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Sample records for mri dgemric method

  1. Utility of delayed gadolinium-enhanced MRI (dGEMRIC) for qualitative evaluation of articular cartilage of patellofemoral joint.

    PubMed

    Nojiri, Takehiro; Watanabe, Nobuyoshi; Namura, Takehiko; Narita, Wataru; Ikoma, Kazuya; Suginoshita, Takehiko; Takamiya, Hisatake; Komiyama, Hiroto; Ito, Hirotoshi; Nishimura, Tsunehiko; Kubo, Toshikazu

    2006-08-01

    Delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) was used for the measurement of relative proteoglycan depletion of articular cartilage in the patellofemoral (PF) joint following a proprietary protocol, which was compared with the X-ray images, proton density weighted MR images (PDWI) and arthroscopic findings. The study examined 30 knees. The ages ranged from 16 to 74 (average 40.3) years. The Gd-DTPA(2-)containing contrast medium was used in a single dose. The subjects were made to exercise the knee joint for 10 min; and MR images were taken 2 h after intravenous injection of contrast medium. T1-calculated images were produced and the region of interest (ROI) was set as follows. (1) ROI1: entire articular cartilage in a slice through the center of the patella. (2) ROI2: low signal region in T1-calculated images, which were set in a blind fashion by two observers. (3) ROI3: articular cartilage on one side that includes ROI2 where low signal region were detected (medial or lateral). ROI3 was set to examine the contrast of ROI2 with surrounding articular cartilage. The average T1 values of ROI1 was 393.5+/-33.6 ms for radiographic grade 0 and 361.3+/-11.1 ms for grade I, which showed a significant difference (P=0.036). The T1 value of ROI2 was 351.6+/-28.2 ms for grade I, 361.9+/-38.3 ms for grade II, 362.1+/-67.7 ms for grade III, and 297.8+/-54.1 ms for grade IV according to arthroscopic Outerbridge classification. All cases, that demonstrated decrease of T1 values on dGEMRIC (ROI2), showed abnormal arthroscopic or direct viewing findings. The ratio (ROI3/ROI2) in cases of only slight damage classified as Outerbridge grade I (6 cases) was an average of 1.04+/-0.02 and was 1.0 or greater in all cases, thereby indicating well-defined contrast with the surrounding cartilage. The diagnosis of damage in articular cartilage was possible in all 16 cases with radiographic K-L grade I on dGEMRIC, while the intensity changes were not found in 10 of 16 cases on PDWI

  2. Current knowledge and importance of dGEMRIC techniques in diagnosis of hip joint diseases.

    PubMed

    Zilkens, Christoph; Tiderius, Carl Johann; Krauspe, Rüdiger; Bittersohl, Bernd

    2015-08-01

    Accurate assessment of early hip joint cartilage alterations may help optimize patient selection and follow-up of hip joint preservation surgery. Delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) is sensitive to the glycosaminoglycan content in cartilage that is lost early in the development of osteoarthritis (OA). Hence, the dGEMRIC technique holds promise for the development of new diagnostic and therapeutic procedures. However, because of the location of the hip joint deep within the body and due to the fairly thin cartilage layers that require high spatial resolution, the diagnosis of early hip joint cartilage alterations may be problematic. The purpose of this review is to outline the current status of dGEMRIC in the assessment of hip joint cartilage. A literature search was performed with PubMed, using the terms "cartilage, osteoarthritis, hip joint, MRI, and dGEMRIC", considering all levels of studies. This review revealed that dGEMRIC can be reliably used in the evaluation of early stage cartilage pathology in various hip joint disorders. Modifications in the technique, such as the operation of three-dimensional imaging and dGEMRIC after intra-articular contrast medium administration, have expanded the range of application. Notably, the studies differ considerably in patient selection and technical prerequisites. Furthermore, there is a need for multicenter prospective studies with the required technical conditions in place to establish outcome based dGEMRIC data to obtain, in conjunction with clinical data, reliable threshold values for normal and abnormal cartilage, and for hips that may benefit from conservative or surgical treatment.

  3. Quantitative assessment of intervertebral disc glycosaminoglycan distribution by gadolinium-enhanced MRI in orthopedic patients.

    PubMed

    Vaga, Stefania; Raimondi, Manuela Teresa; Caiani, Enrico Gianluca; Costa, Francesco; Giordano, Carmen; Perona, Franco; Zerbi, Alberto; Fornari, Maurizio

    2008-01-01

    Our hypothesis was that the enhanced MRI of cartilage (dGEMRIC) imaging protocol could be used in patients to quantify the sulfated glycosaminoglycan (sGAG) in intervertebral discs (IVD). To test this hypothesis, 23 patients with degenerative disc pathology scheduled for surgery were studied by a specific dGEMRIC protocol: each patient underwent two MRI scans, before and 3.5 hr after Gd(DTPA)2-injection of a nonconventional dose of 40 mL. Then, T(1PRE-ENH) and T(1POST-ENH) parametric images of the disc were obtained, from which a new index DeltaT(1) of the molecular status of the IVD was computed (T(1PRE-ENH) - T(1POST-ENH)). A total of 31 tissue samples (one or two from each patient) obtained at herniectomy were collected and biochemically analyzed for sGAG content and used as the gold standard for comparison. DeltaT(1) values in correspondence to degenerated sectors were higher (158 +/- 36 ms) compared to normal sectors (80 +/- 13 ms). Linear regression analysis between MRI-derived and biochemistry-derived measurements resulted in a significant correlation (r = 0.73, P < 0.0001). The DeltaT(1) parametric images, calculated using the modified dGEMRIC technique, provided noninvasive quantitative information about sGAG content within discal tissue in vivo, which resulted in agreement with biochemical analysis. The application of this new MRI method could provide diagnostic information for standard treatment of lumbar discopathy and for innovative therapies of regenerative medicine. PMID:18050346

  4. Sodium MRI: Methods and applications

    PubMed Central

    Madelin, Guillaume; Lee, Jae-Seung; Regatte, Ravinder R.; Jerschow, Alexej

    2014-01-01

    Sodium NMR spectroscopy and MRI have become popular in recent years through the increased availability of high-field MRI scanners, advanced scanner hardware and improved methodology. Sodium MRI is being evaluated for stroke and tumor detection, for breast cancer studies, and for the assessment of osteoarthritis and muscle and kidney functions, to name just a few. In this article, we aim to present an up-to-date review of the theoretical background, the methodology, the challenges and limitations, and current and potential new applications of sodium MRI. PMID:24815363

  5. Quantitative rotating frame relaxometry methods in MRI.

    PubMed

    Gilani, Irtiza Ali; Sepponen, Raimo

    2016-06-01

    Macromolecular degeneration and biochemical changes in tissue can be quantified using rotating frame relaxometry in MRI. It has been shown in several studies that the rotating frame longitudinal relaxation rate constant (R1ρ ) and the rotating frame transverse relaxation rate constant (R2ρ ) are sensitive biomarkers of phenomena at the cellular level. In this comprehensive review, existing MRI methods for probing the biophysical mechanisms that affect the rotating frame relaxation rates of the tissue (i.e. R1ρ and R2ρ ) are presented. Long acquisition times and high radiofrequency (RF) energy deposition into tissue during the process of spin-locking in rotating frame relaxometry are the major barriers to the establishment of these relaxation contrasts at high magnetic fields. Therefore, clinical applications of R1ρ and R2ρ MRI using on- or off-resonance RF excitation methods remain challenging. Accordingly, this review describes the theoretical and experimental approaches to the design of hard RF pulse cluster- and adiabatic RF pulse-based excitation schemes for accurate and precise measurements of R1ρ and R2ρ . The merits and drawbacks of different MRI acquisition strategies for quantitative relaxation rate measurement in the rotating frame regime are reviewed. In addition, this review summarizes current clinical applications of rotating frame MRI sequences. Copyright © 2016 John Wiley & Sons, Ltd.

  6. Low Field Squid MRI Devices, Components and Methods

    NASA Technical Reports Server (NTRS)

    Penanen, Konstantin I. (Inventor); Eom, Byeong H. (Inventor); Hahn, Inseob (Inventor)

    2014-01-01

    Low field SQUID MRI devices, components and methods are disclosed. They include a portable low field (SQUID)-based MRI instrument and a portable low field SQUID-based MRI system to be operated under a bed where a subject is adapted to be located. Also disclosed is a method of distributing wires on an image encoding coil system adapted to be used with an NMR or MRI device for analyzing a sample or subject and a second order superconducting gradiometer adapted to be used with a low field SQUID-based MRI device as a sensing component for an MRI signal related to a subject or sample.

  7. Low field SQUID MRI devices, components and methods

    NASA Technical Reports Server (NTRS)

    Penanen, Konstantin I. (Inventor); Eom, Byeong H (Inventor); Hahn, Inseob (Inventor)

    2010-01-01

    Low field SQUID MRI devices, components and methods are disclosed. They include a portable low field (SQUID)-based MRI instrument and a portable low field SQUID-based MRI system to be operated under a bed where a subject is adapted to be located. Also disclosed is a method of distributing wires on an image encoding coil system adapted to be used with an NMR or MRI device for analyzing a sample or subject and a second order superconducting gradiometer adapted to be used with a low field SQUID-based MRI device as a sensing component for an MRI signal related to a subject or sample.

  8. Low Field Squid MRI Devices, Components and Methods

    NASA Technical Reports Server (NTRS)

    Penanen, Konstantin I. (Inventor); Eom, Byeong H. (Inventor); Hahn, Inseob (Inventor)

    2013-01-01

    Low field SQUID MRI devices, components and methods are disclosed. They include a portable low field (SQUID)-based MRI instrument and a portable low field SQUID-based MRI system to be operated under a bed where a subject is adapted to be located. Also disclosed is a method of distributing wires on an image encoding coil system adapted to be used with an NMR or MRI device for analyzing a sample or subject and a second order superconducting gradiometer adapted to be used with a low field SQUID-based MRI device as a sensing component for an MRI signal related to a subject or sample.

  9. Low field SQUID MRI devices, components and methods

    NASA Technical Reports Server (NTRS)

    Penanen, Konstantin I. (Inventor); Eom, Byeong H. (Inventor); Hahn, Inseob (Inventor)

    2011-01-01

    Low field SQUID MRI devices, components and methods are disclosed. They include a portable low field (SQUID)-based MRI instrument and a portable low field SQUID-based MRI system to be operated under a bed where a subject is adapted to be located. Also disclosed is a method of distributing wires on an image encoding coil system adapted to be used with an NMR or MRI device for analyzing a sample or subject and a second order superconducting gradiometer adapted to be used with a low field SQUID-based MRI device as a sensing component for an MRI signal related to a subject or sample.

  10. SAR measurement in MRI: an improved method

    NASA Astrophysics Data System (ADS)

    Romano, Rocco; Acernese, Fausto; Indovina, Pietro Luigi; Barone, Fabrizio

    2009-03-01

    During an MR procedure, the patient absorbs a portion of the transmitted RF energy, which may result in tissue heating and other adverse effects, such as alterations in visual, auditory and neural functions. The Specific Absorption Rate (SAR), in W/kg, is the RF power absorbed per unit mass of tissue and is one of the most important parameters related with thermal effects and acts as a guideline for MRI safety. Strict limits to the SAR levels are imposed by patient safety international regulations (CEI - EN 60601 - 2 - 33) and SAR measurements are required in order to verify its respect. The recommended methods for mean SAR measurement are quite problematic and often require a maintenance man intervention and long stop machine. For example, in the CEI recommended pulse energy method, the presence of a maintenance man is required in order to correctly connect the required instrumentation; furthermore, the procedure is complex and requires remarkable processing and calculus. Simpler are the calorimetric methods, also if in this case long acquisition times are required in order to have significant temperature variations and accurate heat capacity knowledge (CEI - EN 60601 - 2- 33). The phase transition method is a new method to measure SAR in MRI which has the advantages to be very simple and to overcome all the typical calorimetric method problems. It does not require in gantry temperature measurements, any specific heat or heat capacity knowledge, but only mass and time measurement. Furthermore, in this method, it is possible to show that all deposited SAR power can be considered acquired and measured.

  11. COMPARISON OF THE COMPLETE FOURIER DIRECT MRI WITH EXISTING DIFFUSION WEIGHTED MRI METHODS

    PubMed Central

    Özcan, Alpay

    2011-01-01

    The Complete Fourier Direct (CFD) MRI method introduced in earlier work for modeling the diffusion weighted MRI signal is compared with the existing methods. The preservation of Hermitian symmetry in the diffusion weighted MRI signal without affecting its energy is the key point that differentiates CFD–MRI from the existing methods. By keeping the correct Fourier relationship intact, the joint distribution function is represented ‘as it is’, without any constraints, e.g. being symmetric. The necessity to model or assume models for spin motion and try to fit the model to the samples of the Fourier transform as in case of model matching methods is not required because the Discrete Fourier Transform applied to correctly processed signal in CFD–MRI gives more accurate results. PMID:21918715

  12. An MRI-based attenuation correction method for combined PET/MRI applications

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Yang, Xiaofeng; Wang, Hesheng

    2009-02-01

    We are developing MRI-based attenuation correction methods for PET images. PET has high sensitivity but relatively low resolution and little anatomic details. MRI can provide excellent anatomical structures with high resolution and high soft tissue contrast. MRI can be used to delineate tumor boundaries and to provide an anatomic reference for PET, thereby improving quantitation of PET data. Combined PET/MRI can offer metabolic, functional and anatomic information and thus can provide a powerful tool to study the mechanism of a variety of diseases. Accurate attenuation correction represents an essential component for the reconstruction of artifact-free, quantitative PET images. Unfortunately, the present design of hybrid PET/MRI does not offer measured attenuation correction using a transmission scan. This problem may be solved by deriving attenuation maps from corresponding anatomic MR images. Our approach combines image registration, classification, and attenuation correction in a single scheme. MR images and the preliminary reconstruction of PET data are first registered using our automatic registration method. MRI images are then classified into different tissue types using our multiscale fuzzy C-mean classification method. The voxels of classified tissue types are assigned theoretical tissue-dependent attenuation coefficients to generate attenuation correction factors. Corrected PET emission data are then reconstructed using a threedimensional filtered back projection method and an order subset expectation maximization method. Results from simulated images and phantom data demonstrated that our attenuation correction method can improve PET data quantitation and it can be particularly useful for combined PET/MRI applications.

  13. Background and Mathematical Analysis of Diffusion MRI Methods.

    PubMed

    Ozcan, Alpay; Wong, Kenneth H; Larson-Prior, Linda; Cho, Zang-Hee; Mun, Seong K

    2012-03-01

    The addition of a pair of magnetic field gradient pulses had initially provided the measurement of spin motion with nuclear magnetic resonance (NMR) techniques. In the adaptation of DW-NMR techniques to magnetic resonance imaging (MRI), the taxonomy of mathematical models is divided in two categories: model matching and spectral methods. In this review, the methods are summarized starting from early diffusion weighted (DW) NMR models followed up with their adaptation to DW MRI. Finally, a newly introduced Fourier analysis based unifying theory, so-called Complete Fourier Direct MRI, is included to explain the mechanisms of existing methods.

  14. MRI segmentation of the human brain: challenges, methods, and applications.

    PubMed

    Despotović, Ivana; Goossens, Bart; Philips, Wilfried

    2015-01-01

    Image segmentation is one of the most important tasks in medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, image segmentation is commonly used for measuring and visualizing the brain's anatomical structures, for analyzing brain changes, for delineating pathological regions, and for surgical planning and image-guided interventions. In the last few decades, various segmentation techniques of different accuracy and degree of complexity have been developed and reported in the literature. In this paper we review the most popular methods commonly used for brain MRI segmentation. We highlight differences between them and discuss their capabilities, advantages, and limitations. To address the complexity and challenges of the brain MRI segmentation problem, we first introduce the basic concepts of image segmentation. Then, we explain different MRI preprocessing steps including image registration, bias field correction, and removal of nonbrain tissue. Finally, after reviewing different brain MRI segmentation methods, we discuss the validation problem in brain MRI segmentation.

  15. NMR and MRI apparatus and method

    DOEpatents

    Clarke, John; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Myers, Whittier; McDermott, Robert; ten Haken, Bernard; Pines, Alexander; Trabesinger, Andreas

    2007-03-06

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. Additional signal to noise benefits are obtained by use of a low noise polarization coil, comprising litz wire or superconducting materials. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  16. Iterative method for predistortion of MRI gradient waveforms.

    PubMed

    Harkins, Kevin D; Does, Mark D; Grissom, William A

    2014-08-01

    The purpose of this work is to correct for transient gradient waveform errors in magnetic resonance imaging (MRI), whether from eddy currents, group delay, or gradient amplifier nonlinearities, which are known to affect image quality. An iterative method is proposed to minimize error between desired and measured gradient waveforms, whose success does not depend on accurate knowledge of the gradient system impulse response. The method was applied to half-pulse excitation for 2-D ultra-short echo time (UTE) imaging on a small animal MRI system and to spiral 2-D excitation on a human 7T MRI system. Predistorted gradient waveforms reduced temporal signal variation caused by excitation gradient trajectory errors in 2-D UTE, and improved the quality of excitation patterns produced by spiral excitation pulses. Iterative gradient predistortion is useful for minimizing transient gradient errors without requiring accurate characterization of the gradient system impulse response. PMID:24801945

  17. MRI

    MedlinePlus

    MRI does not use ionizing radiation. No side effects from the magnetic fields and radio waves have been reported. The most common type of contrast (dye) used is gadolinium. It is very safe. Allergic reactions rarely ...

  18. A new method for assessing PET-MRI coregistration

    NASA Astrophysics Data System (ADS)

    DeLorenzo, Christine; Klein, Arno; Mikhno, Arthur; Gray, Neil; Zanderigo, Francesca; Mann, J. John; Parsey, Ramin V.

    2009-02-01

    Positron emission tomography (PET) images are acquired for many purposes, from diagnostic assessment to aiding in the development of novel therapies. Whatever the intended use, it is often necessary to distinguish between different anatomical regions within these images. Because of this, magnetic resonance images (MRIs) are generally acquired to provide an anatomical reference. This reference will only be accurate if the PET image is properly coregistered to the MRI; yet currently, a method to evaluate PET-MRI coregistration accuracy does not exist. This problem is compounded by the fact that two visually indistinguishable coregistration results can produce estimates of ligand binding that vary significantly. Therefore, the focus of this work was to develop a method that can evaluate coregistration performance based on measured ligand binding within certain regions of the coregistered PET image. The evaluation method is based on the premise that a more accurate coregistration will result in higher ligand binding in certain anatomical regions defined by the MRI. This fully automated method was able to assess coregistration results within the variance of an expert manual rater and shows promise as a possible coregistration cost function.

  19. Comparison of regularization methods for human cardiac diffusion tensor MRI.

    PubMed

    Frindel, Carole; Robini, Marc; Croisille, Pierre; Zhu, Yue-Min

    2009-06-01

    Diffusion tensor MRI (DT-MRI) is an imaging technique that is gaining importance in clinical applications. However, there is very little work concerning the human heart. When applying DT-MRI to in vivo human hearts, the data have to be acquired rapidly to minimize artefacts due to cardiac and respiratory motion and to improve patient comfort, often at the expense of image quality. This results in diffusion weighted (DW) images corrupted by noise, which can have a significant impact on the shape and orientation of tensors and leads to diffusion tensor (DT) datasets that are not suitable for fibre tracking. This paper compares regularization approaches that operate either on diffusion weighted images or on diffusion tensors. Experiments on synthetic data show that, for high signal-to-noise ratio (SNR), the methods operating on DW images produce the best results; they substantially reduce noise error propagation throughout the diffusion calculations. However, when the SNR is low, Rician Cholesky and Log-Euclidean DT regularization methods handle the bias introduced by Rician noise and ensure symmetry and positive definiteness of the tensors. Results based on a set of sixteen ex vivo human hearts show that the different regularization methods tend to provide equivalent results. PMID:19356971

  20. Asymmetric MRI magnet design using a hybrid numerical method.

    PubMed

    Zhao, H; Crozier, S; Doddrell, D M

    1999-12-01

    This paper describes a hybrid numerical method for the design of asymmetric magnetic resonance imaging magnet systems. The problem is formulated as a field synthesis and the desired current density on the surface of a cylinder is first calculated by solving a Fredholm equation of the first kind. Nonlinear optimization methods are then invoked to fit practical magnet coils to the desired current density. The field calculations are performed using a semi-analytical method. A new type of asymmetric magnet is proposed in this work. The asymmetric MRI magnet allows the diameter spherical imaging volume to be positioned close to one end of the magnet. The main advantages of making the magnet asymmetric include the potential to reduce the perception of claustrophobia for the patient, better access to the patient by attending physicians, and the potential for reduced peripheral nerve stimulation due to the gradient coil configuration. The results highlight that the method can be used to obtain an asymmetric MRI magnet structure and a very homogeneous magnetic field over the central imaging volume in clinical systems of approximately 1.2 m in length. Unshielded designs are the focus of this work. This method is flexible and may be applied to magnets of other geometries.

  1. The phase transition method for SAR measurement in MRI

    NASA Astrophysics Data System (ADS)

    Romano, R.; Canonico, R.; Acernese, F.; Giordano, G.; Barone, F.

    2014-03-01

    During an MR procedure, the patient absorbs a portion of the transmitted RF energy, which may result in tissue heating and other adverse effects, such as alterations in visual, auditory and neural functions. The Specific Absorption Rate (SAR), in W/kg, is the RF power absorbed per unit mass of tissue and is one of the most important parameters related with thermal effects and acts as a guideline for MRI safety. Strict limits to the SAR levels are imposed by patient safety international regulations (CEI - EN 60601 - 2 - 33) and SAR measurements are required in order to verify its respect. The recommended methods for mean SAR measurement are quite problematic and often require a maintenance man intervention and long stop machine. For example, in the CEI recommended pulse energy method, the presence of a maintenance man is required in order to correctly connect the required instrumentation; furthermore, the procedure is complex and requires remarkable processing and calculus. Simpler are the calorimetric methods, also if in this case long acquisition times are required in order to have significant temperature variations and accurate heat capacity knowledge (CEI - EN 60601 - 2 - 33). The phase transition method is a new method to measure SAR in MRI which has the advantages to be very simple and to overcome all the typical calorimetric method problems. It does not require in gantry temperature measurements, any specific heat or heat capacity knowledge, but only mass and time measurement. Nevertheless, in order to consider this method it is necessary to verify that all deposited SAR power can be considered acquired and measured. In this paper considerations about this aspect are conducted.

  2. A no-calorimetric method for measuring SAR in MRI

    NASA Astrophysics Data System (ADS)

    Romano, Rocco; Acernese, Fausto; Barone, Fabrizio

    2011-04-01

    During an MR procedure, the patient absorbs a portion of the transmitted RF energy, which may result in tissue heating and other adverse effects, such as alterations in visual, auditory and neural functions. The Specific Absorption Rate (SAR), in W/kg, is the RF power absorbed per unit mass of tissue and is one of the most important parameters related with thermal effects and acts as a guideline for MRI safety. Strict limits to the SAR levels are imposed by patient safety international regulations (CEI - EN 60601 - 2 - 33) and SAR measurements are required in order to verify its respect. The recommended methods for mean SAR measurement are quite problematic and often require a maintenance man intervention and long stop machine. For example, in the CEI recommended pulse energy method, the presence of a maintenance man is required in order to correctly connect the required instrumentation; furthermore, the procedure is complex and requires remarkable processing and calculus. Simpler are the calorimetric methods, also if in this case long acquisition times are required in order to have significant temperature variations and accurate heat capacity knowledge (CEI - EN 60601 - 2 - 33). The phase transition method is a new no-calorimetric method to measure SAR in MRI which has the advantages to be very simple and to overcome all the typical calorimetric method problems. It does not require in gantry temperature measurements, any specific heat or heat capacity knowledge, but only mass and time measurement. On the other hand, it is necessary to establish if all deposited power SAR can be considered acquired and measured. In this paper, that will be shown.

  3. The phase transition method for SAR measurement in MRI

    NASA Astrophysics Data System (ADS)

    Romano, Rocco; Acernese, Fausto; Vilasi, Silvia; Barone, Fabrizio

    2010-03-01

    During an MR procedure, the patient absorbs a portion of the transmitted RF energy, which may result in tissue heating and other adverse effects, such as alterations in visual, auditory and neural functions. The Specific Absorption Rate (SAR), in W/kg, is the RF power absorbed per unit mass of tissue and is one of the most important parameters related with thermal effects and acts as a guideline for MRI safety. Strict limits to the SAR levels are imposed by patient safety international regulations (CEI - EN 60601 - 2 - 33) and SAR measurements are required in order to verify its respect. The recommended methods for mean SAR measurement are quite problematic and often require a maintenance man intervention and long stop machine. For example, in the CEI recommended pulse energy method, the presence of a maintenance man is required in order to correctly connect the required instrumentation; furthermore, the procedure is complex and requires remarkable processing and calculus. Simpler are the calorimetric methods, also if in this case long acquisition times are required in order to have significant temperature variations and accurate heat capacity knowledge (CEI - EN 60601 - 2 - 33). The phase transition method is a new method to measure SAR in MRI which has the advantages to be very simple and to overcome all the typical calorimetric method problems. It does not require in gantry temperature measurements, any specific heat or heat capacity knowledge, but only mass and time measurement. On the other hand, it is necessary to establish if all deposited power SAR can be considered acquired and measured. In this paper, that will be shown.

  4. Rapid MRI method for mapping the longitudinal relaxation time

    NASA Astrophysics Data System (ADS)

    Hsu, Jung-Jiin; Glover, Gary H.

    2006-07-01

    A novel method for mapping the longitudinal relaxation time in a clinically acceptable time is developed based on a recent proposal [J.-J. Hsu, I.J. Lowe, Spin-lattice relaxation and a fast T1-map acquisition method in MRI with transient-state magnetization, J. Magn. Reson. 169 (2004) 270-278] and the speed of the spiral pulse sequence. The method acquires multiple curve-fitting samples with one RF pulse train. It does not require RF pulses of specific flip angles (e.g., 90° or 180°), nor are the long recovery waiting time and the measurement of the magnetization at thermal equilibrium needed. Given the value of the flip angle, the curve fitting is semi-logarithmic and not computationally intensive. On a heterogeneous phantom, the average percentage difference between measurements of the present method and those of an inversion-recovery method is below 2.7%. In mapping the human brain, the present method, for example, can obtain four curve-fitting samples for five 128 × 128 slices in less than 3.2 s and the results are in agreement with other studies in the literature.

  5. Reproducibility of MRI segmentation using a feature space method

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Windham, Joe P.; Scarpace, Lisa; Murnock, Tanya

    1998-06-01

    This paper presents reproducibility studies for the segmentation results obtained by our optimal MRI feature space method. The steps of the work accomplished are as follows. (1) Eleven patients with brain tumors were imaged by a 1.5 T General Electric Signa MRI System. Four T2- weighted and two T1-weighted images (before and after Gadolinium injection) were acquired for each patient. (2) Images of a slice through the center of the tumor were selected for processing. (3) Patient information was removed from the image headers and new names (unrecognizable by the image analysts) were given to the images. These images were blindly analyzed by the image analysts. (4) Segmentation results obtained by the two image analysts at two time points were compared to assess the reproducibility of the segmentation method. For each tissue segmented in each patient study, a comparison was done by kappa statistics and a similarity measure (an approximation of kappa statistics used by other researchers), to evaluate the number of pixels that were in both of the segmentation results obtained by the two image analysts (agreement) relative to the number of pixels that were not in both (disagreement). An overall agreement comparison was done by finding means and standard deviations of kappa statistics and the similarity measure found for each tissue type in the studies. The kappa statistics for white matter was the largest (0.80) followed by those of gray matter (0.68), partial volume (0.67), total lesion (0.66), and CSF (0.44). The similarity measure showed the same trend but it was always higher than kappa statistics. It was 0.85 for white matter, 0.77 for gray matter, 0.73 for partial volume, 0.72 for total lesion, and 0.47 for CSF.

  6. Review of methods for functional brain connectivity detection using fMRI

    PubMed Central

    Li, Kaiming; Guo, Lei; Nie, Jingxin; Li, Gang; Liu, Tianming

    2009-01-01

    Since the mid of 1990s, functional connectivity study using fMRI (fcMRI) has drawn increasing attention of neuroscientists and computer scientists, since it opens a new window to explore functional network of human brain with relatively high resolution. A variety of methods for fcMRI study have been proposed. This paper intends to provide a technical review on computational methodologies developed for fcMRI analysis. From our perspective, these computational methods are classified into two general categories: model-driven methods and data-driven methods. Data-driven methods are a large family, and thus are further sub-classified into decomposition-based methods and clustering analysis methods. For each type of methods, principles, main contributors, and their advantages and drawbacks are discussed. Finally, potential applications of fcMRI are overviewed. PMID:19111443

  7. Data on the verification and validation of segmentation and registration methods for diffusion MRI.

    PubMed

    Esteban, Oscar; Zosso, Dominique; Daducci, Alessandro; Bach-Cuadra, Meritxell; Ledesma-Carbayo, María J; Thiran, Jean-Philippe; Santos, Andres

    2016-09-01

    The verification and validation of segmentation and registration methods is a necessary assessment in the development of new processing methods. However, verification and validation of diffusion MRI (dMRI) processing methods is challenging for the lack of gold-standard data. The data described here are related to the research article entitled "Surface-driven registration method for the structure-informed segmentation of diffusion MR images" [1], in which publicly available data are used to derive golden-standard reference-data to validate and evaluate segmentation and registration methods in dMRI. PMID:27508235

  8. Data on the verification and validation of segmentation and registration methods for diffusion MRI.

    PubMed

    Esteban, Oscar; Zosso, Dominique; Daducci, Alessandro; Bach-Cuadra, Meritxell; Ledesma-Carbayo, María J; Thiran, Jean-Philippe; Santos, Andres

    2016-09-01

    The verification and validation of segmentation and registration methods is a necessary assessment in the development of new processing methods. However, verification and validation of diffusion MRI (dMRI) processing methods is challenging for the lack of gold-standard data. The data described here are related to the research article entitled "Surface-driven registration method for the structure-informed segmentation of diffusion MR images" [1], in which publicly available data are used to derive golden-standard reference-data to validate and evaluate segmentation and registration methods in dMRI.

  9. Longitudinal fMRI analysis: A review of methods

    PubMed Central

    Skup, Martha

    2010-01-01

    Functional magnetic resonance imaging (fMRI) investigations of a longitudinal nature, where participants are scanned repeatedly over time and imaging data are obtained at more than one time-point, are essential to understanding functional changes and development in healthy and pathological brains. The main objective of this paper is to provide a brief summary of common longitudinal analysis approaches, develop an overview of fMRI by introducing how such data manifest, and explore the statistical challenges that arise at the intersection of these two techniques. PMID:21691445

  10. Longitudinal fMRI analysis: A review of methods

    PubMed Central

    Skup, Martha

    2011-01-01

    Functional magnetic resonance imaging (fMRI) investigations of a longitudinal nature, where participants are scanned repeatedly over time and imaging data are obtained at more than one time-point, are essential to understanding functional changes and development in healthy and pathological brains. The main objective of this paper is to provide a brief summary of common longitudinal analysis approaches, develop an overview of fMRI by introducing how such data manifest, and explore the statistical challenges that arise at the intersection of these two techniques. PMID:22655113

  11. An Introduction to Normalization and Calibration Methods in Functional MRI

    ERIC Educational Resources Information Center

    Liu, Thomas T.; Glover, Gary H.; Mueller, Bryon A.; Greve, Douglas N.; Brown, Gregory G.

    2013-01-01

    In functional magnetic resonance imaging (fMRI), the blood oxygenation level dependent (BOLD) signal is often interpreted as a measure of neural activity. However, because the BOLD signal reflects the complex interplay of neural, vascular, and metabolic processes, such an interpretation is not always valid. There is growing evidence that changes…

  12. Validation of computational fluid dynamics methods with anatomically exact, 3D printed MRI phantoms and 4D pcMRI.

    PubMed

    Anderson, Jeff R; Diaz, Orlando; Klucznik, Richard; Zhang, Y Jonathan; Britz, Gavin W; Grossman, Robert G; Lv, Nan; Huang, Qinghai; Karmonik, Christof

    2014-01-01

    A new concept of rapid 3D prototyping was implemented using cost-effective 3D printing for creating anatomically correct replica of cerebral aneurysms. With a dedicated flow loop set-up in a full body human MRI scanner, flow measurements were performed using 4D phase contrast magnetic resonance imaging to visualize and quantify intra-aneurysmal flow patterns. Ultrashort TE sequences were employed to obtain high-resolution 3D image data to visualize the lumen inside the plastic replica. In-vitro results were compared with retrospectively obtained in-vivo data and results from computational fluid dynamics simulations (CFD). Rapid prototyping of anatomically realistic 3D models may have future impact in treatment planning, design of image acquisition methods for MRI and angiographic systems and for the design and testing of advanced image post-processing technologies.

  13. Ag/AgCl electrodes in the EEG/fMRI method in 3T MRI scanner

    NASA Astrophysics Data System (ADS)

    Akay, Cengiz; Kepceoğlu, Abdullah

    2013-10-01

    This study focuses on the comparison of two different types of EEG electrodes (the first B10-S-150 Ag/AgCl sintered ring electrode with 1, 5 mm touch proof safety socket and 150 cm heavy-duty lead wire and the second, B12-LS-100 Ag/AgCl sintered FE-electrode with 100 cm light-duty lead wire and 1, 5 mm touch proof safety socket with 5 kΩ resistor near sensor) used in the EEG/fMRI method in 3T MRI scanner. We compared these electrodes by their specific absorption rate (SAR) simulation values and the temperature change calculated by PRF method. The experimental setup of the study is described as follows: a phantom is prepared and the electrodes are placed on it. Then, a simulation for SAR values is realized. The temperature change is calculated by MR thermometer. As a result of this study, Ag/AgCl pin electrode is better to be use in EEG/fMRI; because the measured temperature change is expected to be low.

  14. A parietal memory network revealed by multiple MRI methods.

    PubMed

    Gilmore, Adrian W; Nelson, Steven M; McDermott, Kathleen B

    2015-09-01

    The manner by which the human brain learns and recognizes stimuli is a matter of ongoing investigation. Through examination of meta-analyses of task-based functional MRI and resting state functional connectivity MRI, we identified a novel network strongly related to learning and memory. Activity within this network at encoding predicts subsequent item memory, and at retrieval differs for recognized and unrecognized items. The direction of activity flips as a function of recent history: from deactivation for novel stimuli to activation for stimuli that are familiar due to recent exposure. We term this network the 'parietal memory network' (PMN) to reflect its broad involvement in human memory processing. We provide a preliminary framework for understanding the key functional properties of the network. PMID:26254740

  15. A method to determine activation thresholds in fMRI paradigms.

    PubMed

    Arndt, S; Gold, S; Cizadlo, T; Zheng, J; Ehrhardt, J C; Flaum, M

    1997-08-01

    Determining meaningful activation thresholds in functional magnetic resonance imaging (fMRI) paradigms is complicated by several factors. These include the time-series nature of the data, the influence of physiological rhythms (e.g. respiration) and vacillations introduced by the experimental design (e.g. cueing). We present an empirical threshold for each subject and each fMRI experiment that takes these factors into account. The method requires an additional fMRI data set as similar to the experimental paradigm as possible without dichotomously varying the experimental task of interest. A letter fluency task was used to illustrate this method. This technique differs from classical methods since the Pearson correlation probability values tabulated from statistical theory are not used. Rather each subject defines his or her own set of threshold probability values for correlations. It is against these empirical thresholds, not Pearson's, that an experimental fMRI correlation is assessed.

  16. An Atlas-Based Electron Density Mapping Method for Magnetic Resonance Imaging (MRI)-Alone Treatment Planning and Adaptive MRI-Based Prostate Radiation Therapy

    SciTech Connect

    Dowling, Jason A.; Lambert, Jonathan; Parker, Joel; Salvado, Olivier; Fripp, Jurgen; Capp, Anne; Wratten, Chris; Denham, James W.; Greer, Peter B.

    2012-05-01

    Purpose: Prostate radiation therapy dose planning directly on magnetic resonance imaging (MRI) scans would reduce costs and uncertainties due to multimodality image registration. Adaptive planning using a combined MRI-linear accelerator approach will also require dose calculations to be performed using MRI data. The aim of this work was to develop an atlas-based method to map realistic electron densities to MRI scans for dose calculations and digitally reconstructed radiograph (DRR) generation. Methods and Materials: Whole-pelvis MRI and CT scan data were collected from 39 prostate patients. Scans from 2 patients showed significantly different anatomy from that of the remaining patient population, and these patients were excluded. A whole-pelvis MRI atlas was generated based on the manually delineated MRI scans. In addition, a conjugate electron-density atlas was generated from the coregistered computed tomography (CT)-MRI scans. Pseudo-CT scans for each patient were automatically generated by global and nonrigid registration of the MRI atlas to the patient MRI scan, followed by application of the same transformations to the electron-density atlas. Comparisons were made between organ segmentations by using the Dice similarity coefficient (DSC) and point dose calculations for 26 patients on planning CT and pseudo-CT scans. Results: The agreement between pseudo-CT and planning CT was quantified by differences in the point dose at isocenter and distance to agreement in corresponding voxels. Dose differences were found to be less than 2%. Chi-squared values indicated that the planning CT and pseudo-CT dose distributions were equivalent. No significant differences (p > 0.9) were found between CT and pseudo-CT Hounsfield units for organs of interest. Mean {+-} standard deviation DSC scores for the atlas-based segmentation of the pelvic bones were 0.79 {+-} 0.12, 0.70 {+-} 0.14 for the prostate, 0.64 {+-} 0.16 for the bladder, and 0.63 {+-} 0.16 for the rectum

  17. Robust registration method for interventional MRI-guided thermal ablation of prostate cancer

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Wheaton, Andrew; Lee, Zhenghong; Nagano, Kenichi; Duerk, Jeffrey L.; Wilson, David L.

    2001-05-01

    We are investigating methods to register live-time interventional magnetic resonance imaging (iMRI) slice images with a previously obtained, high resolution MRI image volume. The immediate application is for iMRI-guided treatments of prostate cancer. We created and evaluated a slice-to-volume mutual information registration algorithm for MR images with special features to improve robustness. Features included a multi-resolution approach and automatic restarting to avoid local minima. We acquired 3D volume images from a 1.5 T MRI system and simulated iMRI images. To assess the quality of registration, we calculated 3D displacement on a voxel-by-voxel basis over a volume of interest between slice-to-volume registration and volume-to- volume registrations that were previously shown to be quite accurate. More than 500 registration experiments were performed on MR images of volunteers. The slice-to-volume registration algorithm was very robust for transverse images covering the prostate. A 100% success rate was achieved with an acceptance criterion of <1.0 mm displacement error over the prostate. Our automatic slice-to-volume mutual information registration algorithm is robust and probably sufficiently accurate to aid in the application of iMRI- guided thermal ablation of prostate cancer.

  18. Volumetric and fiber-tracing MRI methods for gray and white matter.

    PubMed

    Larvie, Mykol; Fischl, Bruce

    2016-01-01

    Magnetic resonance imaging (MRI) is capable of generating high-resolution brain images with fine anatomic detail and unique tissue contrasts that reveal structures that are not visible to the eye. Sharply defined gray- and white-matter interfaces allow for quantitative anatomic analysis that can be accurately performed with largely automated segmentation methods. In an analogous fashion, diffusion MRI in the brain provides structural information based on contrasts derived from the diffusivity of water in brain tissue, which can highlight the orientation of neuronal axons. Also using largely automated methods, diffusion MRI can be used to generate models of white-matter tracts throughout the brain, a method known as tractography, as well as characterize the microstructural integrity of neuronal axons. Tractographic analysis has helped to define connectivity in the brain that powerfully informs understanding of brain function, and, together with other diffusion metrics, is useful in evaluation of the normal and diseased brain. The quantitative methods of brain segmentation, tractography, and diffusion MRI extend MRI into a realm beyond visual inspection and provide otherwise unachievable sensitivity and specificity in the analysis of brain structure and function.

  19. Volumetric and fiber-tracing MRI methods for gray and white matter.

    PubMed

    Larvie, Mykol; Fischl, Bruce

    2016-01-01

    Magnetic resonance imaging (MRI) is capable of generating high-resolution brain images with fine anatomic detail and unique tissue contrasts that reveal structures that are not visible to the eye. Sharply defined gray- and white-matter interfaces allow for quantitative anatomic analysis that can be accurately performed with largely automated segmentation methods. In an analogous fashion, diffusion MRI in the brain provides structural information based on contrasts derived from the diffusivity of water in brain tissue, which can highlight the orientation of neuronal axons. Also using largely automated methods, diffusion MRI can be used to generate models of white-matter tracts throughout the brain, a method known as tractography, as well as characterize the microstructural integrity of neuronal axons. Tractographic analysis has helped to define connectivity in the brain that powerfully informs understanding of brain function, and, together with other diffusion metrics, is useful in evaluation of the normal and diseased brain. The quantitative methods of brain segmentation, tractography, and diffusion MRI extend MRI into a realm beyond visual inspection and provide otherwise unachievable sensitivity and specificity in the analysis of brain structure and function. PMID:27432659

  20. A new fast and unsynchronized method for MRI of viscoelastic properties of soft tissues.

    PubMed

    Lewa, C J; Roth, M; Nicol, L; Franconi, J M; de Certaines, J D

    2000-11-01

    Quantitative measurement of mechanical properties of biologic tissues may have several applications for diagnosis or biomechanic modeling in sports medicine, traumatology, or computer-guided surgery. The magnetic resonance imaging (MRI) methods previously tested for these applications all required synchronization between MRI acquisition pulses and the mechanical stimulation. A new unsynchronized method operating with no prior knowledge of intensity, direction, and frequency of the mechanical waves is proposed. A specifically modified SPAMM (SPAtial Modulation of Magnetization) sequence has been used, operating on a 0.2-T MRI system. The experimental results obtained on test objects fit well with theoretical calculations. The new proposed method is very fast (a less than 5-second acquisition time) for routine clinical use. PMID:11050651

  1. An empirical comparison of different LDA methods in fMRI-based brain states decoding.

    PubMed

    Xia, Maogeng; Song, Sutao; Yao, Li; Long, Zhiying

    2015-01-01

    Decoding brain states from response patterns with multivariate pattern recognition techniques is a popular method for detecting multivoxel patterns of brain activation. These patterns are informative with respect to a subject's perceptual or cognitive states. Linear discriminant analysis (LDA) cannot be directly applied to fMRI data analysis because of the "few samples and large features" nature of functional magnetic resonance imaging (fMRI) data. Although several improved LDA methods have been used in fMRI-based decoding, little is known regarding the relative performance of different LDA classifiers on fMRI data. In this study, we compared five LDA classifiers using both simulated data with varied noise levels and real fMRI data. The compared LDA classifiers include LDA combined with PCA (LDA-PCA), LDA with three types of regularizations (identity matrix, diagonal matrix and scaled identity matrix) and LDA with optimal-shrinkage covariance estimator using Ledoit and Wolf lemma (LDA-LW). The results indicated that LDA-LW was the most robust to noises. Moreover, LDA-LW and LDA with scaled identity matrix showed better stability and classification accuracy than the other methods. LDA-LW demonstrated the best overall performance. PMID:26405876

  2. An empirical comparison of different LDA methods in fMRI-based brain states decoding.

    PubMed

    Xia, Maogeng; Song, Sutao; Yao, Li; Long, Zhiying

    2015-01-01

    Decoding brain states from response patterns with multivariate pattern recognition techniques is a popular method for detecting multivoxel patterns of brain activation. These patterns are informative with respect to a subject's perceptual or cognitive states. Linear discriminant analysis (LDA) cannot be directly applied to fMRI data analysis because of the "few samples and large features" nature of functional magnetic resonance imaging (fMRI) data. Although several improved LDA methods have been used in fMRI-based decoding, little is known regarding the relative performance of different LDA classifiers on fMRI data. In this study, we compared five LDA classifiers using both simulated data with varied noise levels and real fMRI data. The compared LDA classifiers include LDA combined with PCA (LDA-PCA), LDA with three types of regularizations (identity matrix, diagonal matrix and scaled identity matrix) and LDA with optimal-shrinkage covariance estimator using Ledoit and Wolf lemma (LDA-LW). The results indicated that LDA-LW was the most robust to noises. Moreover, LDA-LW and LDA with scaled identity matrix showed better stability and classification accuracy than the other methods. LDA-LW demonstrated the best overall performance.

  3. MRI-Based Computed Tomography Metal Artifact Correction Method for Improving Proton Range Calculation Accuracy

    SciTech Connect

    Park, Peter C.; Schreibmann, Eduard; Roper, Justin; Elder, Eric; Crocker, Ian; Fox, Tim; Zhu, X. Ronald; Dong, Lei; Dhabaan, Anees

    2015-03-15

    Purpose: Computed tomography (CT) artifacts can severely degrade dose calculation accuracy in proton therapy. Prompted by the recently increased popularity of magnetic resonance imaging (MRI) in the radiation therapy clinic, we developed an MRI-based CT artifact correction method for improving the accuracy of proton range calculations. Methods and Materials: The proposed method replaces corrupted CT data by mapping CT Hounsfield units (HU number) from a nearby artifact-free slice, using a coregistered MRI. MRI and CT volumetric images were registered with use of 3-dimensional (3D) deformable image registration (DIR). The registration was fine-tuned on a slice-by-slice basis by using 2D DIR. Based on the intensity of paired MRI pixel values and HU from an artifact-free slice, we performed a comprehensive analysis to predict the correct HU for the corrupted region. For a proof-of-concept validation, metal artifacts were simulated on a reference data set. Proton range was calculated using reference, artifactual, and corrected images to quantify the reduction in proton range error. The correction method was applied to 4 unique clinical cases. Results: The correction method resulted in substantial artifact reduction, both quantitatively and qualitatively. On respective simulated brain and head and neck CT images, the mean error was reduced from 495 and 370 HU to 108 and 92 HU after correction. Correspondingly, the absolute mean proton range errors of 2.4 cm and 1.7 cm were reduced to less than 2 mm in both cases. Conclusions: Our MRI-based CT artifact correction method can improve CT image quality and proton range calculation accuracy for patients with severe CT artifacts.

  4. A novel image analysis method based on Bayesian segmentation for event-related functional MRI

    NASA Astrophysics Data System (ADS)

    Huang, Lejian; Comer, Mary L.; Talavage, Thomas M.

    2008-02-01

    This paper presents the application of the expectation-maximization/maximization of the posterior marginals (EM/MPM) algorithm to signal detection for functional MRI (fMRI). On basis of assumptions for fMRI 3-D image data, a novel analysis method is proposed and applied to synthetic data and human brain data. Synthetic data analysis is conducted using two statistical noise models (white and autoregressive of order 1) and, for low contrast-to-noise ratio (CNR) data, reveals better sensitivity and specificity for the new method than for the traditional General Linear Model (GLM) approach. When applied to human brain data, functional activation regions are found to be consistent with those obtained using the GLM approach.

  5. Termination of the MRI via parasitic instabilities in core-collapse supernovae: influence of numerical methods

    NASA Astrophysics Data System (ADS)

    Rembiasz, T.; Obergaulinger, M.; Cerdá-Durán, P.; Aloy, M. Á.; Müller, E.

    2016-05-01

    We study the influence of numerical methods and grid resolution on the termination of the magnetorotational instability (MRI) by means of parasitic instabilities in threedimensional shearing-disc simulations reproducing typical conditions found in core-collapse supernovae. Whether or not the MRI is able to amplify weak magnetic fields in this context strongly depends, among other factors, on the amplitude at which its growth terminates. The qualitative results of our study do not depend on the numerical scheme. In all our models, MRI termination is caused by Kelvin-Helmholtz instabilities, consistent with theoretical predictions. Quantitatively, however, there are differences, but numerical convergence can be achieved even at relatively low grid resolutions if high-order reconstruction methods are used.

  6. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks.

  7. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks. PMID:27656202

  8. Synthesis of ferrofluid with magnetic nanoparticles by sonochemical method for MRI contrast agent

    NASA Astrophysics Data System (ADS)

    Hee Kim, Eun; Sook Lee, Hyo; Kook Kwak, Byung; Kim, Byung-Kee

    2005-03-01

    Superparamagnetic iron oxide nanoparticles (SPIO) having high magnetization (83 emu/g) and crystallinity were synthesized by using a sonochemical method. Ferrofluids from these nanoparticles coated with oleic acid as a surfactant were prepared for magnetic resonance imaging (MRI) contrast agent. The coated SPIO could be easily dispersed in chitosan, and the hydrodynamic diameter of the coated SPIO in the chitosan solution was estimated to be 65 nm. The ferrofluids of various concentrations did not agglomerate for 30 days, indicating their good stability. The T1- and T2-weighted MR images of these ferrofluids were obtained and the MRI image contrasts were similar to those of Resovist ®.

  9. A new method for joint susceptibility artefact correction and super-resolution for dMRI

    NASA Astrophysics Data System (ADS)

    Ruthotto, Lars; Mohammadi, Siawoosh; Weiskopf, Nikolaus

    2014-03-01

    Diffusion magnetic resonance imaging (dMRI) has become increasingly relevant in clinical research and neuroscience. It is commonly carried out using the ultra-fast MRI acquisition technique Echo-Planar Imaging (EPI). While offering crucial reduction of acquisition times, two limitations of EPI are distortions due to varying magnetic susceptibilities of the object being imaged and its limited spatial resolution. In the recent years progress has been made both for susceptibility artefact correction and increasing of spatial resolution using image processing and reconstruction methods. However, so far, the interplay between both problems has not been studied and super-resolution techniques could only be applied along one axis, the slice-select direction, limiting the potential gain in spatial resolution. In this work we describe a new method for joint susceptibility artefact correction and super-resolution in EPI-MRI that can be used to increase resolution in all three spatial dimensions and in particular increase in-plane resolutions. The key idea is to reconstruct a distortion-free, high-resolution image from a number of low-resolution EPI data that are deformed in different directions. Numerical results on dMRI data of a human brain indicate that this technique has the potential to provide for the first time in-vivo dMRI at mesoscopic spatial resolution (i.e. 500μm) a spatial resolution that could bridge the gap between white-matter information from ex-vivo histology (≍1μm) and in-vivo dMRI (≍2000μm).

  10. Associations between the properties of the cartilage matrix and findings from quantitative MRI in human osteoarthritic cartilage of the knee.

    PubMed

    Wei, Bo; Du, Xiaotao; Liu, Jun; Mao, Fengyong; Zhang, Xiang; Liu, Shuai; Xu, Yan; Zang, Fengchao; Wang, Liming

    2015-01-01

    The aim of this study was to investigate the associations between the properties of the cartilage matrix and the results of T2 mapping and delayed gadolinium-enhanced magnetic resonance imaging (dGEMRIC) in human knee osteoarthritic cartilage. Osteochondral samples were harvested from the middle part of the femoral condyle and tibial plateaus of 20 patients with knee osteoarthritis (OA) during total knee arthroplasty. Sagittal T2 mapping, T1pre, and T1Gd were performed using 7.0T magnetic resonance imaging (MRI). Glycosaminoglycan (GAG) distribution was evaluated by OARSI, collagen anisotropy was assessed by polarized light microscopy (PLM), and biochemical analyses measured water, GAG, and collagen content. Associations between properties of the cartilage matrix and T2 and ΔR1 (1/T1Gd-1/T1pre) values were explored using correlation analysis. T2 and ΔR1 values were significantly correlated with the degree of cartilage degeneration (OARSI grade; Ρ = 0.53 and 0.77). T2 values were significantly correlated with water content (r = 0.69; P < 0.001), GAG content (r = -0.43; P < 0.001), and PLM grade (r = 0.47; P < 0.001), but not with collagen content (r = -0.02; P = 0.110). ΔR1 values were significantly correlated with GAG content (r = -0.84; P < 0.001) and PLM grade (r = 0.41; P < 0.001). Taken together, T2 mapping and dGEMRIC results were correlated with the properties of the cartilage matrix in human knee osteoarthritic cartilage. Combination T2 mapping and dGEMRIC represents a potential non-invasive monitoring technique to detect the progress of knee OA. PMID:26097577

  11. Method of performing MRI with an atomic magnetometer

    DOEpatents

    Savukov, Igor Mykhaylovich; Matlashov, Andrei Nikolaevich; Espy, Michelle A.; Volegov, Petr Lvovich; Kraus, Jr., Robert Henry; Zotev, Vadim Sergeyevich

    2012-11-06

    A method and apparatus are provided for performing an in-situ magnetic resonance imaging of an object. The method includes the steps of providing an atomic magnetometer, coupling a magnetic field generated by magnetically resonating samples of the object through a flux transformer to the atomic magnetometer and measuring a magnetic resonance of the atomic magnetometer.

  12. Method of performing MRI with an atomic magnetometer

    SciTech Connect

    Savukov, Igor Mykhaylovich; Matlashov, Andrei Nikolaevich; Espy, Michelle A; Volegov, Petr Lvovich; Kraus, Jr., Robert Henry; Zotev, Vadim Sergeyevich

    2013-08-27

    A method and apparatus are provided for performing an in-situ magnetic resonance imaging of an object. The method includes the steps of providing an atomic magnetometer, coupling a magnetic field generated by magnetically resonating samples of the object through a flux transformer to the atomic magnetometer and measuring a magnetic resonance of the atomic magnetometer.

  13. Multisensory integration of dynamic emotional faces and voices: method for simultaneous EEG-fMRI measurements

    PubMed Central

    Schelenz, Patrick D.; Klasen, Martin; Reese, Barbara; Regenbogen, Christina; Wolf, Dhana; Kato, Yutaka; Mathiak, Klaus

    2013-01-01

    Combined EEG-fMRI analysis correlates time courses from single electrodes or independent EEG components with the hemodynamic response. Implementing information from only one electrode, however, may miss relevant information from complex electrophysiological networks. Component based analysis, in turn, depends on a priori knowledge of the signal topography. Complex designs such as studies on multisensory integration of emotions investigate subtle differences in distributed networks based on only a few trials per condition. Thus, they require a sensitive and comprehensive approach which does not rely on a-priori knowledge about the underlying neural processes. In this pilot study, feasibility and sensitivity of source localization-driven analysis for EEG-fMRI was tested using a multisensory integration paradigm. Dynamic audiovisual stimuli consisting of emotional talking faces and pseudowords with emotional prosody were rated in a delayed response task. The trials comprised affectively congruent and incongruent displays. In addition to event-locked EEG and fMRI analyses, induced oscillatory EEG responses at estimated cortical sources and in specific temporo-spectral windows were correlated with the corresponding BOLD responses. EEG analysis showed high data quality with less than 10% trial rejection. In an early time window, alpha oscillations were suppressed in bilateral occipital cortices and fMRI analysis confirmed high data quality with reliable activation in auditory, visual and frontal areas to the presentation of multisensory stimuli. In line with previous studies, we obtained reliable correlation patterns for event locked occipital alpha suppression and BOLD signal time course. Our results suggest a valid methodological approach to investigate complex stimuli using the present source localization driven method for EEG-fMRI. This novel procedure may help to investigate combined EEG-fMRI data from novel complex paradigms with high spatial and temporal

  14. New method for predicting estrogen receptor status utilizing breast MRI texture kinetic analysis

    NASA Astrophysics Data System (ADS)

    Chaudhury, Baishali; Hall, Lawrence O.; Goldgof, Dmitry B.; Gatenby, Robert A.; Gillies, Robert; Drukteinis, Jennifer S.

    2014-03-01

    Magnetic Resonance Imaging (MRI) of breast cancer typically shows that tumors are heterogeneous with spatial variations in blood flow and cell density. Here, we examine the potential link between clinical tumor imaging and the underlying evolutionary dynamics behind heterogeneity in the cellular expression of estrogen receptors (ER) in breast cancer. We assume, in an evolutionary environment, that ER expression will only occur in the presence of significant concentrations of estrogen, which is delivered via the blood stream. Thus, we hypothesize, the expression of ER in breast cancer cells will correlate with blood flow on gadolinium enhanced breast MRI. To test this hypothesis, we performed quantitative analysis of blood flow on dynamic contrast enhanced MRI (DCE-MRI) and correlated it with the ER status of the tumor. Here we present our analytic methods, which utilize a novel algorithm to analyze 20 volumetric DCE-MRI breast cancer tumors. The algorithm generates post initial enhancement (PIE) maps from DCE-MRI and then performs texture features extraction from the PIE map, feature selection, and finally classification of tumors into ER positive and ER negative status. The combined gray level co-occurrence matrices, gray level run length matrices and local binary pattern histogram features allow quantification of breast tumor heterogeneity. The algorithm predicted ER expression with an accuracy of 85% using a Naive Bayes classifier in leave-one-out cross-validation. Hence, we conclude that our data supports the hypothesis that imaging characteristics can, through application of evolutionary principles, provide insights into the cellular and molecular properties of cancer cells.

  15. An adaptive MR-CT registration method for MRI-guided prostate cancer radiotherapy

    NASA Astrophysics Data System (ADS)

    Zhong, Hualiang; Wen, Ning; Gordon, James J.; Elshaikh, Mohamed A.; Movsas, Benjamin; Chetty, Indrin J.

    2015-04-01

    Magnetic Resonance images (MRI) have superior soft tissue contrast compared with CT images. Therefore, MRI might be a better imaging modality to differentiate the prostate from surrounding normal organs. Methods to accurately register MRI to simulation CT images are essential, as we transition the use of MRI into the routine clinic setting. In this study, we present a finite element method (FEM) to improve the performance of a commercially available, B-spline-based registration algorithm in the prostate region. Specifically, prostate contours were delineated independently on ten MRI and CT images using the Eclipse treatment planning system. Each pair of MRI and CT images was registered with the B-spline-based algorithm implemented in the VelocityAI system. A bounding box that contains the prostate volume in the CT image was selected and partitioned into a tetrahedral mesh. An adaptive finite element method was then developed to adjust the displacement vector fields (DVFs) of the B-spline-based registrations within the box. The B-spline and FEM-based registrations were evaluated based on the variations of prostate volume and tumor centroid, the unbalanced energy of the generated DVFs, and the clarity of the reconstructed anatomical structures. The results showed that the volumes of the prostate contours warped with the B-spline-based DVFs changed 10.2% on average, relative to the volumes of the prostate contours on the original MR images. This discrepancy was reduced to 1.5% for the FEM-based DVFs. The average unbalanced energy was 2.65 and 0.38 mJ cm-3, and the prostate centroid deviation was 0.37 and 0.28 cm, for the B-spline and FEM-based registrations, respectively. Different from the B-spline-warped MR images, the FEM-warped MR images have clear boundaries between prostates and bladders, and their internal prostatic structures are consistent with those of the original MR images. In summary, the developed adaptive FEM method preserves the prostate volume

  16. A hybrid method for classifying cognitive states from fMRI data.

    PubMed

    Parida, S; Dehuri, S; Cho, S-B; Cacha, L A; Poznanski, R R

    2015-09-01

    Functional magnetic resonance imaging (fMRI) makes it possible to detect brain activities in order to elucidate cognitive-states. The complex nature of fMRI data requires under-standing of the analyses applied to produce possible avenues for developing models of cognitive state classification and improving brain activity prediction. While many models of classification task of fMRI data analysis have been developed, in this paper, we present a novel hybrid technique through combining the best attributes of genetic algorithms (GAs) and ensemble decision tree technique that consistently outperforms all other methods which are being used for cognitive-state classification. Specifically, this paper illustrates the combined effort of decision-trees ensemble and GAs for feature selection through an extensive simulation study and discusses the classification performance with respect to fMRI data. We have shown that our proposed method exhibits significant reduction of the number of features with clear edge classification accuracy over ensemble of decision-trees.

  17. A hybrid method for classifying cognitive states from fMRI data.

    PubMed

    Parida, S; Dehuri, S; Cho, S-B; Cacha, L A; Poznanski, R R

    2015-09-01

    Functional magnetic resonance imaging (fMRI) makes it possible to detect brain activities in order to elucidate cognitive-states. The complex nature of fMRI data requires under-standing of the analyses applied to produce possible avenues for developing models of cognitive state classification and improving brain activity prediction. While many models of classification task of fMRI data analysis have been developed, in this paper, we present a novel hybrid technique through combining the best attributes of genetic algorithms (GAs) and ensemble decision tree technique that consistently outperforms all other methods which are being used for cognitive-state classification. Specifically, this paper illustrates the combined effort of decision-trees ensemble and GAs for feature selection through an extensive simulation study and discusses the classification performance with respect to fMRI data. We have shown that our proposed method exhibits significant reduction of the number of features with clear edge classification accuracy over ensemble of decision-trees. PMID:26455882

  18. Signal-to-noise ratio comparison of encoding methods for hyperpolarized noble gas MRI

    NASA Technical Reports Server (NTRS)

    Zhao, L.; Venkatesh, A. K.; Albert, M. S.; Panych, L. P.

    2001-01-01

    Some non-Fourier encoding methods such as wavelet and direct encoding use spatially localized bases. The spatial localization feature of these methods enables optimized encoding for improved spatial and temporal resolution during dynamically adaptive MR imaging. These spatially localized bases, however, have inherently reduced image signal-to-noise ratio compared with Fourier or Hadamad encoding for proton imaging. Hyperpolarized noble gases, on the other hand, have quite different MR properties compared to proton, primarily the nonrenewability of the signal. It could be expected, therefore, that the characteristics of image SNR with respect to encoding method will also be very different from hyperpolarized noble gas MRI compared to proton MRI. In this article, hyperpolarized noble gas image SNRs of different encoding methods are compared theoretically using a matrix description of the encoding process. It is shown that image SNR for hyperpolarized noble gas imaging is maximized for any orthonormal encoding method. Methods are then proposed for designing RF pulses to achieve normalized encoding profiles using Fourier, Hadamard, wavelet, and direct encoding methods for hyperpolarized noble gases. Theoretical results are confirmed with hyperpolarized noble gas MRI experiments. Copyright 2001 Academic Press.

  19. Unsupervised nonlinear dimensionality reduction machine learning methods applied to multiparametric MRI in cerebral ischemia: preliminary results

    NASA Astrophysics Data System (ADS)

    Parekh, Vishwa S.; Jacobs, Jeremy R.; Jacobs, Michael A.

    2014-03-01

    The evaluation and treatment of acute cerebral ischemia requires a technique that can determine the total area of tissue at risk for infarction using diagnostic magnetic resonance imaging (MRI) sequences. Typical MRI data sets consist of T1- and T2-weighted imaging (T1WI, T2WI) along with advanced MRI parameters of diffusion-weighted imaging (DWI) and perfusion weighted imaging (PWI) methods. Each of these parameters has distinct radiological-pathological meaning. For example, DWI interrogates the movement of water in the tissue and PWI gives an estimate of the blood flow, both are critical measures during the evolution of stroke. In order to integrate these data and give an estimate of the tissue at risk or damaged; we have developed advanced machine learning methods based on unsupervised non-linear dimensionality reduction (NLDR) techniques. NLDR methods are a class of algorithms that uses mathematically defined manifolds for statistical sampling of multidimensional classes to generate a discrimination rule of guaranteed statistical accuracy and they can generate a two- or three-dimensional map, which represents the prominent structures of the data and provides an embedded image of meaningful low-dimensional structures hidden in their high-dimensional observations. In this manuscript, we develop NLDR methods on high dimensional MRI data sets of preclinical animals and clinical patients with stroke. On analyzing the performance of these methods, we observed that there was a high of similarity between multiparametric embedded images from NLDR methods and the ADC map and perfusion map. It was also observed that embedded scattergram of abnormal (infarcted or at risk) tissue can be visualized and provides a mechanism for automatic methods to delineate potential stroke volumes and early tissue at risk.

  20. Image homogenization using pre-emphasis method for high field MRI

    PubMed Central

    Li, Ye; Wang, Chunsheng; Yu, Baiying; Vigneron, Daniel; Chen, Wei

    2013-01-01

    Radiofrequency (RF) field (B1) inhomogeneity due to shortened wavelength at high field is a major cause of magnetic resonance imaging (MRI) nonuniformity in high dielectric biological samples (e.g., human body). In this work, we propose a method to improve the B1 and MRI homogeneity by using pre-emphasized non-uniform B1 distribution. The intrinsic B1 distribution that could be generated by a RF volume coil, specifically a microstrip transmission line (MTL) coil used in this work, was pre-emphasized in the sample’s periphery region of interest to compensate for the central brightness induced by high frequency interference effect due to shortened wave length. This pre-emphasized non-uniform B1 can be realized by varying the parameters of microstrip elements, such as the substrate thickness of MTL volume coil. Both numerical simulation and phantom MR imaging studies were carried out to investigate the feasibility and merit of the proposed method in achieving homogeneous MR images. The simulation results demonstrate that by using a pre-emphasized B1 distribution generated by the MTL volume coil, relatively uniform B1 distribution and homogeneous MR image (98% homogeneity) within the spherical phantom (15 cm diameter) were achieved with 4.5 mm thickness. The B1 and MRI intensity distributions of a 16-element MTL volume coil with fixed substrate thickness and five varied saline loads were modeled and experimentally tested. Similar results from both simulation and experiments were obtained, suggesting substantial improvements of B1 and MRI homogeneities within the phantom containing 125 mM saline. The overall results demonstrate an efficient B1 shimming approach for improving high field MRI. PMID:24040618

  1. k-t Group sparse: a method for accelerating dynamic MRI.

    PubMed

    Usman, M; Prieto, C; Schaeffter, T; Batchelor, P G

    2011-10-01

    Compressed sensing (CS) is a data-reduction technique that has been applied to speed up the acquisition in MRI. However, the use of this technique in dynamic MR applications has been limited in terms of the maximum achievable reduction factor. In general, noise-like artefacts and bad temporal fidelity are visible in standard CS MRI reconstructions when high reduction factors are used. To increase the maximum achievable reduction factor, additional or prior information can be incorporated in the CS reconstruction. Here, a novel CS reconstruction method is proposed that exploits the structure within the sparse representation of a signal by enforcing the support components to be in the form of groups. These groups act like a constraint in the reconstruction. The information about the support region can be easily obtained from training data in dynamic MRI acquisitions. The proposed approach was tested in two-dimensional cardiac cine MRI with both downsampled and undersampled data. Results show that higher acceleration factors (up to 9-fold), with improved spatial and temporal quality, can be obtained with the proposed approach in comparison to the standard CS reconstructions. PMID:21394781

  2. An optimized target-field method for MRI transverse biplanar gradient coil design

    NASA Astrophysics Data System (ADS)

    Zhang, Rui; Xu, Jing; Fu, Youyi; Li, Yangjing; Huang, Kefu; Zhang, Jue; Fang, Jing

    2011-12-01

    Gradient coils are essential components of magnetic resonance imaging (MRI) systems. In this paper, we present an optimized target-field method for designing a transverse biplanar gradient coil with high linearity, low inductance and small resistance, which can well satisfy the requirements of permanent-magnet MRI systems. In this new method, the current density is expressed by trigonometric basis functions with unknown coefficients in polar coordinates. Following the standard procedures, we construct an objective function with respect to the total square errors of the magnetic field at all target-field points with the penalty items associated with the stored magnetic energy and the dissipated power. By adjusting the two penalty factors and minimizing the objective function, the appropriate coefficients of the current density are determined. Applying the stream function method to the current density, the specific winding patterns on the planes can be obtained. A novel biplanar gradient coil has been designed using this method to operate in a permanent-magnet MRI system. In order to verify the validity of the proposed approach, the gradient magnetic field generated by the resulted current density has been calculated via the Biot-Savart law. The results have demonstrated the effectiveness and advantage of this proposed method.

  3. Electromagnetic fields inside a lossy, multilayered spherical head phantom excited by MRI coils: models and methods.

    PubMed

    Liu, Feng; Crozier, Stuart

    2004-05-21

    The precise evaluation of electromagnetic field (EMF) distributions inside biological samples is becoming an increasingly important design requirement for high field MRI systems. In evaluating the induced fields caused by magnetic field gradients and RF transmitter coils, a multilayered dielectric spherical head model is proposed to provide a better understanding of electromagnetic interactions when compared to a traditional homogeneous head phantom. This paper presents Debye potential (DP) and Dyadic Green's function (DGF)-based solutions of the EMFs inside a head-sized, stratified sphere with similar radial conductivity and permittivity profiles as a human head. The DP approach is formulated for the symmetric case in which the source is a circular loop carrying a harmonic-formed current over a wide frequency range. The DGF method is developed for generic cases in which the source may be any kind of RF coil whose current distribution can be evaluated using the method of moments. The calculated EMFs can then be used to deduce MRI imaging parameters. The proposed methods, while not representing the full complexity of a head model, offer advantages in rapid prototyping as the computation times are much lower than a full finite difference time domain calculation using a complex head model. Test examples demonstrate the capability of the proposed models/methods. It is anticipated that this model will be of particular value for high field MRI applications, especially the rapid evaluation of RF resonator (surface and volume coils) and high performance gradient set designs.

  4. A new method based on Dempster-Shafer theory and fuzzy c-means for brain MRI segmentation

    NASA Astrophysics Data System (ADS)

    Liu, Jie; Lu, Xi; Li, Yunpeng; Chen, Xiaowu; Deng, Yong

    2015-10-01

    In this paper, a new method is proposed to decrease sensitiveness to motion noise and uncertainty in magnetic resonance imaging (MRI) segmentation especially when only one brain image is available. The method is approached with considering spatial neighborhood information by fusing the information of pixels with their neighbors with Dempster-Shafer (DS) theory. The basic probability assignment (BPA) of each single hypothesis is obtained from the membership function of applying fuzzy c-means (FCM) clustering to the gray levels of the MRI. Then multiple hypotheses are generated according to the single hypothesis. Then we update the objective pixel’s BPA by fusing the BPA of the objective pixel and those of its neighbors to get the final result. Some examples in MRI segmentation are demonstrated at the end of the paper, in which our method is compared with some previous methods. The results show that the proposed method is more effective than other methods in motion-blurred MRI segmentation.

  5. A Quantitative MRI Method for Imaging Blood-Brain Barrier Leakage in Experimental Traumatic Brain Injury

    PubMed Central

    Watts, Lora Talley; Jiang, Zhao; Shen, Qiang; Li, Yunxia; Duong, Timothy Q.

    2014-01-01

    Blood-brain barrier (BBB) disruption is common following traumatic brain injury (TBI). Dynamic contrast enhanced (DCE) MRI can longitudinally measure the transport coefficient Ktrans which reflects BBB permeability. Ktrans measurements however are not widely used in TBI research because it is generally considered to be noisy and possesses low spatial resolution. We improved spatiotemporal resolution and signal sensitivity of Ktrans MRI in rats by using a high-sensitivity surface transceiver coil. To overcome the signal drop off profile of the surface coil, a pre-scan module was used to map the flip angle (B1 field) and magnetization (M0) distributions. A series of T1-weighted gradient echo images were acquired and fitted to the extended Kety model with reversible or irreversible leakage, and the best model was selected using F-statistics. We applied this method to study the rat brain one hour following controlled cortical impact (mild to moderate TBI), and observed clear depiction of the BBB damage around the impact regions, which matched that outlined by Evans Blue extravasation. Unlike the relatively uniform T2 contrast showing cerebral edema, Ktrans shows a pronounced heterogeneous spatial profile in and around the impact regions, displaying a nonlinear relationship with T2. This improved Ktrans MRI method is also compatible with the use of high-sensitivity surface coil and the high-contrast two-coil arterial spin-labeling method for cerebral blood flow measurement, enabling more comprehensive investigation of the pathophysiology in TBI. PMID:25478693

  6. Real-time 2D spatially selective MRI experiments: Comparative analysis of optimal control design methods.

    PubMed

    Maximov, Ivan I; Vinding, Mads S; Tse, Desmond H Y; Nielsen, Niels Chr; Shah, N Jon

    2015-05-01

    There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community.

  7. Real-time 2D spatially selective MRI experiments: Comparative analysis of optimal control design methods

    NASA Astrophysics Data System (ADS)

    Maximov, Ivan I.; Vinding, Mads S.; Tse, Desmond H. Y.; Nielsen, Niels Chr.; Shah, N. Jon

    2015-05-01

    There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community.

  8. A high accuracy multi-image registration method for tracking MRI-guided robots

    NASA Astrophysics Data System (ADS)

    Shang, Weijian; Fischer, Gregory S.

    2012-02-01

    Recent studies have demonstrated an increasing number of functional surgical robots and other devices operating in the Magnetic Resonance Imaging (MRI) environment. Calibration and tracking of the robotic device is essential during such MRI-guided procedures. A fiducial tracking module is placed on the base or the end effector of the robot to localize it within the scanner, and thus the patient coordinate system. The fiducial frame represents a Z shape and is made of seven tubes filled with high contrast fluid. The frame is highlighted in the MR images and is used in localization. Compared to the former single image registration method, multiple images are used in this algorithm to calculate the position and orientation of the frame, and thus the robot. By using multiple images together, measurement error is reduced and the rigid requirement of slow to acquire high quality of images is not required. Accuracy and performance were evaluated in experiments which were operated with a Philips 3T MRI scanner. Presented is an accuracy comparison of the new method with varied number of images, and a comparison to more traditional single image registration techniques.

  9. Real-time 2D spatially selective MRI experiments: Comparative analysis of optimal control design methods.

    PubMed

    Maximov, Ivan I; Vinding, Mads S; Tse, Desmond H Y; Nielsen, Niels Chr; Shah, N Jon

    2015-05-01

    There is an increasing need for development of advanced radio-frequency (RF) pulse techniques in modern magnetic resonance imaging (MRI) systems driven by recent advancements in ultra-high magnetic field systems, new parallel transmit/receive coil designs, and accessible powerful computational facilities. 2D spatially selective RF pulses are an example of advanced pulses that have many applications of clinical relevance, e.g., reduced field of view imaging, and MR spectroscopy. The 2D spatially selective RF pulses are mostly generated and optimised with numerical methods that can handle vast controls and multiple constraints. With this study we aim at demonstrating that numerical, optimal control (OC) algorithms are efficient for the design of 2D spatially selective MRI experiments, when robustness towards e.g. field inhomogeneity is in focus. We have chosen three popular OC algorithms; two which are gradient-based, concurrent methods using first- and second-order derivatives, respectively; and a third that belongs to the sequential, monotonically convergent family. We used two experimental models: a water phantom, and an in vivo human head. Taking into consideration the challenging experimental setup, our analysis suggests the use of the sequential, monotonic approach and the second-order gradient-based approach as computational speed, experimental robustness, and image quality is key. All algorithms used in this work were implemented in the MATLAB environment and are freely available to the MRI community. PMID:25863895

  10. Appraising the Role of Iron in Brain Aging and Cognition: Promises and Limitations of MRI Methods

    PubMed Central

    Daugherty, Ana M; Raz, Naftali

    2015-01-01

    Age-related increase in frailty is accompanied by a fundamental shift in cellular iron homeostasis. By promoting oxidative stress, the intracellular accumulation of non-heme iron outside of binding complexes contributes to chronic inflammation and interferes with normal brain metabolism. In the absence of direct non-invasive biomarkers of brain oxidative stress, iron accumulation estimated in vivo may serve as its proxy indicator. Hence, developing reliable in vivo measurements of brain iron content via magnetic resonance imaging (MRI) is of significant interest in human neuroscience. To date, by estimating brain iron content through various MRI methods, significant age differences and age-related increases in iron content of the basal ganglia have been revealed across multiple samples. Less consistent are the findings that pertain to the relationship between elevated brain iron content and systemic indices of vascular and metabolic dysfunction. Only a handful of cross-sectional investigations have linked high iron content in various brain regions and poor performance on assorted cognitive tests. The even fewer longitudinal studies indicate that iron accumulation may precede shrinkage of the basal ganglia and thus predict poor maintenance of cognitive functions. This rapidly developing field will benefit from introduction of higher-field MRI scanners, improvement in iron-sensitive and -specific acquisition sequences and post-processing analytic and computational methods, as well as accumulation of data from long-term longitudinal investigations. This review describes the potential advantages and promises of MRI-based assessment of brain iron, summarizes recent findings and highlights the limitations of the current methodology. PMID:26248580

  11. Appraising the Role of Iron in Brain Aging and Cognition: Promises and Limitations of MRI Methods.

    PubMed

    Daugherty, Ana M; Raz, Naftali

    2015-09-01

    Age-related increase in frailty is accompanied by a fundamental shift in cellular iron homeostasis. By promoting oxidative stress, the intracellular accumulation of non-heme iron outside of binding complexes contributes to chronic inflammation and interferes with normal brain metabolism. In the absence of direct non-invasive biomarkers of brain oxidative stress, iron accumulation estimated in vivo may serve as its proxy indicator. Hence, developing reliable in vivo measurements of brain iron content via magnetic resonance imaging (MRI) is of significant interest in human neuroscience. To date, by estimating brain iron content through various MRI methods, significant age differences and age-related increases in iron content of the basal ganglia have been revealed across multiple samples. Less consistent are the findings that pertain to the relationship between elevated brain iron content and systemic indices of vascular and metabolic dysfunction. Only a handful of cross-sectional investigations have linked high iron content in various brain regions and poor performance on assorted cognitive tests. The even fewer longitudinal studies indicate that iron accumulation may precede shrinkage of the basal ganglia and thus predict poor maintenance of cognitive functions. This rapidly developing field will benefit from introduction of higher-field MRI scanners, improvement in iron-sensitive and -specific acquisition sequences and post-processing analytic and computational methods, as well as accumulation of data from long-term longitudinal investigations. This review describes the potential advantages and promises of MRI-based assessment of brain iron, summarizes recent findings and highlights the limitations of the current methodology.

  12. fMRI contrast at high and ultrahigh magnetic fields: insight from complementary methods.

    PubMed

    Ciobanu, Luisa; Solomon, Eddy; Pyatigorskaya, Nadya; Roussel, Tangi; Le Bihan, Denis; Frydman, Lucio

    2015-06-01

    This manuscript examines the origins and nature of the function-derived activation detected by magnetic resonance imaging at ultrahigh fields using different encoding methods. A series of preclinical high field (7 T) and ultra-high field (17.2 T) fMRI experiments were performed using gradient echo EPI, spin echo EPI and spatio-temporally encoded (SPEN) strategies. The dependencies of the fMRI signal change on the strength of the magnetic field and on different acquisition and sequence parameters were investigated. Artifact-free rat brain images with good resolution in all areas, as well as significant localized activation maps upon forepaw stimulation, were obtained in a single scan using fully refocused SPEN sequences devoid of T2* effects. Our results showed that, besides the normal T2-weighted BOLD contribution that arises in spin-echo sequences, fMRI SPEN signals contain a strong component caused by apparent T1-related effects, demonstrating the potential of such technique for exploring functional activation in rodents and on humans at ultrahigh fields. PMID:25795340

  13. A method to reduce the Gibbs ringing artifact in MRI scans while keeping tissue boundary integrity.

    PubMed

    Archibald, Rick; Gelb, Anne

    2002-04-01

    Gibbs ringing is a well known artifact that effects reconstruction of images having discontinuities. This is a problem in the reconstruction of magnetic resonance imaging (MRI) data due to the many different tissues normally present in each scan. The Gibbs ringing artifact manifests itself at the boundaries of the tissues, making it difficult to determine the structure of the brain tissue. The Gegenbauer reconstruction method has been shown to effectively eliminate the effects of Gibbs ringing in other applications. This paper presents the application of the Gegenbauer reconstruction method to neuro-imaging. PMID:12022619

  14. The efficiency of fMRI region of interest analysis methods for detecting group differences

    PubMed Central

    Hutchison, Joanna L.; Hubbard, Nicholas A.; Brigante, Ryan M.; Turner, Monroe; Sandoval, Traci I.; Hillis, G. Andrew J.; Weaver, Travis; Rypma, Bart

    2014-01-01

    Background Using a standard space brain template is an efficient way of determining region-of-interest (ROI) boundaries for functional magnetic resonance imaging (fMRI) data analyses. However, ROIs based on landmarks on subject-specific (i.e., native space) brain surfaces are anatomically accurate and probably best reflect the regional blood oxygen level dependent (BOLD) response for the individual. Unfortunately, accurate native space ROIs are often time-intensive to delineate even when using automated methods. New Method We compared analyses of group differences when using standard versus native space ROIs using both volume and surface-based analyses. Collegiate and military-veteran participants completed a button press task and a digit-symbol verification task during fMRI acquisition. Data were analyzed within ROIs representing left and right motor and prefrontal cortices, in native and standard space. Volume and surface-based analysis results were also compared using both functional (i.e., percent signal change) and structural (i.e., voxel or node count) approaches. Results and Comparison with Existing Method(s) Results suggest that transformation into standard space can affect the outcome of structural and functional analyses (inflating/minimizing differences, based on cortical geography), and these transformations can affect conclusions regarding group differences with volumetric data. Conclusions Caution is advised when applying standard space ROIs to volumetric fMRI data. However, volumetric analyses show group differences and are appropriate in circumstances when time is limited. Surface-based analyses using functional ROIs generated the greatest group differences and were less susceptible to differences between native and standard space. We conclude that surface-based analyses are preferable with adequate time and computing resources. PMID:24487017

  15. Automated Robust Image Segmentation: Level Set Method Using Nonnegative Matrix Factorization with Application to Brain MRI.

    PubMed

    Dera, Dimah; Bouaynaya, Nidhal; Fathallah-Shaykh, Hassan M

    2016-07-01

    We address the problem of fully automated region discovery and robust image segmentation by devising a new deformable model based on the level set method (LSM) and the probabilistic nonnegative matrix factorization (NMF). We describe the use of NMF to calculate the number of distinct regions in the image and to derive the local distribution of the regions, which is incorporated into the energy functional of the LSM. The results demonstrate that our NMF-LSM method is superior to other approaches when applied to synthetic binary and gray-scale images and to clinical magnetic resonance images (MRI) of the human brain with and without a malignant brain tumor, glioblastoma multiforme. In particular, the NMF-LSM method is fully automated, highly accurate, less sensitive to the initial selection of the contour(s) or initial conditions, more robust to noise and model parameters, and able to detect as small distinct regions as desired. These advantages stem from the fact that the proposed method relies on histogram information instead of intensity values and does not introduce nuisance model parameters. These properties provide a general approach for automated robust region discovery and segmentation in heterogeneous images. Compared with the retrospective radiological diagnoses of two patients with non-enhancing grade 2 and 3 oligodendroglioma, the NMF-LSM detects earlier progression times and appears suitable for monitoring tumor response. The NMF-LSM method fills an important need of automated segmentation of clinical MRI. PMID:27417984

  16. Hybrid ICA-Seed-Based Methods for fMRI Functional Connectivity Assessment: A Feasibility Study

    PubMed Central

    Kelly, Robert E.; Wang, Zhishun; Alexopoulos, George S.; Gunning, Faith M.; Murphy, Christopher F.; Morimoto, Sarah Shizuko; Kanellopoulos, Dora; Jia, Zhiru; Lim, Kelvin O.; Hoptman, Matthew J.

    2010-01-01

    Brain functional connectivity (FC) is often assessed from fMRI data using seed-based methods, such as those of detecting temporal correlation between a predefined region (seed) and all other regions in the brain; or using multivariate methods, such as independent component analysis (ICA). ICA is a useful data-driven tool, but reproducibility issues complicate group inferences based on FC maps derived with ICA. These reproducibility issues can be circumvented with hybrid methods that use information from ICA-derived spatial maps as seeds to produce seed-based FC maps. We report results from five experiments to demonstrate the potential advantages of hybrid ICA-seed-based FC methods, comparing results from regressing fMRI data against task-related a priori time courses, with “back-reconstruction” from a group ICA, and with five hybrid ICA-seed-based FC methods: ROI-based with (1) single-voxel, (2) few-voxel, and (3) many-voxel seed; and dual-regression-based with (4) single ICA map and (5) multiple ICA map seed. PMID:20689712

  17. Principal Component Analysis of breast DCE-MRI Adjusted with a Model Based Method

    PubMed Central

    Eyal, Erez.; Badikhi, Daria; Furman-Haran, Edna; Kelcz, Fredrick; Kirshenbaum, Kevin J.; Degani, Hadassa

    2010-01-01

    Purpose To investigate a fast, objective and standardized method for analyzing breast DCE-MRI applying principal component analysis (PCA) adjusted with a model based method. Materials and Methods 3D gradient-echo dynamic contrast-enhanced breast images of 31 malignant and 38 benign lesions, recorded on a 1.5 Tesla scanner were retrospectively analyzed by PCA and by the model based three-time-point (3TP) method. Results Intensity scaled (IS) and enhancement scaled (ES) datasets were reduced by PCA yielding a 1st IS-eigenvector that captured the signal variation between fat and fibroglandular tissue; two IS-eigenvectors and the two first ES-eigenvectors that captured contrast-enhanced changes, whereas the remaining eigenvectors captured predominantly noise changes. Rotation of the two contrast related eigenvectors led to a high congruence between the projection coefficients and the 3TP parameters. The ES-eigenvectors and the rotation angle were highly reproducible across malignant lesions enabling calculation of a general rotated eigenvector base. ROC curve analysis of the projection coefficients of the two eigenvectors indicated high sensitivity of the 1st rotated eigenvector to detect lesions (AUC>0.97) and of the 2nd rotated eigenvector to differentiate malignancy from benignancy (AUC=0.87). Conclusion PCA adjusted with a model-based method provided a fast and objective computer-aided diagnostic tool for breast DCE-MRI. PMID:19856419

  18. 3-dimensional throat region segmentation from MRI data based on Fourier interpolation and 3-dimensional level set methods.

    PubMed

    Campbell, Sean; Doshi, Trushali; Soraghan, John; Petropoulakis, Lykourgos; Di Caterina, Gaetano; Grose, Derek; MacKenzie, Kenneth

    2015-01-01

    A new algorithm for 3D throat region segmentation from magnetic resonance imaging (MRI) is presented. The proposed algorithm initially pre-processes the MRI data to increase the contrast between the throat region and its surrounding tissues and to reduce artifacts. Isotropic 3D volume is reconstructed using the Fourier interpolation. Furthermore, a cube encompassing the throat region is evolved using level set method to form a smooth 3D boundary of the throat region. The results of the proposed algorithm on real and synthetic MRI data are used to validate the robustness and accuracy of the algorithm.

  19. Heart MRI

    MedlinePlus

    Magnetic resonance imaging - cardiac; Magnetic resonance imaging - heart; Nuclear magnetic resonance - cardiac; NMR - cardiac; MRI of the heart; Cardiomyopathy - MRI; Heart failure - MRI; Congenital heart disease - MRI

  20. An empirical Bayes normalization method for connectivity metrics in resting state fMRI

    PubMed Central

    Chen, Shuo; Kang, Jian; Wang, Guoqing

    2015-01-01

    Functional connectivity analysis using resting-state functional magnetic resonance imaging (rs-fMRI) has emerged as a powerful technique for investigating functional brain networks. The functional connectivity is often quantified by statistical metrics (e.g., Pearson correlation coefficient), which may be affected by many image acquisition and preprocessing steps such as the head motion correction and the global signal regression. The appropriate quantification of the connectivity metrics is essential for meaningful and reproducible scientific findings. We propose a novel empirical Bayes method to normalize the functional brain connectivity metrics on a posterior probability scale. Moreover, the normalization function maps the original connectivity metrics to values between zero and one, which is well-suited for the graph theory based network analysis and avoids the information loss due to the (negative value) hard thresholding step. We apply the normalization method to a simulation study and the simulation results show that our normalization method effectively improves the robustness and reliability of the quantification of brain functional connectivity and provides more powerful group difference (biomarkers) detection. We illustrate our method on an analysis of a rs-fMRI dataset from the Autism Brain Imaging Data Exchange (ABIDE) study. PMID:26441493

  1. Evaluating pH in the Extracellular Tumor Microenvironment Using CEST MRI and Other Imaging Methods

    PubMed Central

    Chen, Liu Qi; Pagel, Mark D.

    2016-01-01

    Tumor acidosis is a consequence of altered metabolism, which can lead to chemoresistance and can be a target of alkalinizing therapies. Noninvasive measurements of the extracellular pH (pHe) of the tumor microenvironment can improve diagnoses and treatment decisions. A variety of noninvasive imaging methods have been developed for measuring tumor pHe. This review provides a detailed description of the advantages and limitations of each method, providing many examples from previous research reports. A substantial emphasis is placed on methods that use MR spectroscopy and MR imaging, including recently developed methods that use chemical exchange saturation transfer MRI that combines some advantages of MR spectroscopy and imaging. Together, this review provides a comprehensive overview of methods for measuring tumor pHe, which may facilitate additional creative approaches in this research field. PMID:27761517

  2. Two Methods of Mechanical Noise Reduction of Recorded Speech During Phonation in an MRI device

    NASA Astrophysics Data System (ADS)

    Přibil, J.; Horáček, J.; Horák, P.

    2011-01-01

    The paper presents two methods of noise reduction of speech signal recorded in an MRI device during phonation for the human vocal tract modelling. The applied approach of noise speech signal cleaning is based on cepstral speech analysis and synthesis because the noise is mainly produced by gradient coils, has a mechanical character, and can be processed in spectral domain. Our first noise reduction method is using real cepstrum limitation and clipping the "peaks" corresponding to the harmonic frequencies of mechanical noise. The second method is coming out from substation of the short-time spectra of two signals recorded withal: the first includes speech and noise, and the second consists of noise only. The resulting speech quality was compared by spectrogram and mean periodogram methods.

  3. Sub-band denoising and spline curve fitting method for hemodynamic measurement in perfusion MRI

    NASA Astrophysics Data System (ADS)

    Lin, Hong-Dun; Huang, Hsiao-Ling; Hsu, Yuan-Yu; Chen, Chi-Chen; Chen, Ing-Yi; Wu, Liang-Chi; Liu, Ren-Shyan; Lin, Kang-Ping

    2003-05-01

    In clinical research, non-invasive MR perfusion imaging is capable of investigating brain perfusion phenomenon via various hemodynamic measurements, such as cerebral blood volume (CBV), cerebral blood flow (CBF), and mean trasnit time (MTT). These hemodynamic parameters are useful in diagnosing brain disorders such as stroke, infarction and periinfarct ischemia by further semi-quantitative analysis. However, the accuracy of quantitative analysis is usually affected by poor signal-to-noise ratio image quality. In this paper, we propose a hemodynamic measurement method based upon sub-band denoising and spline curve fitting processes to improve image quality for better hemodynamic quantitative analysis results. Ten sets of perfusion MRI data and corresponding PET images were used to validate the performance. For quantitative comparison, we evaluate gray/white matter CBF ratio. As a result, the hemodynamic semi-quantitative analysis result of mean gray to white matter CBF ratio is 2.10 +/- 0.34. The evaluated ratio of brain tissues in perfusion MRI is comparable to PET technique is less than 1-% difference in average. Furthermore, the method features excellent noise reduction and boundary preserving in image processing, and short hemodynamic measurement time.

  4. A Method for Safety Testing of Radiofrequency/Microwave-Emitting Devices Using MRI

    PubMed Central

    Alon, Leeor; Cho, Gene Y.; Yang, Xing; Sodickson, Daniel K.; Deniz, Cem M.

    2015-01-01

    Purpose Strict regulations are imposed on the amount of radiofrequency (RF) energy that devices can emit to prevent excessive deposition of RF energy into the body. In this study, we investigated the application of MR temperature mapping and 10-g average specific absorption rate (SAR) computation for safety evaluation of RF-emitting devices. Methods Quantification of the RF power deposition was shown for an MRI-compatible dipole antenna and a non–MRI-compatible mobile phone via phantom temperature change measurements. Validation of the MR temperature mapping method was demonstrated by comparison with physical temperature measurements and electromagnetic field simulations. MR temperature measurements alongside physical property measurements were used to reconstruct 10-g average SAR. Results The maximum temperature change for a dipole antenna and the maximum 10-g average SAR were 1.83° C and 12.4 W/kg, respectively, for simulations and 1.73° C and 11.9 W/kg, respectively, for experiments. The difference between MR and probe thermometry was <0.15° C. The maximum temperature change and the maximum 10-g average SAR for a cell phone radiating at maximum output for 15 min was 1.7° C and 0.54 W/kg, respectively. Conclusion Information acquired using MR temperature mapping and thermal property measurements can assess RF/microwave safety with high resolution and fidelity. PMID:25424724

  5. Comparison of multi-subject ICA methods for analysis of fMRI data.

    PubMed

    Erhardt, Erik Barry; Rachakonda, Srinivas; Bedrick, Edward J; Allen, Elena A; Adali, Tülay; Calhoun, Vince D

    2011-12-01

    Spatial independent component analysis (ICA) applied to functional magnetic resonance imaging (fMRI) data identifies functionally connected networks by estimating spatially independent patterns from their linearly mixed fMRI signals. Several multi-subject ICA approaches estimating subject-specific time courses (TCs) and spatial maps (SMs) have been developed, however, there has not yet been a full comparison of the implications of their use. Here, we provide extensive comparisons of four multi-subject ICA approaches in combination with data reduction methods for simulated and fMRI task data. For multi-subject ICA, the data first undergo reduction at the subject and group levels using principal component analysis (PCA). Comparisons of subject-specific, spatial concatenation, and group data mean subject-level reduction strategies using PCA and probabilistic PCA (PPCA) show that computationally intensive PPCA is equivalent to PCA, and that subject-specific and group data mean subject-level PCA are preferred because of well-estimated TCs and SMs. Second, aggregate independent components are estimated using either noise-free ICA or probabilistic ICA (PICA). Third, subject-specific SMs and TCs are estimated using back-reconstruction. We compare several direct group ICA (GICA) back-reconstruction approaches (GICA1-GICA3) and an indirect back-reconstruction approach, spatio-temporal regression (STR, or dual regression). Results show the earlier group ICA (GICA1) approximates STR, however STR has contradictory assumptions and may show mixed-component artifacts in estimated SMs. Our evidence-based recommendation is to use GICA3, introduced here, with subject-specific PCA and noise-free ICA, providing the most robust and accurate estimated SMs and TCs in addition to offering an intuitive interpretation.

  6. Head MRI

    MedlinePlus

    ... the head; MRI - cranial; NMR - cranial; Cranial MRI; Brain MRI; MRI - brain; MRI - head ... the test, tell your provider if you have: Brain aneurysm clips An artificial heart valves Heart defibrillator ...

  7. SU-E-J-221: A Novel Expansion Method for MRI Based Target Delineation in Prostate Radiotherapy

    SciTech Connect

    Ruiz, B; Feng, Y; Shores, R; Fung, C

    2015-06-15

    Purpose: To compare a novel bladder/rectum carveout expansion method on MRI delineated prostate to standard CT and expansion based methods for maintaining prostate coverage while providing superior bladder and rectal sparing. Methods: Ten prostate cases were planned to include four trials: MRI vs CT delineated prostate/proximal seminal vesicles, and each image modality compared to both standard expansions (8mm 3D expansion and 5mm posterior, i.e. ∼8mm) and carveout method expansions (5mm 3D expansion, 4mm posterior for GTV-CTV excluding expansion into bladder/rectum followed by additional 5mm 3D expansion to PTV, i.e. ∼1cm). All trials were planned to total dose 7920 cGy via IMRT. Evaluation and comparison was made using the following criteria: QUANTEC constraints for bladder/rectum including analysis of low dose regions, changes in PTV volume, total control points, and maximum hot spot. Results: ∼8mm MRI expansion consistently produced the most optimal plan with lowest total control points and best bladder/rectum sparing. However, this scheme had the smallest prostate (average 22.9% reduction) and subsequent PTV volume, consistent with prior literature. ∼1cm MRI had an average PTV volume comparable to ∼8mm CT at 3.79% difference. Bladder QUANTEC constraints were on average less for the ∼1cm MRI as compared to the ∼8mm CT and observed as statistically significant with 2.64% reduction in V65. Rectal constraints appeared to follow the same trend. Case-by-case analysis showed variation in rectal V30 with MRI delineated prostate being most favorable regardless of expansion type. ∼1cm MRI and ∼8mm CT had comparable plan quality. Conclusion: MRI delineated prostate with standard expansions had the smallest PTV leading to margins that may be too tight. Bladder/rectum carveout expansion method on MRI delineated prostate was found to be superior to standard CT based methods in terms of bladder and rectal sparing while maintaining prostate coverage

  8. MRI methods for the evaluation of high intensity focused ultrasound tumor treatment: Current status and future needs.

    PubMed

    Hectors, Stefanie J C G; Jacobs, Igor; Moonen, Chrit T W; Strijkers, Gustav J; Nicolay, Klaas

    2016-01-01

    Thermal ablation with high intensity focused ultrasound (HIFU) is an emerging noninvasive technique for the treatment of solid tumors. HIFU treatment of malignant tumors requires accurate treatment planning, monitoring and evaluation, which can be facilitated by performing the procedure in an MR-guided HIFU system. The MR-based evaluation of HIFU treatment is most often restricted to contrast-enhanced T1 -weighted imaging, while it has been shown that the non-perfused volume may not reflect the extent of nonviable tumor tissue after HIFU treatment. There are multiple studies in which more advanced MRI methods were assessed for their suitability for the evaluation of HIFU treatment. While several of these methods seem promising regarding their sensitivity to HIFU-induced tissue changes, there is still ample room for improvement of MRI protocols for HIFU treatment evaluation. In this review article, we describe the major acute and delayed effects of HIFU treatment. For each effect, the MRI methods that have been-or could be-used to detect the associated tissue changes are described. In addition, the potential value of multiparametric MRI for the evaluation of HIFU treatment is discussed. The review ends with a discussion on future directions for the MRI-based evaluation of HIFU treatment.

  9. SU-E-J-196: New Visualization Methods for Longitudinal MRI Registrations and Segmentations

    SciTech Connect

    Veeraraghavan, H; Deasy, J

    2014-06-01

    Purpose: To develop visualization techniques to facilitate easy assessment of (a) registration and (b) tracking volumetric changes in structures during radiation therapy from MRI. Method: The frequently used method for visualizing registrations between scans is a multi-color overlay technique or deformation vector fields. However, the overlay technique is unintuitive and does not help to appreciate the quality of registration particularly when the registration mismatches are not very large. Similarly, the deformation fields give an indication of extent of deformation but do not help to assess the differences in registration. We present a mirroring and edge-augmented mirroring technique that places the fixed and moving image next to each other and allows the user to quickly assess the small differences in registration. Next, we present a volumetric intersection based 3D model to visualize the changes in diseased lymph node volumes in head and neck cancer. 3D model-based visualization provides more information about the location-specific changes in volume rather than the simplistic one dimensional information obtained from 2D plot of nodal volume changes. Result: We show results comparing our approach with the standard colorbased overlay method for comparing registrations of intra-patient registrations using T2-MRI. Upon comparing the mirroring technique with the color-overlay, one can more easily appreciate the differences in registration. Adding edge-based mirroring seems to further assist in evaluating the registration. Our approach for viewing registrations seems to be more intuitive and easy to use in order to help assess the quality of registration compared to color-based overlays. Similarly, the change volumetric model together with a 2D plot reveals more information including the locations undergoing changes and responding to treatment. Conclusions: Better approaches are necessary for assessing the quality of registrations and changes in diseased structures

  10. An accurate heart beat detection method in the EKG recorded in fMRI system.

    PubMed

    Oh, Sung Suk; Chung, Jun-Young; Yoon, Hyo Woon; Park, HyunWook

    2007-01-01

    The simultaneous recording of functional magnetic resonance imaging (fMRI) and electroencephalogram (EEG) provides an efficient signal for the high spatiotemporal brain mapping because each modality provides complementary information. The peak detection in the EEG signal measured in the MR scanner is necessary for removal of the ballistocardiac artifact. Especially, it would be affected by the quality of the EKG signal and the variation of the heart beat rate. Therefore, we propose the peak detection method using a K-teager energy operator (K-TEO) as well as further refinement processes in order to detect precise peaks. We applied this technique to the analysis of simulation waves with random noise and abrupt heat beat changes.

  11. Method for Simultaneous fMRI/EEG Data Collection during a Focused Attention Suggestion for Differential Thermal Sensation

    PubMed Central

    Douglas, Pamela K.; Pisani, Maureen; Reid, Rory; Head, Austin; Lau, Edward; Mirakhor, Ebrahim; Bramen, Jennifer; Gordon, Billi; Anderson, Ariana; Kerr, Wesley T.; Cheong, Chajoon; Cohen, Mark S.

    2014-01-01

    In the present work, we demonstrate a method for concurrent collection of EEG/fMRI data. In our setup, EEG data are collected using a high-density 256-channel sensor net. The EEG amplifier itself is contained in a field isolation containment system (FICS), and MRI clock signals are synchronized with EEG data collection for subsequent MR artifact characterization and removal. We demonstrate this method first for resting state data collection. Thereafter, we demonstrate a protocol for EEG/fMRI data recording, while subjects listen to a tape asking them to visualize that their left hand is immersed in a cold-water bath and referred to, here, as the cold glove paradigm. Thermal differentials between each hand are measured throughout EEG/fMRI data collection using an MR compatible temperature sensor that we developed for this purpose. We collect cold glove EEG/fMRI data along with simultaneous differential hand temperature measurements both before and after hypnotic induction. Between pre and post sessions, single modality EEG data are collected during the hypnotic induction and depth assessment process. Our representative results demonstrate that significant changes in the EEG power spectrum can be measured during hypnotic induction, and that hand temperature changes during the cold glove paradigm can be detected rapidly using our MR compatible differential thermometry device. PMID:24429915

  12. Efficacy Evaluation of Different Wavelet Feature Extraction Methods on Brain MRI Tumor Detection

    NASA Astrophysics Data System (ADS)

    Nabizadeh, Nooshin; John, Nigel; Kubat, Miroslav

    2014-03-01

    Automated Magnetic Resonance Imaging brain tumor detection and segmentation is a challenging task. Among different available methods, feature-based methods are very dominant. While many feature extraction techniques have been employed, it is still not quite clear which of feature extraction methods should be preferred. To help improve the situation, we present the results of a study in which we evaluate the efficiency of using different wavelet transform features extraction methods in brain MRI abnormality detection. Applying T1-weighted brain image, Discrete Wavelet Transform (DWT), Discrete Wavelet Packet Transform (DWPT), Dual Tree Complex Wavelet Transform (DTCWT), and Complex Morlet Wavelet Transform (CMWT) methods are applied to construct the feature pool. Three various classifiers as Support Vector Machine, K Nearest Neighborhood, and Sparse Representation-Based Classifier are applied and compared for classifying the selected features. The results show that DTCWT and CMWT features classified with SVM, result in the highest classification accuracy, proving of capability of wavelet transform features to be informative in this application.

  13. Measuring the subjective value of risky and ambiguous options using experimental economics and functional MRI methods.

    PubMed

    Levy, Ifat; Rosenberg Belmaker, Lior; Manson, Kirk; Tymula, Agnieszka; Glimcher, Paul W

    2012-09-19

    Most of the choices we make have uncertain consequences. In some cases the probabilities for different possible outcomes are precisely known, a condition termed "risky". In other cases when probabilities cannot be estimated, this is a condition described as "ambiguous". While most people are averse to both risk and ambiguity(1,2), the degree of those aversions vary substantially across individuals, such that the subjective value of the same risky or ambiguous option can be very different for different individuals. We combine functional MRI (fMRI) with an experimental economics-based method(3 )to assess the neural representation of the subjective values of risky and ambiguous options(4). This technique can be now used to study these neural representations in different populations, such as different age groups and different patient populations. In our experiment, subjects make consequential choices between two alternatives while their neural activation is tracked using fMRI. On each trial subjects choose between lotteries that vary in their monetary amount and in either the probability of winning that amount or the ambiguity level associated with winning. Our parametric design allows us to use each individual's choice behavior to estimate their attitudes towards risk and ambiguity, and thus to estimate the subjective values that each option held for them. Another important feature of the design is that the outcome of the chosen lottery is not revealed during the experiment, so that no learning can take place, and thus the ambiguous options remain ambiguous and risk attitudes are stable. Instead, at the end of the scanning session one or few trials are randomly selected and played for real money. Since subjects do not know beforehand which trials will be selected, they must treat each and every trial as if it and it alone was the one trial on which they will be paid. This design ensures that we can estimate the true subjective value of each option to each subject. We

  14. Optimizing methods for linking cinematic features to fMRI data.

    PubMed

    Kauttonen, Janne; Hlushchuk, Yevhen; Tikka, Pia

    2015-04-15

    One of the challenges of naturalistic neurosciences using movie-viewing experiments is how to interpret observed brain activations in relation to the multiplicity of time-locked stimulus features. As previous studies have shown less inter-subject synchronization across viewers of random video footage than story-driven films, new methods need to be developed for analysis of less story-driven contents. To optimize the linkage between our fMRI data collected during viewing of a deliberately non-narrative silent film 'At Land' by Maya Deren (1944) and its annotated content, we combined the method of elastic-net regularization with the model-driven linear regression and the well-established data-driven independent component analysis (ICA) and inter-subject correlation (ISC) methods. In the linear regression analysis, both IC and region-of-interest (ROI) time-series were fitted with time-series of a total of 36 binary-valued and one real-valued tactile annotation of film features. The elastic-net regularization and cross-validation were applied in the ordinary least-squares linear regression in order to avoid over-fitting due to the multicollinearity of regressors, the results were compared against both the partial least-squares (PLS) regression and the un-regularized full-model regression. Non-parametric permutation testing scheme was applied to evaluate the statistical significance of regression. We found statistically significant correlation between the annotation model and 9 ICs out of 40 ICs. Regression analysis was also repeated for a large set of cubic ROIs covering the grey matter. Both IC- and ROI-based regression analyses revealed activations in parietal and occipital regions, with additional smaller clusters in the frontal lobe. Furthermore, we found elastic-net based regression more sensitive than PLS and un-regularized regression since it detected a larger number of significant ICs and ROIs. Along with the ISC ranking methods, our regression analysis proved

  15. Optimizing methods for linking cinematic features to fMRI data.

    PubMed

    Kauttonen, Janne; Hlushchuk, Yevhen; Tikka, Pia

    2015-04-15

    One of the challenges of naturalistic neurosciences using movie-viewing experiments is how to interpret observed brain activations in relation to the multiplicity of time-locked stimulus features. As previous studies have shown less inter-subject synchronization across viewers of random video footage than story-driven films, new methods need to be developed for analysis of less story-driven contents. To optimize the linkage between our fMRI data collected during viewing of a deliberately non-narrative silent film 'At Land' by Maya Deren (1944) and its annotated content, we combined the method of elastic-net regularization with the model-driven linear regression and the well-established data-driven independent component analysis (ICA) and inter-subject correlation (ISC) methods. In the linear regression analysis, both IC and region-of-interest (ROI) time-series were fitted with time-series of a total of 36 binary-valued and one real-valued tactile annotation of film features. The elastic-net regularization and cross-validation were applied in the ordinary least-squares linear regression in order to avoid over-fitting due to the multicollinearity of regressors, the results were compared against both the partial least-squares (PLS) regression and the un-regularized full-model regression. Non-parametric permutation testing scheme was applied to evaluate the statistical significance of regression. We found statistically significant correlation between the annotation model and 9 ICs out of 40 ICs. Regression analysis was also repeated for a large set of cubic ROIs covering the grey matter. Both IC- and ROI-based regression analyses revealed activations in parietal and occipital regions, with additional smaller clusters in the frontal lobe. Furthermore, we found elastic-net based regression more sensitive than PLS and un-regularized regression since it detected a larger number of significant ICs and ROIs. Along with the ISC ranking methods, our regression analysis proved

  16. Investigation of a method for generating synthetic CT models from MRI scans of the head and neck for radiation therapy

    NASA Astrophysics Data System (ADS)

    Hsu, Shu-Hui; Cao, Yue; Huang, Ke; Feng, Mary; Balter, James M.

    2013-12-01

    Magnetic resonance (MR) images often provide superior anatomic and functional information over computed tomography (CT) images, but generally are not used alone without CT images for radiotherapy treatment planning and image guidance. This study aims to investigate the potential of probabilistic classification of voxels from multiple MRI contrasts to generate synthetic CT (‘MRCT’) images. The method consists of (1) acquiring multiple MRI volumes: T1-weighted, T2-weighted, two echoes from a ultra-short echo time (UTE) sequence, and calculated fat and water image volumes using a Dixon method, (2) classifying tissues using fuzzy c-means clustering with a spatial constraint, (3) assigning attenuation properties with weights based on the probability of individual tissue classes being present in each voxel, and (4) generating a MRCT image volume from the sum of attenuation properties in each voxel. The capability of each MRI contrast to differentiate tissues of interest was investigated based on a retrospective analysis of ten patients. For one prospective patient, the correlation of skull intensities between CT and MR was investigated, the discriminatory power of MRI in separating air from bone was evaluated, and the generated MRCT image volume was qualitatively evaluated. Our analyses showed that one MRI volume was not sufficient to separate all tissue types, and T2-weighted images was more sensitive to bone density variation compared to other MRI image types. The short echo UTE image showed significant improvement in contrasting air versus bone, but could not completely separate air from bone without false labeling. Generated MRCT and CT images showed similar contrast between bone and soft/solid tissues. These results demonstrate the potential of the presented method to generate synthetic CT images to support the workflow of radiation oncology treatment planning and image guidance.

  17. Breast MRI, digital mammography and breast tomosynthesis: Comparison of three methods for early detection of breast cancer

    PubMed Central

    Roganovic, Dragana; Djilas, Dragana; Vujnovic, Sasa; Pavic, Dag; Stojanov, Dragan

    2015-01-01

    Breast cancer is the most common malignancy in women and early detection is important for its successful treatment. The aim of this study was to investigate the sensitivity and specificity of three methods for early detection of breast cancer: breast magnetic resonance imaging (MRI), digital mammography, and breast tomosynthesis in comparison to histopathology, as well as to investigate the intraindividual variability between these modalities. We included 57 breast lesions, each detected by three diagnostic modalities: digital mammography, breast MRI, and breast tomosynthesis, and subsequently confirmed by histopathology. Breast Imaging-Reporting and Data System (BI-RADS) was used for characterizing the lesions. One experienced radiologist interpreted all three diagnostic modalities. Twenty-nine of the breast lesions were malignant while 28 were benign. The sensitivity for digital mammography, breast MRI, and breast tomosynthesis, was 72.4%, 93.1%, and 100%, respectively; while the specificity was 46.4%, 60.7%, and 75%, respectively. Receiver operating characteristics (ROC) curve analysis showed an overall diagnostic advantage of breast tomosynthesis over both breast MRI and digital mammography. with significant difference between breast tomosynthesis and digital mammography (p<0.001), while the difference between breast tomosynthesis and breast MRI was not significant (p = 0.20). PMID:26614855

  18. Common MRI acquisition non-idealities significantly impact the output of the boundary shift integral method of measuring brain atrophy on serial MRI.

    PubMed

    Preboske, Gregory M; Gunter, Jeff L; Ward, Chadwick P; Jack, Clifford R

    2006-05-01

    Measuring rates of brain atrophy from serial magnetic resonance imaging (MRI) studies is an attractive way to assess disease progression in neurodegenerative disorders, particularly Alzheimer's disease (AD). A widely recognized approach is the boundary shift integral (BSI). The objective of this study was to evaluate how several common scan non-idealities affect the output of the BSI algorithm. We created three types of image non-idealities between the image volumes in a serial pair used to measure between-scan change: inconsistent image contrast between serial scans, head motion, and poor signal-to-noise (SNR). In theory the BSI volume difference measured between each pair of images should be zero and any deviation from zero should represent corruption of the BSI measurement by some non-ideality intentionally introduced into the second scan in the pair. Two different BSI measures were evaluated, whole brain and ventricle. As the severity of motion, noise, and non-congruent image contrast increased in the second scan, the calculated BSI values deviated progressively more from the expected value of zero. This study illustrates the magnitude of the error in measures of change in brain and ventricle volume across serial MRI scans that can result from commonly encountered deviations from ideal image quality. The magnitudes of some of the measurement errors seen in this study exceed the disease effect in AD shown in various publications, which range from 1% to 2.78% per year for whole brain atrophy and 5.4% to 13.8% per year for ventricle expansion (Table 1). For example, measurement error may exceed 100% if image contrast properties dramatically differ between the two scans in a measurement pair. Methods to maximize consistency of image quality over time are an essential component of any quantitative serial MRI study.

  19. A wavelet method for modeling and despiking motion artifacts from resting-state fMRI time series

    PubMed Central

    Patel, Ameera X.; Kundu, Prantik; Rubinov, Mikail; Jones, P. Simon; Vértes, Petra E.; Ersche, Karen D.; Suckling, John; Bullmore, Edward T.

    2014-01-01

    The impact of in-scanner head movement on functional magnetic resonance imaging (fMRI) signals has long been established as undesirable. These effects have been traditionally corrected by methods such as linear regression of head movement parameters. However, a number of recent independent studies have demonstrated that these techniques are insufficient to remove motion confounds, and that even small movements can spuriously bias estimates of functional connectivity. Here we propose a new data-driven, spatially-adaptive, wavelet-based method for identifying, modeling, and removing non-stationary events in fMRI time series, caused by head movement, without the need for data scrubbing. This method involves the addition of just one extra step, the Wavelet Despike, in standard pre-processing pipelines. With this method, we demonstrate robust removal of a range of different motion artifacts and motion-related biases including distance-dependent connectivity artifacts, at a group and single-subject level, using a range of previously published and new diagnostic measures. The Wavelet Despike is able to accommodate the substantial spatial and temporal heterogeneity of motion artifacts and can consequently remove a range of high and low frequency artifacts from fMRI time series, that may be linearly or non-linearly related to physical movements. Our methods are demonstrated by the analysis of three cohorts of resting-state fMRI data, including two high-motion datasets: a previously published dataset on children (N = 22) and a new dataset on adults with stimulant drug dependence (N = 40). We conclude that there is a real risk of motion-related bias in connectivity analysis of fMRI data, but that this risk is generally manageable, by effective time series denoising strategies designed to attenuate synchronized signal transients induced by abrupt head movements. The Wavelet Despiking software described in this article is freely available for download at www

  20. A method to determine the necessity for global signal regression in resting-state fMRI studies.

    PubMed

    Chen, Gang; Chen, Guangyu; Xie, Chunming; Ward, B Douglas; Li, Wenjun; Antuono, Piero; Li, Shi-Jiang

    2012-12-01

    In resting-state functional MRI studies, the global signal (operationally defined as the global average of resting-state functional MRI time courses) is often considered a nuisance effect and commonly removed in preprocessing. This global signal regression method can introduce artifacts, such as false anticorrelated resting-state networks in functional connectivity analyses. Therefore, the efficacy of this technique as a correction tool remains questionable. In this article, we establish that the accuracy of the estimated global signal is determined by the level of global noise (i.e., non-neural noise that has a global effect on the resting-state functional MRI signal). When the global noise level is low, the global signal resembles the resting-state functional MRI time courses of the largest cluster, but not those of the global noise. Using real data, we demonstrate that the global signal is strongly correlated with the default mode network components and has biological significance. These results call into question whether or not global signal regression should be applied. We introduce a method to quantify global noise levels. We show that a criteria for global signal regression can be found based on the method. By using the criteria, one can determine whether to include or exclude the global signal regression in minimizing errors in functional connectivity measures.

  1. A correlation-based method for extracting subject-specific components and artifacts from group-fMRI data.

    PubMed

    Pamilo, Siina; Malinen, Sanna; Hotta, Jaakko; Seppä, Mika

    2015-11-01

    We present a simple but effective correlation-based method (maxCorr) for extracting subject-specific components from group-fMRI data. The method finds signal components that correlate maximally with the data set of one subject and minimally with the data sets of the other subjects. We show that such subject-specific components are often related to movement and physiological noise (e.g. cardiac cycle, respiration). We further demonstrate that removing the most subject-specific components for each subject reduces the overall data variance and improves the statistical identification of true fMRI activations. We compare the performance of maxCorr with CompCor, a commonly used artifact-finding method in fMRI analysis. We show that maxCorr is less likely than CompCor to remove actual stimulus-related activity, especially when no information about the stimulus is available. MaxCorr operates without stimulus information and is therefore well suitable for analyses of fMRI experiments employing naturalistic stimuli, such as movies, where stimulus regressors are difficult to construct, and for brain decoding techniques benefiting from reduced subject-specific variance in each subject's data.

  2. Concurrent NIRS-fMRI activation studies by using a new method for BOLD signal analysis

    NASA Astrophysics Data System (ADS)

    Sassaroli, Angelo; Frederick, Bruce d.; Tong, Yunjie; Renshaw, Perry F.; Fantini, Sergio

    2007-05-01

    We propose a new method for BOLD signal calculation that is more meaningful for comparison with NIRS data. We provide evidence that BOLD signal can be highly localized within the region of activation not only in terms of the amplitude of activation but also for the nuances of the temporal trend. Therefore, in order to take into account of the spatial dependence of BOLD signal we propose to introduce a weighting function given by a photon hitting density function calculated for a given optical source-detector pair. In one case study, after we define this new method of BOLD calculation and extract a BOLD trend for each optical source-detector pairs we show that there is an high correlation between this BOLD signal and the changes of oxy and deoxy hemoglobin calculated at the same source-detector pair; however the correlation becomes poorer when the newly defined BOLD signal is compared with the changes of oxy and deoxy hemoglobin occurring in different channels. This results is consistent with the fact that for this experiment (which used a 3T MRI machine) the BOLD and NIRS signals were sensitive to changes occurring in the same locations and in similar vascular compartments.

  3. Predicting response before initiation of neoadjuvant chemotherapy in breast cancer using new methods for the analysis of dynamic contrast enhanced MRI (DCE MRI) data

    NASA Astrophysics Data System (ADS)

    DeGrandchamp, Joseph B.; Whisenant, Jennifer G.; Arlinghaus, Lori R.; Abramson, V. G.; Yankeelov, Thomas E.; Cárdenas-Rodríguez, Julio

    2016-03-01

    The pharmacokinetic parameters derived from dynamic contrast enhanced (DCE) MRI have shown promise as biomarkers for tumor response to therapy. However, standard methods of analyzing DCE MRI data (Tofts model) require high temporal resolution, high signal-to-noise ratio (SNR), and the Arterial Input Function (AIF). Such models produce reliable biomarkers of response only when a therapy has a large effect on the parameters. We recently reported a method that solves the limitations, the Linear Reference Region Model (LRRM). Similar to other reference region models, the LRRM needs no AIF. Additionally, the LRRM is more accurate and precise than standard methods at low SNR and slow temporal resolution, suggesting LRRM-derived biomarkers could be better predictors. Here, the LRRM, Non-linear Reference Region Model (NRRM), Linear Tofts model (LTM), and Non-linear Tofts Model (NLTM) were used to estimate the RKtrans between muscle and tumor (or the Ktrans for Tofts) and the tumor kep,TOI for 39 breast cancer patients who received neoadjuvant chemotherapy (NAC). These parameters and the receptor statuses of each patient were used to construct cross-validated predictive models to classify patients as complete pathological responders (pCR) or non-complete pathological responders (non-pCR) to NAC. Model performance was evaluated using area under the ROC curve (AUC). The AUC for receptor status alone was 0.62, while the best performance using predictors from the LRRM, NRRM, LTM, and NLTM were AUCs of 0.79, 0.55, 0.60, and 0.59 respectively. This suggests that the LRRM can be used to predict response to NAC in breast cancer.

  4. Imaging transplanted stem cells in real time using an MRI dual-contrast method

    PubMed Central

    Ngen, Ethel J.; Wang, Lee; Kato, Yoshinori; Krishnamachary, Balaji; Zhu, Wenlian; Gandhi, Nishant; Smith, Barbara; Armour, Michael; Wong, John; Gabrielson, Kathleen; Artemov, Dmitri

    2015-01-01

    Stem cell therapies are currently being investigated for the repair of brain injuries. Although exogenous stem cell labelling with superparamagnetic iron oxide nanoparticles (SPIONs) prior to transplantation provides a means to noninvasively monitor stem cell transplantation by magnetic resonance imaging (MRI), monitoring cell death is still a challenge. Here, we investigate the feasibility of using an MRI dual-contrast technique to detect cell delivery, cell migration and cell death after stem cell transplantation. Human mesenchymal stem cells were dual labelled with SPIONs and gadolinium-based chelates (GdDTPA). The viability, proliferation rate, and differentiation potential of the labelled cells were then evaluated. The feasibility of this MRI technique to distinguish between live and dead cells was next evaluated using MRI phantoms, and in vivo using both immune-competent and immune-deficient mice, following the induction of brain injury in the mice. All results were validated with bioluminescence imaging. In live cells, a negative (T2/T2*) MRI contrast predominates, and is used to track cell delivery and cell migration. Upon cell death, a diffused positive (T1) MRI contrast is generated in the vicinity of the dead cells, and serves as an imaging marker for cell death. Ultimately, this technique could be used to manage stem cell therapies. PMID:26330231

  5. Imaging transplanted stem cells in real time using an MRI dual-contrast method.

    PubMed

    Ngen, Ethel J; Wang, Lee; Kato, Yoshinori; Krishnamachary, Balaji; Zhu, Wenlian; Gandhi, Nishant; Smith, Barbara; Armour, Michael; Wong, John; Gabrielson, Kathleen; Artemov, Dmitri

    2015-09-02

    Stem cell therapies are currently being investigated for the repair of brain injuries. Although exogenous stem cell labelling with superparamagnetic iron oxide nanoparticles (SPIONs) prior to transplantation provides a means to noninvasively monitor stem cell transplantation by magnetic resonance imaging (MRI), monitoring cell death is still a challenge. Here, we investigate the feasibility of using an MRI dual-contrast technique to detect cell delivery, cell migration and cell death after stem cell transplantation. Human mesenchymal stem cells were dual labelled with SPIONs and gadolinium-based chelates (GdDTPA). The viability, proliferation rate, and differentiation potential of the labelled cells were then evaluated. The feasibility of this MRI technique to distinguish between live and dead cells was next evaluated using MRI phantoms, and in vivo using both immune-competent and immune-deficient mice, following the induction of brain injury in the mice. All results were validated with bioluminescence imaging. In live cells, a negative (T2/T2*) MRI contrast predominates, and is used to track cell delivery and cell migration. Upon cell death, a diffused positive (T1) MRI contrast is generated in the vicinity of the dead cells, and serves as an imaging marker for cell death. Ultimately, this technique could be used to manage stem cell therapies.

  6. An improved hybrid MoM/FDTD technique for MRI RF coils modeling using Huygen's equivalent surface method.

    PubMed

    Li, Bing Keong; Liu, Feng; Weber, Ewald; Padhi, Shantanu; Crozier, Stuart

    2007-01-01

    In this work, an improved hybrid MoM/FDTD algorithm for modeling low to ultra high field MRI RF coil/sample interactions has been proposed. In our previous hybrid MoM/FDTD method, the accuracy of modeling MRI RF coils is generally hindered by two major issues, staircasing errors and rough approximation of the coil current distortions by electromagnetic reflections from sample. In view of this, a Huygen's equivalent surface method has been proposed to effectively bridge MoM and FDTD. In the improved hybrid MoM/FDTD algorithm, staircasing errors are eliminated, and most importantly the complex coil/tissue interactions are explicitly accounted for. The accuracy of the improved hybrid MoM/FDTD method is numerically verified with a well established hybrid Green function/MoM solution and also experimentally underpinned with MR images obtained using a prototype rotary phased array head coil.

  7. Iterative reconstruction method for three-dimensional non-cartesian parallel MRI

    NASA Astrophysics Data System (ADS)

    Jiang, Xuguang

    Parallel magnetic resonance imaging (MRI) with non-Cartesian sampling pattern is a promising technique that increases the scan speed using multiple receiver coils with reduced samples. However, reconstruction is challenging due to the increased complexity. Three reconstruction methods were evaluated: gridding, blocked uniform resampling (BURS) and non-uniform FFT (NUFFT). Computer simulations of parallel reconstruction were performed. Root mean square error (RMSE) of the reconstructed images to the simulated phantom were used as image quality criterion. Gridding method showed best RMSE performance. Two type of a priori constraints to reduce noise and artifacts were evaluated: edge preserving penalty, which suppresses noise and aliasing artifact in image while preventing over-smoothness, and object support penalty, which reduces background noise amplification. A trust region based step-ratio method that iteratively calculates the penalty coefficient was proposed for the penalty functions. Two methods to alleviate computation burden were evaluated: smaller over sampling ratio, and interpolation coefficient matrix compression. The performance were individually tested using computer simulations. Edge preserving penalty and object support penalty were shown to have consistent improvement on RMSE. The performance of calculated penalty coefficients on the two penalties were close to the best RMSE. Oversampling ratio as low as 1.125 was shown to have impact of less than one percent on RMSE for the radial sampling pattern reconstruction. The value reduced the three dimensional data requirement to less than 1/5 of what the conventional 2x grid needed. Interpolation matrix compression with compression ratio up to 50 percent showed small impact on RMSE. The proposed method was validated on 25MR data set from a GEMR scanner. Six image quality metrics were used to evaluate the performance. RMSE, normalized mutual information (NMI) and joint entropy (JE) relative to a reference

  8. Integrating fMRI and SNP data for biomarker identification for schizophrenia with a sparse representation based variable selection method

    PubMed Central

    2013-01-01

    Background In recent years, both single-nucleotide polymorphism (SNP) array and functional magnetic resonance imaging (fMRI) have been widely used for the study of schizophrenia (SCZ). In addition, a few studies have been reported integrating both SNPs data and fMRI data for comprehensive analysis. Methods In this study, a novel sparse representation based variable selection (SRVS) method has been proposed and tested on a simulation data set to demonstrate its multi-resolution properties. Then the SRVS method was applied to an integrative analysis of two different SCZ data sets, a Single-nucleotide polymorphism (SNP) data set and a functional resonance imaging (fMRI) data set, including 92 cases and 116 controls. Biomarkers for the disease were identified and validated with a multivariate classification approach followed by a leave one out (LOO) cross-validation. Then we compared the results with that of a previously reported sparse representation based feature selection method. Results Results showed that biomarkers from our proposed SRVS method gave significantly higher classification accuracy in discriminating SCZ patients from healthy controls than that of the previous reported sparse representation method. Furthermore, using biomarkers from both data sets led to better classification accuracy than using single type of biomarkers, which suggests the advantage of integrative analysis of different types of data. Conclusions The proposed SRVS algorithm is effective in identifying significant biomarkers for complicated disease as SCZ. Integrating different types of data (e.g. SNP and fMRI data) may identify complementary biomarkers benefitting the diagnosis accuracy of the disease. PMID:24565219

  9. A New Method for Preparing Mesenchymal Stem Cells and Labeling with Ferumoxytol for Cell Tracking by MRI

    PubMed Central

    Liu, Li; Tseng, Lanya; Ye, Qing; Wu, Yijen L.; Bain, Daniel J.; Ho, Chien

    2016-01-01

    Mesenchymal stem cells (MSCs) are among the major stem cells used for cell therapy and regenerative medicine. In-vivo cell-tracking by magnetic resonance imaging (MRI) is crucial for regenerative medicine, allowing verification that the transplanted cells reach the targeted sites. Cellular MRI combined with superparamagnetic iron-oxide (SPIO) contrast agents is an effective cell-tracking method. Here, we are reporting a new “bio-mimicry” method by making use of the “in-vivo environment” of MSCs to prepare native MSCs, so that (i) the phagocytic activity of cultured MSCs can be recovered and expanded MSCs can be ex-vivo labeled with Ferumoxytol, which is currently the only FDA approved SPIO nanoparticles for human use. Using our new method, 7-day cultured MSCs regain the capability to take up Ferumoxytol and exhibit an intracellular iron concentration of 2.50 ± 0.50 pg/MSC, comparable to that obtained by using Ferumoxytol-heparin-protamine nanocomplex; and (ii) cells can be re-sized to more native size, reducing from 32.0 ± 7.2 μm to 19.5 ± 5.2 μm. Our method can be very useful for expanding MSCs and labeling with Ferumoxytol, without the need for transfection agents and/or electroporation, allowing cell-tracking by MRI in both pre-clinical and clinical studies. PMID:27188664

  10. Multimodal Visualization of DTI and fMRI Data Using Illustrative Methods

    NASA Astrophysics Data System (ADS)

    Born, Silvia; Jainek, Werner; Hlawitschka, Mario; Scheuermann, Gerik; Trantakis, Christos; Meixensberger, Jürgen; Bartz, Dirk

    Designing multimodal visualizations combining anatomical and functional brain data is a demanding task. [1] applied illustrative rendering techniques to obtain a high-quality representation of the location and characteristic of brain activation areas (derived from MRI and fMRI). Here, we present the integration of DTI data into this system. Reconstructed nerve fibers connecting functional areas with each other and lower brain areas are embedded into the complex rendering pipeline. Further, we enhanced perception of depth and shape by applying silhouettes and dithered halftoning.

  11. A novel fMRI group data analysis method based on data-driven reference extracting from group subjects.

    PubMed

    Shi, Yuhu; Zeng, Weiming; Wang, Nizhuan; Chen, Dongtailang

    2015-12-01

    Group-independent component analysis (GICA) is a well-established blind source separation technique that has been widely applied to study multi-subject functional magnetic resonance imaging (fMRI) data. The group-independent components (GICs) represent the commonness of all of the subjects in the group. Similar to independent component analysis on the single-subject level, the performance of GICA can be improved for multi-subject fMRI data analysis by incorporating a priori information; however, a priori information is not always considered while looking for GICs in existing GICA methods, especially when no obvious or specific knowledge about an unknown group is available. In this paper, we present a novel method to extract the group intrinsic reference from all of the subjects of the group and then incorporate it into the GICA extraction procedure. Comparison experiments between FastICA and GICA with intrinsic reference (GICA-IR) are implemented on the group level with regard to the simulated, hybrid and real fMRI data. The experimental results show that the GICs computed by GICA-IR have a higher correlation with the corresponding independent component of each subject in the group, and the accuracy of activation regions detected by GICA-IR was also improved. These results have demonstrated the advantages of the GICA-IR method, which can better reflect the commonness of the subjects in the group. PMID:26387634

  12. Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure

    PubMed Central

    Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M.; Komlosh, Michal E.; İrfanoğlu, M. Okan; Pierpaoli, Carlo; Basser, Peter J.

    2014-01-01

    Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in “q-space,” and the corresponding “mean apparent propagator (MAP)” describing molecular displacements in “r-space.” We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit “displacement” sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions—the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP-MRI

  13. Battlefield MRI

    SciTech Connect

    Espy, Michelle

    2015-06-01

    Magnetic Resonance Imaging is the best method for non-invasive imaging of soft tissue anatomy, saving countless lives each year. It is regarded as the gold standard for diagnosis of mild to moderate traumatic brain injuries. Furthermore, conventional MRI relies on very high, fixed strength magnetic fields (> 1.5 T) with parts-per-million homogeneity, which requires very large and expensive magnets.

  14. MRI and low back pain

    MedlinePlus

    Backache - MRI; Low back pain - MRI; Lumbar pain - MRI; Back strain - MRI; Lumbar radiculopathy - MRI; Herniated intervertebral disk - MRI; Prolapsed intervertebral disk - MRI; Slipped disk - MRI; Ruptured ...

  15. An aqueous method for the controlled manganese (Mn(2+)) substitution in superparamagnetic iron oxide nanoparticles for contrast enhancement in MRI.

    PubMed

    Ereath Beeran, Ansar; Nazeer, Shaiju S; Fernandez, Francis Boniface; Muvvala, Krishna Surendra; Wunderlich, Wilfried; Anil, Sukumaran; Vellappally, Sajith; Ramachandra Rao, M S; John, Annie; Jayasree, Ramapurath S; Varma, P R Harikrishna

    2015-02-14

    Despite the success in the use of superparamagnetic iron oxide nanoparticles (SPION) for various scientific applications, its potential in biomedical fields has not been exploited to its full potential. In this context, an in situ substitution of Mn(2+) was performed in SPION and a series of ferrite particles, MnxFe1-xFe2O4 with a varying molar ratio of Mn(2+) : Fe(2+) where 'x' varies from 0-0.75. The ferrite particles obtained were further studied in MRI contrast applications and showed appreciable enhancement in their MRI contrast properties. Manganese substituted ferrite nanocrystals (MnIOs) were synthesized using a novel, one-step aqueous co-precipitation method based on the use of a combination of sodium hydroxide and trisodium citrate (TSC). This approach yielded the formation of highly crystalline, superparamagnetic MnIOs with good control over their size and bivalent Mn ion crystal substitution. The presence of a TSC hydrophilic layer on the surface facilitated easy dispersion of the materials in an aqueous media. Primary characterizations such as structural, chemical and magnetic properties demonstrated the successful formation of manganese substituted ferrite. More significantly, the MRI relaxivity of the MnIOs improved fourfold when compared to SPION crystals imparting high potential for use as an MRI contrast agent. Further, the cytocompatibility and blood compatibility evaluations demonstrated excellent cell morphological integrity even at high concentrations of nanoparticles supporting the non-toxic nature of nanoparticles. These results open new horizons for the design of biocompatible water dispersible ferrite nanoparticles with good relaxivity properties via a versatile and easily scalable co-precipitation route. PMID:25586703

  16. Three-band MRI image fusion utilizing the wavelet-based method optimized with two quantitative fusion metrics

    NASA Astrophysics Data System (ADS)

    Zheng, Yufeng; Elmaghraby, Adel S.; Frigui, Hichem

    2006-03-01

    In magnetic resonance imaging (MRI), there are three bands of images ("MRI triplet") available, which are T1-, T2- and PD-weighted images. The three images of a MRI triplet provide complementary structure information and therefore it is useful for diagnosis and subsequent analysis to combine three-band images into one. We propose an advanced discrete wavelet transform (αDWT) for three-band MRI image fusion and the αDWT algorithm is further optimized utilizing two quantitative fusion metrics - the image quality index (IQI) and ratio spatial frequency error (rSFe). In the aDWT method, principle component analysis (PCA) and morphological processing are incorporated into a regular DWT fusion algorithm. Furthermore, the αDWT has two adjustable parameters - the level of DWT decomposition (L d) and the length of the selected wavelet (L w) that determinately affect the fusion result. The fused image quality can be quantitatively measured with the established metrics - IQI and rSFe. Varying the control parameters (L d and L w), an iterative fusion procedure can be implemented and running until an optimized fusion is achieved. We fused and analyzed several MRI triplets from the Visible Human Project ® female dataset. From the quantitative and qualitative evaluations of fused images, we found that (1) the αDWTi-IQI algorithm produces a smoothed image whereas the αDWTi-rSFe algorithm yields a sharpened image, (2) fused image "T1+T2" is the most informative one in comparison with other two-in-one fusions (PD+T1 and PD+T2), (3) for three-in-one fusions, no significant difference is observed among the three fusions of (PD+T1)+T2, (PD+T2)+T1 and (T1+T2)+PD, thus the order of fusion does not play an important role. The fused images can significantly benefit medical diagnosis and also the further image processing such as multi-modality image fusion (with CT images), visualization (colorization), segmentation, classification and computer-aided diagnosis (CAD).

  17. Temperature mapping in bread dough using SE and GE two-point MRI methods: experimental and theoretical estimation of uncertainty.

    PubMed

    Lucas, Tiphaine; Musse, Maja; Bornert, Mélanie; Davenel, Armel; Quellec, Stéphane

    2012-04-01

    Two-dimensional (2D)-SE, 2D-GE and tri-dimensional (3D)-GE two-point T(1)-weighted MRI methods were evaluated in this study in order to maximize the accuracy of temperature mapping of bread dough during thermal processing. Uncertainties were propagated throughout each protocol of measurement, and comparisons demonstrated that all the methods with comparable acquisition times minimized the temperature uncertainty to similar extent. The experimental uncertainties obtained with low-field MRI were also compared to the theoretical estimations. Some discrepancies were reported between experimental and theoretical values of uncertainties of temperature; however, experimental and theoretical trends with varying parameters agreed to a large extent for both SE and GE methods. The 2D-SE method was chosen for further applications on prefermented dough because of its lower sensitivity to susceptibility differences in porous media. It was applied for temperature mapping in prefermented dough during chilling prior to freezing and compared locally to optical fiber measurements.

  18. Temperature mapping in bread dough using SE and GE two-point MRI methods: experimental and theoretical estimation of uncertainty.

    PubMed

    Lucas, Tiphaine; Musse, Maja; Bornert, Mélanie; Davenel, Armel; Quellec, Stéphane

    2012-04-01

    Two-dimensional (2D)-SE, 2D-GE and tri-dimensional (3D)-GE two-point T(1)-weighted MRI methods were evaluated in this study in order to maximize the accuracy of temperature mapping of bread dough during thermal processing. Uncertainties were propagated throughout each protocol of measurement, and comparisons demonstrated that all the methods with comparable acquisition times minimized the temperature uncertainty to similar extent. The experimental uncertainties obtained with low-field MRI were also compared to the theoretical estimations. Some discrepancies were reported between experimental and theoretical values of uncertainties of temperature; however, experimental and theoretical trends with varying parameters agreed to a large extent for both SE and GE methods. The 2D-SE method was chosen for further applications on prefermented dough because of its lower sensitivity to susceptibility differences in porous media. It was applied for temperature mapping in prefermented dough during chilling prior to freezing and compared locally to optical fiber measurements. PMID:22227351

  19. Multi-parametric MRI characterization of enzymatically degraded articular cartilage.

    PubMed

    Nissi, Mikko J; Salo, Elli-Noora; Tiitu, Virpi; Liimatainen, Timo; Michaeli, Shalom; Mangia, Silvia; Ellermann, Jutta; Nieminen, Miika T

    2016-07-01

    Several laboratory and rotating frame quantitative MRI parameters were evaluated and compared for detection of changes in articular cartilage following selective enzymatic digestion. Bovine osteochondral specimens were subjected to 44 h incubation in control medium or in collagenase or chondroitinase ABC to induce superficial collagen or proteoglycan (glycosaminoglycan) alterations. The samples were scanned at 9.4 T for T1 , T1 Gd (dGEMRIC), T2 , adiabatic T1 ρ , adiabatic T2 ρ , continuous-wave T1 ρ , TRAFF2 , and T1 sat relaxation times and for magnetization transfer ratio (MTR). For reference, glycosaminoglycan content, collagen fibril orientation and biomechanical properties were determined. Changes primarily in the superficial cartilage were noted after enzymatic degradation. Most of the studied parameters were sensitive to the destruction of collagen network, whereas glycosaminoglycan depletion was detected only by native T1 and T1 Gd relaxation time constants throughout the tissue and by MTR superficially. T1 , adiabatic T1 ρ , adiabatic T2 ρ , continuous-wave T1 ρ , and T1 sat correlated significantly with the biomechanical properties while T1 Gd correlated with glycosaminoglycan staining. The findings indicated that most of the studied MRI parameters were sensitive to both glycosaminoglycan content and collagen network integrity, with changes due to enzymatic treatment detected primarily in the superficial tissue. Strong correlation of T1 , adiabatic T1ρ , adiabatic T2 ρ , continuous-wave T1 ρ , and T1 sat with the altered biomechanical properties, reflects that these parameters were sensitive to critical functional properties of cartilage. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1111-1120, 2016. PMID:26662555

  20. MRI Scans

    MedlinePlus

    Magnetic resonance imaging (MRI) uses a large magnet and radio waves to look at organs and structures inside your body. Health care professionals use MRI scans to diagnose a variety of conditions, from torn ...

  1. Comparison of dynamic susceptibility contrast-MRI perfusion quantification methods in the presence of delay and dispersion

    NASA Astrophysics Data System (ADS)

    Maan, Bianca; Simões, Rita Lopes; Meijer, Frederick J. A.; Klaas Jan Renema, W.; Slump, Cornelis H.

    2011-03-01

    The perfusion of the brain is essential to maintain brain function. Stroke is an example of a decrease in blood flow and reduced perfusion. During ischemic stroke the blood flow to tissue is hampered due to a clot inside a vessel. To investigate the recovery of stroke patients, follow up studies are necessary. MRI is the preferred imaging modality for follow up because of the absence of radiation dose concerns, contrary to CT. Dynamic Susceptibility Contrast (DSC) MRI is an imaging technique used for measuring perfusion of the brain, however, is not standard applied in the clinical routine due to lack of immediate patient benefit. Several post processing algorithms are described in the literature to obtain cerebral blood flow (CBF). The quantification of CBF relies on the deconvolution of a tracer concentration-time curve in an arterial and a tissue voxel. There are several methods to obtain this deconvolution based on singular-value decomposition (SVD). This contribution describes a comparison between the different approaches as currently there is no best practice for (all) clinical relevant situations. We investigate the influence of tracer delay, dispersion and recirculation on the performance of the methods. In the presence of negative delays, the truncated SVD approach overestimates the CBF. Block-circulant and reformulated SVD are delay-independent. Due to its delay dependent behavior, the truncated SVD approach performs worse in the presence of dispersion as well. However all SVD approaches are dependent on the amount of dispersion. Moreover, we observe that the optimal truncation parameter varies when recirculation is added to noisy data, suggesting that, in practice, these methods are not immune to tracer recirculation. Finally, applying the methods to clinical data resulted in a large variability of the CBF estimates. Block-circulant SVD will work in all situations and is the method with the highest potential.

  2. Applicability of Greulich-Pyle and Tanner-Whitehouse grading methods to MRI when assessing hand bone age in forensic age estimation: A pilot study.

    PubMed

    Urschler, Martin; Krauskopf, Astrid; Widek, Thomas; Sorantin, Erich; Ehammer, Thomas; Borkenstein, Martin; Yen, Kathrin; Scheurer, Eva

    2016-09-01

    Determination of skeletal development is a key pillar in forensic age estimation of living persons. Radiological assessment of hand bone age is widely used until the age of about 17-18 years, applying visual grading techniques to hand radiographs. This study investigated whether Greulich-Pyle (GP) and Tanner-Whitehouse (TW2) grading can be equally used for magnetic resonance imaging (MRI) data, which would offer the huge benefit of avoiding ionizing radiation. In 18 subjects aged between 7 and 17 years a radiograph and an MRI scan of the hand were performed. Epiphyseal ossification of hand bones was rated by two blinded radiologists with both GP and TW2. Correlation between hand MRIs and radiographs was analyzed by linear regression and inter-observer agreement was assessed. Correlation between age estimates from MRI and radiographs was high for both GP (r(2)=0.98) and TW2 (r(2)=0.93). MRI showed a tendency to estimate age slightly lower for 14-18 year-olds, which would be favorable regarding majority age determination in case this result could be reproduced using a currently not existing reference estimation method based on MRI data. Inter-observer agreement was similar for GP in radiographs and MRI, while for TW2, agreement in MRI was lower than in radiographs. In spite of limitations regarding sample size and recruited subjects, our results indicate that the use of GP and TW2 on MRI data offers the possibility of hand bone age estimation without the need for ionizing radiation. PMID:27344264

  3. Applicability of Greulich-Pyle and Tanner-Whitehouse grading methods to MRI when assessing hand bone age in forensic age estimation: A pilot study.

    PubMed

    Urschler, Martin; Krauskopf, Astrid; Widek, Thomas; Sorantin, Erich; Ehammer, Thomas; Borkenstein, Martin; Yen, Kathrin; Scheurer, Eva

    2016-09-01

    Determination of skeletal development is a key pillar in forensic age estimation of living persons. Radiological assessment of hand bone age is widely used until the age of about 17-18 years, applying visual grading techniques to hand radiographs. This study investigated whether Greulich-Pyle (GP) and Tanner-Whitehouse (TW2) grading can be equally used for magnetic resonance imaging (MRI) data, which would offer the huge benefit of avoiding ionizing radiation. In 18 subjects aged between 7 and 17 years a radiograph and an MRI scan of the hand were performed. Epiphyseal ossification of hand bones was rated by two blinded radiologists with both GP and TW2. Correlation between hand MRIs and radiographs was analyzed by linear regression and inter-observer agreement was assessed. Correlation between age estimates from MRI and radiographs was high for both GP (r(2)=0.98) and TW2 (r(2)=0.93). MRI showed a tendency to estimate age slightly lower for 14-18 year-olds, which would be favorable regarding majority age determination in case this result could be reproduced using a currently not existing reference estimation method based on MRI data. Inter-observer agreement was similar for GP in radiographs and MRI, while for TW2, agreement in MRI was lower than in radiographs. In spite of limitations regarding sample size and recruited subjects, our results indicate that the use of GP and TW2 on MRI data offers the possibility of hand bone age estimation without the need for ionizing radiation.

  4. A functional network estimation method of resting-state fMRI using a hierarchical Markov random field.

    PubMed

    Liu, Wei; Awate, Suyash P; Anderson, Jeffrey S; Fletcher, P Thomas

    2014-10-15

    We propose a hierarchical Markov random field model for estimating both group and subject functional networks simultaneously. The model takes into account the within-subject spatial coherence as well as the between-subject consistency of the network label maps. The statistical dependency between group and subject networks acts as a regularization, which helps the network estimation on both layers. We use Gibbs sampling to approximate the posterior density of the network labels and Monte Carlo expectation maximization to estimate the model parameters. We compare our method with two alternative segmentation methods based on K-Means and normalized cuts, using synthetic and real fMRI data. The experimental results show that our proposed model is able to identify both group and subject functional networks with higher accuracy on synthetic data, more robustness, and inter-session consistency on the real data.

  5. A Functional Networks Estimation Method of Resting-State fMRI Using a Hierarchical Markov Random Field

    PubMed Central

    Liu, Wei; Awate, Suyash P.; Anderson, Jeffrey S.; Fletcher, P. Thomas

    2014-01-01

    We propose a hierarchical Markov random field model that estimates both group and subject functional networks simultaneously. The model takes into account the within-subject spatial coherence as well as the between-subject consistency of the network label maps. The statistical dependency between group and subject networks acts as a regularization, which helps the network estimation on both layers. We use Gibbs sampling to approximate the posterior density of the network labels and Monte Carlo expectation maximization to estimate the model parameters. We compare our method with two alternative segmentation methods based on K-Means and normalized cuts, using synthetic and real fMRI data. The experimental results show our proposed model is able to identify both group and subject functional networks with higher accuracy, more robustness, and inter-session consistency. PMID:24954282

  6. Objective evaluation of methods to track motion from clinical cardiac-gated tagged MRI without the use of a gold standard

    NASA Astrophysics Data System (ADS)

    Parages, Felipe M.; Denney, Thomas S.; Brankov, Jovan G.

    2015-03-01

    Cardiac-gated MRI is widely used for the task of measuring parameters related to heart motion. More specifically, gated tagged MRI is the preferred modality to estimate local deformation (strain) and rotational motion (twist) of myocardial tissue. Many methods have been proposed to estimate cardiac motion from gated MRI sequences. However, when dealing with clinical data, evaluation of these methods is problematic due to the absence of gold-standards for cardiac motion. To overcome that, a linear regression scheme known as regression-without-truth (RWT) was proposed in the past. RWT uses priors to model the distribution of true values, thus enabling us to assess image-analysis algorithms without knowledge of the ground-truth. Furthermore, it allows one to rank methods by means of an objective figure-of-merit γ (i.e. precision). In this work we apply RWT to compare the performance of several gated MRI motion-tracking methods (e.g. non-rigid registration, feature based, harmonic phase) at the task of estimating myocardial strain and left-ventricle (LV) twist, from a population of 18 clinical human cardiac-gated tagged MRI studies.

  7. Quantification of fibrosis in infarcted swine hearts by ex vivo late gadolinium-enhancement and diffusion-weighted MRI methods

    NASA Astrophysics Data System (ADS)

    Pop, Mihaela; Ghugre, Nilesh R.; Ramanan, Venkat; Morikawa, Lily; Stanisz, Greg; Dick, Alexander J.; Wright, Graham A.

    2013-08-01

    Many have speculated that MRI signal characteristics can be used to identify regions of heterogeneous infarct associated with an arrhythmogenic substrate; however, direct evidence of this relationship is limited. The aim of this study was to demonstrate the remodelling characteristics of fibrosis by means of histology and high-resolution MR imaging. For this purpose, we performed whole-mount histology in heart samples (n = 9) collected from five swine at six weeks post-infarction and compared the extent of fibrosis in the infarcted areas delineated in these histological images with that obtained ex vivo by MRI using late gadolinium-enhancement (LGE) and diffusion-weighted imaging (DWI) methods. All MR images were obtained at a submillimetre resolution (i.e., voxel size of 0.6×0.6×1.2 mm3). Specifically, in the histology images, we differentiated moderate fibrosis (consisting of a mixture of viable and non-viable myocytes, known as border zone, BZ) from severe fibrosis (i.e., the dense scar). Correspondingly, tissue heterogeneities in the MR images were categorized by a Gaussian mixture model into healthy, BZ and scar. Our results showed that (a) both MRI methods were capable of qualitatively distinguishing sharp edges between dense scar and healthy tissue from regions of heterogeneous BZ; (b) the BZ and dense scar areas had intermediate-to-high increased values of signal intensity in the LGE images and of apparent diffusion coefficient in the DWI, respectively. In addition, as demonstrated by the Picrosirius Red and immunohistochemistry stains, the viable bundles in the BZ were clearly separated by thin collagen strands and had reduced expression of Cx43, whereas the core scar was composed of dense fibrosis. A quantitative analysis demonstrated that the comparison between BZ/scar extent in LGE and DWI to the corresponding areas identified in histology yielded very good correlations (i.e., for the scar identified by LGE, R2 was 0.96 compared to R2 = 0.93 for the

  8. Finite difference time domain (FDTD) method for modeling the effect of switched gradients on the human body in MRI.

    PubMed

    Zhao, Huawei; Crozier, Stuart; Liu, Feng

    2002-12-01

    Numerical modeling of the eddy currents induced in the human body by the pulsed field gradients in MRI presents a difficult computational problem. It requires an efficient and accurate computational method for high spatial resolution analyses with a relatively low input frequency. In this article, a new technique is described which allows the finite difference time domain (FDTD) method to be efficiently applied over a very large frequency range, including low frequencies. This is not the case in conventional FDTD-based methods. A method of implementing streamline gradients in FDTD is presented, as well as comparative analyses which show that the correct source injection in the FDTD simulation plays a crucial rule in obtaining accurate solutions. In particular, making use of the derivative of the input source waveform is shown to provide distinct benefits in accuracy over direct source injection. In the method, no alterations to the properties of either the source or the transmission media are required. The method is essentially frequency independent and the source injection method has been verified against examples with analytical solutions. Results are presented showing the spatial distribution of gradient-induced electric fields and eddy currents in a complete body model.

  9. Shape based MRI prostate image segmentation using local information driven directional distance Bayesian method

    NASA Astrophysics Data System (ADS)

    Gao, Yi; Tannenbaum, Allen

    2010-03-01

    In this paper, we present a shape based segmentation methodology for magnetic resonance prostate images. We first propose a new way to represent shapes via the hyperbolic tangent of the signed distance function. This effectively corrects the drawbacks of the signed distance function and yields very reasonable results for the shape registration and learning. Secondly, under a Bayesian statistical framework, instead of computing the posterior using a uniform prior, a directional distance map is introduced in order to incorporate a priori knowledge of image content as well as the estimated center of target object. Essentially, the image is modeled as a Finsler manifold and the metric is computed out of the directional derivative of the image. Then the directional distance map is computed to suppress the posterior remote from the object center. Thirdly, in the posterior image, a localized region based cost functional is designed to drive the shape based segmentation. Such cost functional utilizes the local regional information and is robust to both image noise and remote/irrelevant disturbances. With these three major components, the entire shape based segmentation procedure is provided as a complete open source pipeline and is applied to magnetic resonance image (MRI) prostate data.

  10. TH-C-BRD-06: A Novel MRI Based CT Artifact Correction Method for Improving Proton Range Calculation in the Presence of Severe CT Artifacts

    SciTech Connect

    Park, P; Schreibmann, E; Fox, T; Roper, J; Elder, E; Tejani, M; Crocker, I; Curran, W; Dhabaan, A

    2014-06-15

    Purpose: Severe CT artifacts can impair our ability to accurately calculate proton range thereby resulting in a clinically unacceptable treatment plan. In this work, we investigated a novel CT artifact correction method based on a coregistered MRI and investigated its ability to estimate CT HU and proton range in the presence of severe CT artifacts. Methods: The proposed method corrects corrupted CT data using a coregistered MRI to guide the mapping of CT values from a nearby artifact-free region. First patient MRI and CT images were registered using 3D deformable image registration software based on B-spline and mutual information. The CT slice with severe artifacts was selected as well as a nearby slice free of artifacts (e.g. 1cm away from the artifact). The two sets of paired MRI and CT images at different slice locations were further registered by applying 2D deformable image registration. Based on the artifact free paired MRI and CT images, a comprehensive geospatial analysis was performed to predict the correct CT HU of the CT image with severe artifact. For a proof of concept, a known artifact was introduced that changed the ground truth CT HU value up to 30% and up to 5cm error in proton range. The ability of the proposed method to recover the ground truth was quantified using a selected head and neck case. Results: A significant improvement in image quality was observed visually. Our proof of concept study showed that 90% of area that had 30% errors in CT HU was corrected to 3% of its ground truth value. Furthermore, the maximum proton range error up to 5cm was reduced to 4mm error. Conclusion: MRI based CT artifact correction method can improve CT image quality and proton range calculation for patients with severe CT artifacts.

  11. The connectivity domain: Analyzing resting state fMRI data using feature-based data-driven and model-based methods

    PubMed Central

    Iraji, Armin; Calhoun, Vince D.; Wiseman, Natalie M.; Davoodi-Bojd, Esmaeil; Avanaki, Mohammad R.N.; Haacke, E. Mark; Kou, Zhifeng

    2016-01-01

    Spontaneous fluctuations of resting state functional MRI (rsfMRI) have been widely used to understand the macro-connectome of the human brain. However, these fluctuations are not synchronized among subjects, which leads to limitations and makes utilization of first-level model-based methods challenging. Considering this limitation of rsfMRI data in the time domain, we propose to transfer the spatiotemporal information of the rsfMRI data to another domain, the connectivity domain, in which each value represents the same effect across subjects. Using a set of seed networks and a connectivity index to calculate the functional connectivity for each seed network, we transform data into the connectivity domain by generating connectivity weights for each subject. Comparison of the two domains using a data-driven method suggests several advantages in analyzing data using data-driven methods in the connectivity domain over the time domain. We also demonstrate the feasibility of applying model-based methods in the connectivity domain, which offers a new pathway for the use of first-level model-based methods on rsfMRI data. The connectivity domain, furthermore, demonstrates a unique opportunity to perform first-level feature-based data-driven and model-based analyses. The connectivity domain can be constructed from any technique that identifies sets of features that are similar across subjects and can greatly help researchers in the study of macro-connectome brain function by enabling us to perform a wide range of model-based and data-driven approaches on rsfMRI data, decreasing susceptibility of analysis techniques to parameters that are not related to brain connectivity information, and evaluating both static and dynamic functional connectivity of the brain from a new perspective. PMID:27079528

  12. ADvanced IMage Algebra (ADIMA): a novel method for depicting multiple sclerosis lesion heterogeneity, as demonstrated by quantitative MRI

    PubMed Central

    Tozer, Daniel J; Schmierer, Klaus; Chard, Declan T; Anderson, Valerie M; Altmann, Daniel R; Miller, David H; Wheeler-Kingshott, Claudia AM

    2013-01-01

    Background: There are modest correlations between multiple sclerosis (MS) disability and white matter lesion (WML) volumes, as measured by T2-weighted (T2w) magnetic resonance imaging (MRI) scans (T2-WML). This may partly reflect pathological heterogeneity in WMLs, which is not apparent on T2w scans. Objective: To determine if ADvanced IMage Algebra (ADIMA), a novel MRI post-processing method, can reveal WML heterogeneity from proton-density weighted (PDw) and T2w images. Methods: We obtained conventional PDw and T2w images from 10 patients with relapsing–remitting MS (RRMS) and ADIMA images were calculated from these. We classified all WML into bright (ADIMA-b) and dark (ADIMA-d) sub-regions, which were segmented. We obtained conventional T2-WML and T1-WML volumes for comparison, as well as the following quantitative magnetic resonance parameters: magnetisation transfer ratio (MTR), T1 and T2. Also, we assessed the reproducibility of the segmentation for ADIMA-b, ADIMA-d and T2-WML. Results: Our study’s ADIMA-derived volumes correlated with conventional lesion volumes (p < 0.05). ADIMA-b exhibited higher T1 and T2, and lower MTR than the T2-WML (p < 0.001). Despite the similarity in T1 values between ADIMA-b and T1-WML, these regions were only partly overlapping with each other. ADIMA-d exhibited quantitative characteristics similar to T2-WML; however, they were only partly overlapping. Mean intra- and inter-observer coefficients of variation for ADIMA-b, ADIMA-d and T2-WML volumes were all < 6 % and < 10 %, respectively. Conclusion: ADIMA enabled the simple classification of WML into two groups having different quantitative magnetic resonance properties, which can be reproducibly distinguished. PMID:23037551

  13. Carbon-wire loop based artifact correction outperforms post-processing EEG/fMRI corrections--A validation of a real-time simultaneous EEG/fMRI correction method.

    PubMed

    van der Meer, Johan N; Pampel, André; Van Someren, Eus J W; Ramautar, Jennifer R; van der Werf, Ysbrand D; Gomez-Herrero, German; Lepsien, Jöran; Hellrung, Lydia; Hinrichs, Hermann; Möller, Harald E; Walter, Martin

    2016-01-15

    Simultaneous EEG-fMRI combines two powerful neuroimaging techniques, but the EEG signal suffers from severe artifacts in the MRI environment that are difficult to remove. These are the MR scanning artifact and the blood-pulsation artifact--strategies to remove them are a topic of ongoing research. Additionally large, unsystematic artifacts are produced across the full frequency spectrum by the magnet's helium pump (and ventilator) systems which are notoriously hard to remove. As a consequence, experimenters routinely deactivate the helium pump during simultaneous EEG-fMRI acquisitions which potentially risks damaging the MRI system and necessitates more frequent and expensive helium refills. We present a novel correction method addressing both helium pump and ballisto-cardiac (BCG) artifacts, consisting of carbon-wire loops (CWL) as additional sensors to accurately track unpredictable artifacts related to subtle movements in the scanner, and an EEGLAB plugin to perform artifact correction. We compare signal-to-noise metrics of EEG data, corrected with CWL and three conventional correction methods, for helium pump off and on measurements. Because the CWL setup records signals in real-time, it fits requirements of applications where immediate correction is necessary, such as neuro-feedback applications or stimulation time-locked to specific sleep oscillations. The comparison metrics in this paper relate to: (1) the EEG signal itself, (2) the "eyes open vs. eyes closed" effect, and (3) an assessment of how the artifact corrections impacts the ability to perform meaningful correlations between EEG alpha power and the BOLD signal. Results show that the CWL correction corrects for He pump artifact and also produces EEG data more comparable to EEG obtained outside the magnet than conventional post-processing methods. PMID:26505301

  14. Carbon-wire loop based artifact correction outperforms post-processing EEG/fMRI corrections--A validation of a real-time simultaneous EEG/fMRI correction method.

    PubMed

    van der Meer, Johan N; Pampel, André; Van Someren, Eus J W; Ramautar, Jennifer R; van der Werf, Ysbrand D; Gomez-Herrero, German; Lepsien, Jöran; Hellrung, Lydia; Hinrichs, Hermann; Möller, Harald E; Walter, Martin

    2016-01-15

    Simultaneous EEG-fMRI combines two powerful neuroimaging techniques, but the EEG signal suffers from severe artifacts in the MRI environment that are difficult to remove. These are the MR scanning artifact and the blood-pulsation artifact--strategies to remove them are a topic of ongoing research. Additionally large, unsystematic artifacts are produced across the full frequency spectrum by the magnet's helium pump (and ventilator) systems which are notoriously hard to remove. As a consequence, experimenters routinely deactivate the helium pump during simultaneous EEG-fMRI acquisitions which potentially risks damaging the MRI system and necessitates more frequent and expensive helium refills. We present a novel correction method addressing both helium pump and ballisto-cardiac (BCG) artifacts, consisting of carbon-wire loops (CWL) as additional sensors to accurately track unpredictable artifacts related to subtle movements in the scanner, and an EEGLAB plugin to perform artifact correction. We compare signal-to-noise metrics of EEG data, corrected with CWL and three conventional correction methods, for helium pump off and on measurements. Because the CWL setup records signals in real-time, it fits requirements of applications where immediate correction is necessary, such as neuro-feedback applications or stimulation time-locked to specific sleep oscillations. The comparison metrics in this paper relate to: (1) the EEG signal itself, (2) the "eyes open vs. eyes closed" effect, and (3) an assessment of how the artifact corrections impacts the ability to perform meaningful correlations between EEG alpha power and the BOLD signal. Results show that the CWL correction corrects for He pump artifact and also produces EEG data more comparable to EEG obtained outside the magnet than conventional post-processing methods.

  15. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods.

    PubMed

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J; Pataky, Rozalia; Sparrow, Sarah A; Wilkinson, A G; Macnaught, Gillian; Semple, Scott I; Boardman, James P

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases 'uniformly' distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  16. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    PubMed Central

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; Macnaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-01-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course. PMID:27010238

  17. Accurate Learning with Few Atlases (ALFA): an algorithm for MRI neonatal brain extraction and comparison with 11 publicly available methods

    NASA Astrophysics Data System (ADS)

    Serag, Ahmed; Blesa, Manuel; Moore, Emma J.; Pataky, Rozalia; Sparrow, Sarah A.; Wilkinson, A. G.; MacNaught, Gillian; Semple, Scott I.; Boardman, James P.

    2016-03-01

    Accurate whole-brain segmentation, or brain extraction, of magnetic resonance imaging (MRI) is a critical first step in most neuroimage analysis pipelines. The majority of brain extraction algorithms have been developed and evaluated for adult data and their validity for neonatal brain extraction, which presents age-specific challenges for this task, has not been established. We developed a novel method for brain extraction of multi-modal neonatal brain MR images, named ALFA (Accurate Learning with Few Atlases). The method uses a new sparsity-based atlas selection strategy that requires a very limited number of atlases ‘uniformly’ distributed in the low-dimensional data space, combined with a machine learning based label fusion technique. The performance of the method for brain extraction from multi-modal data of 50 newborns is evaluated and compared with results obtained using eleven publicly available brain extraction methods. ALFA outperformed the eleven compared methods providing robust and accurate brain extraction results across different modalities. As ALFA can learn from partially labelled datasets, it can be used to segment large-scale datasets efficiently. ALFA could also be applied to other imaging modalities and other stages across the life course.

  18. A fast alignment method for breast MRI follow-up studies using automated breast segmentation and current-prior registration

    NASA Astrophysics Data System (ADS)

    Wang, Lei; Strehlow, Jan; Rühaak, Jan; Weiler, Florian; Diez, Yago; Gubern-Merida, Albert; Diekmann, Susanne; Laue, Hendrik; Hahn, Horst K.

    2015-03-01

    In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process. In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.

  19. A novel passive shimming method for the correction of magnetic fields above the patient bed in MRI.

    PubMed

    Kong, Xia; Zhu, Minhua; Xia, Ling; Crozier, Stuart; Wang, Qiuliang; Ni, Zhipeng; Liu, Feng

    2015-08-01

    This paper presents a novel passive shimming method for the effective correction of static magnetic field (B0) inhomogeneities in Magnetic Resonance Imaging (MRI) systems. Passive shimming is used to find an optimum configuration for the placement of iron pieces applied to improve the B0 uniformity in the predefined imaging region referred to as the diameter of spherical volume (DSV). However, most passive shimming methods neglect to recognize that the space under the patient bed is not in use for imaging. In this work, we present a new algorithm that attempts to avoid the unnecessary shimming of the space under the patient bed. During implementation, the B0 field is still measured over the DSV surface and then mapped onto the effective imaging volume surface; a dedicated sensitivity matrix is generated only for the imaging area above the patient bed. A linear programming optimization procedure is performed for the determination of thicknesses and locations the shim pieces. Our experimental results showed that by revising the shimming target area, the new method provides superior optimization solutions. Compared to a conventional approach, the new method requires smaller amount of iron to correct the B0 inhomogeneities in the imaging area which has the effect of improving thermal stability to the B0 field. It also reduces the complexity of the optimization problem. Our new shimming strategy helps to improve the magnetic field homogeneity within the realistic imaging space, and ultimately improve image quality. PMID:26073600

  20. Stimulus-induced Rotary Saturation (SIRS): a potential method for the detection of neuronal currents with MRI.

    PubMed

    Witzel, Thomas; Lin, Fa-Hsuan; Rosen, Bruce R; Wald, Lawrence L

    2008-10-01

    Neuronal currents produce local transient and oscillatory magnetic fields that can be readily detected by MEG. Previous work attempting to detect these magnetic fields with MR focused on detecting local phase shifts and dephasing in T(2) or T(2)-weighted images. For temporally biphasic and multi-phasic local currents the sensitivity of these methods can be reduced through the cancellation of the accrued phase induced by positive and negative episodes of the neuronal current. The magnitude of the phase shift is also dependent on the distribution of the current within the voxel. Since spins on one side of a current source develop an opposite phase shift relative to those on the other side, there is likely to be significant cancellation within the voxel. We introduce a potential method for detecting neuronal currents though their resonant T(1rho) saturation during a spin-lock preparation period. The method is insensitive to the temporal and spatial cancellation effects since it utilizes the multi-phasic nature of the neuronal currents and thus is not sensitive to the sign of the local field. To produce a T(1)(rho) reduction, the Larmor frequency in the rotating frame, which is set by gammaB(1lock) (typically 20 Hz-5 kHz), must match the major frequency components of the stimulus-induced neuronal currents. We validate the method in MRI phantom studies. The rotary saturation spectra showed a sharp resonance when a current dipole within the phantom was driven at the Larmor frequency in the rotating frame. A 7 min block-design experiment was found to be sensitive to a current dipole strength of 56 nAm, an approximate magnetic field of 1 nT at 1.5 mm from the dipole. This dipole moment is similar to that seen using the phase shift method in a similar experimental setup by Konn et al. [Konn, D., Gowland, P., Bowtell, R., 2003. MRI detection of weak magnetic fields due to an extended current dipole in a conducting sphere: a model for direct detection of neuronal currents in

  1. MRI-based elastic-mapping method for inter-subject comparison of brain FDG-PET images

    SciTech Connect

    Yang, J.; Huang, S.C.; Lin, K.P.; Small, G.; Phelps, M.E.

    1996-12-31

    Inter-subject anatomic differences prohibits direct image-wise statistical evaluation of brain FDG-PET images of Alzheimer`s disease (AD) patients. In this study, we propose a MRI-based elastic-mapping method which enables image-wise evaluation. The method involves intra-subject MR-PET registration, 3-D elastic mapping of two set of MR images, and elastically transforming the co-registered PET images. The MR-PET registration used simulated PET images, which were based on segmentation of MR images. In the 3-D elastic mapping stage, first a global linear scaling was applied to compensate for brain size difference, then a deformation field was obtained by minimizing the regional sum of squared difference between the two sets of MR images. Two groups (AD patient and normal control), each with three subjects, were included in the current study. After processing, images from all subjects have similar shapes. Averaging the images across all subjects (either within the individual group or for both groups) give images indistinguishable from original single subject FDG images (i.e. without much spatial resolution loss), except with lower image noise level. The method is expected to allow statistical image-wise analysis to be performed across different subjects.

  2. Marked effects of intracranial volume correction methods on sex differences in neuroanatomical structures: a HUNT MRI study

    PubMed Central

    Pintzka, Carl W. S.; Hansen, Tor I.; Evensmoen, Hallvard R.; Håberg, Asta K.

    2015-01-01

    To date, there is no consensus whether sexual dimorphism in the size of neuroanatomical structures exists, or if such differences are caused by choice of intracranial volume (ICV) correction method. When investigating volume differences in neuroanatomical structures, corrections for variation in ICV are used. Commonly applied methods are the ICV-proportions, ICV-residuals and ICV as a covariate of no interest, ANCOVA. However, these different methods give contradictory results with regard to presence of sex differences. Our aims were to investigate presence of sexual dimorphism in 18 neuroanatomical volumes unrelated to ICV-differences by using a large ICV-matched subsample of 304 men and women from the HUNT-MRI general population study, and further to demonstrate in the entire sample of 966 healthy subjects, which of the ICV-correction methods gave results similar to the ICV-matched subsample. In addition, sex-specific subsamples were created to investigate whether differences were an effect of head size or sex. Most sex differences were related to volume scaling with ICV, independent of sex. Sex differences were detected in a few structures; amygdala, cerebellar cortex, and 3rd ventricle were larger in men, but the effect sizes were small. The residuals and ANCOVA methods were most effective at removing the effects of ICV. The proportions method suffered from systematic errors due to lack of proportionality between ICV and neuroanatomical volumes, leading to systematic mis-assignment of structures as either larger or smaller than their actual size. Adding additional sexual dimorphic covariates to the ANCOVA gave opposite results of those obtained in the ICV-matched subsample or with the residuals method. The findings in the current study explain some of the considerable variation in the literature on sexual dimorphisms in neuroanatomical volumes. In conclusion, sex plays a minor role for neuroanatomical volume differences; most differences are related to ICV

  3. New methods for MRI denoising based on sparseness and self-similarity.

    PubMed

    Manjón, José V; Coupé, Pierrick; Buades, Antonio; Louis Collins, D; Robles, Montserrat

    2012-01-01

    This paper proposes two new methods for the three-dimensional denoising of magnetic resonance images that exploit the sparseness and self-similarity properties of the images. The proposed methods are based on a three-dimensional moving-window discrete cosine transform hard thresholding and a three-dimensional rotationally invariant version of the well-known nonlocal means filter. The proposed approaches were compared with related state-of-the-art methods and produced very competitive results. Both methods run in less than a minute, making them usable in most clinical and research settings. PMID:21570894

  4. Improving tissue segmentation of human brain MRI through preprocessing by the Gegenbauer reconstruction method.

    PubMed

    Archibald, Rick; Chen, Kewei; Gelb, Anne; Renaut, Rosemary

    2003-09-01

    The Gegenbauer image reconstruction method, previously shown to improve the quality of magnetic resonance images, is utilized in this study as a segmentation preprocessing step. It is demonstrated that, for all simulated and real magnetic resonance images used in this study, the Gegenbauer reconstruction method improves the accuracy of segmentation. Although it is more desirable to use the k-space data for the Gegenbauer reconstruction method, only information acquired from MR images is necessary for the reconstruction, making the procedure completely self-contained and viable for all human brain segmentation algorithms. PMID:14527609

  5. A Dictionary Learning Method with Total Generalized Variation for MRI Reconstruction.

    PubMed

    Lu, Hongyang; Wei, Jingbo; Liu, Qiegen; Wang, Yuhao; Deng, Xiaohua

    2016-01-01

    Reconstructing images from their noisy and incomplete measurements is always a challenge especially for medical MR image with important details and features. This work proposes a novel dictionary learning model that integrates two sparse regularization methods: the total generalized variation (TGV) approach and adaptive dictionary learning (DL). In the proposed method, the TGV selectively regularizes different image regions at different levels to avoid oil painting artifacts largely. At the same time, the dictionary learning adaptively represents the image features sparsely and effectively recovers details of images. The proposed model is solved by variable splitting technique and the alternating direction method of multiplier. Extensive simulation experimental results demonstrate that the proposed method consistently recovers MR images efficiently and outperforms the current state-of-the-art approaches in terms of higher PSNR and lower HFEN values.

  6. A Dictionary Learning Method with Total Generalized Variation for MRI Reconstruction

    PubMed Central

    Lu, Hongyang; Wei, Jingbo; Wang, Yuhao; Deng, Xiaohua

    2016-01-01

    Reconstructing images from their noisy and incomplete measurements is always a challenge especially for medical MR image with important details and features. This work proposes a novel dictionary learning model that integrates two sparse regularization methods: the total generalized variation (TGV) approach and adaptive dictionary learning (DL). In the proposed method, the TGV selectively regularizes different image regions at different levels to avoid oil painting artifacts largely. At the same time, the dictionary learning adaptively represents the image features sparsely and effectively recovers details of images. The proposed model is solved by variable splitting technique and the alternating direction method of multiplier. Extensive simulation experimental results demonstrate that the proposed method consistently recovers MR images efficiently and outperforms the current state-of-the-art approaches in terms of higher PSNR and lower HFEN values. PMID:27110235

  7. A theoretical comparison of two optimization methods for radiofrequency drive schemes in high frequency MRI resonators

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Beck, Barbara L.; Fitzsimmons, Jeffrey R.; Blackband, Stephen J.; Crozier, Stuart

    2005-11-01

    In this paper, numerical simulations are used in an attempt to find optimal source profiles for high frequency radiofrequency (RF) volume coils. Biologically loaded, shielded/unshielded circular and elliptical birdcage coils operating at 170 MHz, 300 MHz and 470 MHz are modelled using the FDTD method for both 2D and 3D cases. Taking advantage of the fact that some aspects of the electromagnetic system are linear, two approaches have been proposed for the determination of the drives for individual elements in the RF resonator. The first method is an iterative optimization technique with a kernel for the evaluation of RF fields inside an imaging plane of a human head model using pre-characterized sensitivity profiles of the individual rungs of a resonator; the second method is a regularization-based technique. In the second approach, a sensitivity matrix is explicitly constructed and a regularization procedure is employed to solve the ill-posed problem. Test simulations show that both methods can improve the B1-field homogeneity in both focused and non-focused scenarios. While the regularization-based method is more efficient, the first optimization method is more flexible as it can take into account other issues such as controlling SAR or reshaping the resonator structures. It is hoped that these schemes and their extensions will be useful for the determination of multi-element RF drives in a variety of applications.

  8. Molecular fMRI

    PubMed Central

    Bartelle, Benjamin B.; Barandov, Ali

    2016-01-01

    Comprehensive analysis of brain function depends on understanding the dynamics of diverse neural signaling processes over large tissue volumes in intact animals and humans. Most existing approaches to measuring brain signaling suffer from limited tissue penetration, poor resolution, or lack of specificity for well-defined neural events. Here we discuss a new brain activity mapping method that overcomes some of these problems by combining MRI with contrast agents sensitive to neural signaling. The goal of this “molecular fMRI” approach is to permit noninvasive whole-brain neuroimaging with specificity and resolution approaching current optical neuroimaging methods. In this article, we describe the context and need for molecular fMRI as well as the state of the technology today. We explain how major types of MRI probes work and how they can be sensitized to neurobiological processes, such as neurotransmitter release, calcium signaling, and gene expression changes. We comment both on past work in the field and on challenges and promising avenues for future development. SIGNIFICANCE STATEMENT Brain researchers currently have a choice between measuring neural activity using cellular-level recording techniques, such as electrophysiology and optical imaging, or whole-brain imaging methods, such as fMRI. Cellular level methods are precise but only address a small portion of mammalian brains; on the other hand, whole-brain neuroimaging techniques provide very little specificity for neural pathways or signaling components of interest. The molecular fMRI techniques we discuss have particular potential to combine the specificity of cellular-level measurements with the noninvasive whole-brain coverage of fMRI. On the other hand, molecular fMRI is only just getting off the ground. This article aims to offer a snapshot of the status and future prospects for development of molecular fMRI techniques. PMID:27076413

  9. Susceptibility and size quantification of small human veins from an MRI method.

    PubMed

    Hsieh, Ching-Yi; Cheng, Yu-Chung N; Xie, He; Haacke, E Mark; Neelavalli, Jaladhar

    2015-12-01

    Recently a method called CISSCO (Complex Image Summation around a Spherical or a Cylindrical Object) was introduced for accurately quantifying the susceptibility and the radius of any narrow cylindrical object at any orientation using a typical two-echo gradient echo sequence. This work further optimizes the method for quantifying oxygen saturation in small cerebral veins in the human brain. The revised method is first validated through numerical simulations and then applied to data from phantom and human brain. The effect of phase high pass filtering on the quantified parameters is studied and procedures for mitigating its adverse effects are suggested. Uncertainty of each measurement is estimated from the error propagation method. It is shown that the revised method allows for accurate quantification of both the vessel size and its oxygen saturation even in the case of a low SNR (signal to noise ratio) in the vein. The results are self consistent across different veins within a given subject with a variation of less than 6%. Finally, imaging parameters and some procedures are suggested for accurate susceptibility and radius quantifications of small human veins. PMID:26248271

  10. A fully automated method for quantitative cerebral hemodynamic analysis using DSC-MRI.

    PubMed

    Bjørnerud, Atle; Emblem, Kyrre E

    2010-05-01

    Dynamic susceptibility contrast (DSC)-based perfusion analysis from MR images has become an established method for analysis of cerebral blood volume (CBV) in glioma patients. To date, little emphasis has, however, been placed on quantitative perfusion analysis of these patients, mainly due to the associated increased technical complexity and lack of sufficient stability in a clinical setting. The aim of our study was to develop a fully automated analysis framework for quantitative DSC-based perfusion analysis. The method presented here generates quantitative hemodynamic maps without user interaction, combined with automatic segmentation of normal-appearing cerebral tissue. Validation of 101 patients with confirmed glioma after surgery gave mean values for CBF, CBV, and MTT, extracted automatically from normal-appearing whole-brain white and gray matter, in good agreement with literature values. The measured age- and gender-related variations in the same parameters were also in agreement with those in the literature. Several established analysis methods were compared and the resulting perfusion metrics depended significantly on method and parameter choice. In conclusion, we present an accurate, fast, and automatic quantitative perfusion analysis method where all analysis steps are based on raw DSC data only. PMID:20087370

  11. Improving the performance of the prony method using a wavelet domain filter for MRI denoising.

    PubMed

    Jaramillo, Rodney; Lentini, Marianela; Paluszny, Marco

    2014-01-01

    The Prony methods are used for exponential fitting. We use a variant of the Prony method for abnormal brain tissue detection in sequences of T 2 weighted magnetic resonance images. Here, MR images are considered to be affected only by Rician noise, and a new wavelet domain bilateral filtering process is implemented to reduce the noise in the images. This filter is a modification of Kazubek's algorithm and we use synthetic images to show the ability of the new procedure to suppress noise and compare its performance with respect to the original filter, using quantitative and qualitative criteria. The tissue classification process is illustrated using a real sequence of T 2 MR images, and the filter is applied to each image before using the variant of the Prony method.

  12. The EM Method in a Probabilistic Wavelet-Based MRI Denoising

    PubMed Central

    2015-01-01

    Human body heat emission and others external causes can interfere in magnetic resonance image acquisition and produce noise. In this kind of images, the noise, when no signal is present, is Rayleigh distributed and its wavelet coefficients can be approximately modeled by a Gaussian distribution. Noiseless magnetic resonance images can be modeled by a Laplacian distribution in the wavelet domain. This paper proposes a new magnetic resonance image denoising method to solve this fact. This method performs shrinkage of wavelet coefficients based on the conditioned probability of being noise or detail. The parameters involved in this filtering approach are calculated by means of the expectation maximization (EM) method, which avoids the need to use an estimator of noise variance. The efficiency of the proposed filter is studied and compared with other important filtering techniques, such as Nowak's, Donoho-Johnstone's, Awate-Whitaker's, and nonlocal means filters, in different 2D and 3D images. PMID:26089959

  13. Improving the Performance of the Prony Method Using a Wavelet Domain Filter for MRI Denoising

    PubMed Central

    Lentini, Marianela; Paluszny, Marco

    2014-01-01

    The Prony methods are used for exponential fitting. We use a variant of the Prony method for abnormal brain tissue detection in sequences of T2 weighted magnetic resonance images. Here, MR images are considered to be affected only by Rician noise, and a new wavelet domain bilateral filtering process is implemented to reduce the noise in the images. This filter is a modification of Kazubek's algorithm and we use synthetic images to show the ability of the new procedure to suppress noise and compare its performance with respect to the original filter, using quantitative and qualitative criteria. The tissue classification process is illustrated using a real sequence of T2 MR images, and the filter is applied to each image before using the variant of the Prony method. PMID:24834108

  14. Method of propulsion of a ferromagnetic core in the cardiovascular system through magnetic gradients generated by an MRI system.

    PubMed

    Mathieu, Jean-Baptiste; Beaudoin, Gilles; Martel, Sylvain

    2006-02-01

    This paper reports the use of a magnetic resonance imaging (MRI) system to propel a ferromagnetic core. The concept was studied for future development of microdevices designed to perform minimally invasive interventions in remote sites accessible through the human cardiovascular system. A mathematical model is described taking into account various parameters such as the size of blood vessels, the velocities and viscous properties of blood, the magnetic properties of the materials, the characteristics of MRI gradient coils, as well as the ratio between the diameter of a spherical core and the diameter of the blood vessels. The concept of magnetic propulsion by MRI is validated experimentally by measuring the flow velocities that magnetized spheres (carbon steel 1010/1020) can withstand inside cylindrical tubes under the different magnetic forces created with a Siemens Magnetom Vision 1.5 T MRI system. The differences between the velocities predicted by the theoretical model and the experiments are approximately 10%. The results indicate that with the technology available today for gradient coils used in clinical MRI systems, it is possible to generate sufficient gradients to propel a ferromagnetic sphere in the larger sections of the arterial system. In other words, the results show that in the larger blood vessels where the diameter of the microdevices could be as large as a couple a millimeters, the few tens of mT/m of gradients required for displacement against the relatively high blood flow rate is well within the limits of clinical MRI systems. On the other hand, although propulsion of a ferromagnetic core with diameter of approximately 600 microm may be possible with existing clinical MRI systems, gradient amplitudes of several T/m would be required to propel a much smaller ferromagnetic core in small vessels such as capillaries and additional gradient coils would be required to upgrade existing MRI systems for operations at such a scale.

  15. SU-C-17A-03: Evaluation of Deformable Image Registration Methods Between MRI and CT for Prostate Cancer Radiotherapy

    SciTech Connect

    Wen, N; Glide-Hurst, C; Zhong, H; Chin, K; Kumarasiri, A; Liu, C; Liu, M; Siddiqui, S

    2014-06-15

    Purpose: We evaluated the performance of two commercially available and one open source B-Spline deformable image registration (DIR) algorithms between T2-weighted MRI and treatment planning CT using the DICE indices. Methods: CT simulation (CT-SIM) and MR simulation (MR-SIM) for four prostate cancer patients were conducted on the same day using the same setup and immobilization devices. CT images (120 kVp, 500 mAs, voxel size = 1.1x1.1x3.0 mm3) were acquired using an open-bore CT scanner. T2-weighted Turbo Spine Echo (T2W-TSE) images (TE/TR/α = 80/4560 ms/90°, voxel size = 0.7×0.7×2.5 mm3) were scanned on a 1.0T high field open MR-SIM. Prostates, seminal vesicles, rectum and bladders were delineated on both T2W-TSE and CT images by the attending physician. T2W-TSE images were registered to CT images using three DIR algorithms, SmartAdapt (Varian), Velocity AI (Velocity) and Elastix (Klein et al 2010) and contours were propagated. DIR results were evaluated quantitatively or qualitatively by image comparison and calculating organ DICE indices. Results: Significant differences in the contours of prostate and seminal vesicles were observed between MR and CT. On average, volume changes of the propagated contours were 5%, 2%, 160% and 8% for the prostate, seminal vesicles, bladder and rectum respectively. Corresponding mean DICE indices were 0.7, 0.5, 0.8, and 0.7. The intraclass correlation coefficient (ICC) was 0.9 among three algorithms for the Dice indices. Conclusion: Three DIR algorithms for CT/MR registration yielded similar results for organ propagation. Due to the different soft tissue contrasts between MRI and CT, organ delineation of prostate and SVs varied significantly, thus efforts to develop other DIR evaluation metrics are warranted. Conflict of interest: Submitting institution has research agreements with Varian Medical System and Philips Healthcare.

  16. New multispectral MRI data fusion technique for white matter lesion segmentation: method and comparison with thresholding in FLAIR images

    PubMed Central

    Ferguson, Karen J.; Chappell, Francesca M.; Wardlaw, Joanna M.

    2010-01-01

    Objective Brain tissue segmentation by conventional threshold-based techniques may have limited accuracy and repeatability in older subjects. We present a new multispectral magnetic resonance (MR) image analysis approach for segmenting normal and abnormal brain tissue, including white matter lesions (WMLs). Methods We modulated two 1.5T MR sequences in the red/green colour space and calculated the tissue volumes using minimum variance quantisation. We tested it on 14 subjects, mean age 73.3 ± 10 years, representing the full range of WMLs and atrophy. We compared the results of WML segmentation with those using FLAIR-derived thresholds, examined the effect of sampling location, WML amount and field inhomogeneities, and tested observer reliability and accuracy. Results FLAIR-derived thresholds were significantly affected by the location used to derive the threshold (P = 0.0004) and by WML volume (P = 0.0003), and had higher intra-rater variability than the multispectral technique (mean difference ± SD: 759 ± 733 versus 69 ± 326 voxels respectively). The multispectral technique misclassified 16 times fewer WMLs. Conclusion Initial testing suggests that the multispectral technique is highly reproducible and accurate with the potential to be applied to routinely collected clinical MRI data. Electronic supplementary material The online version of this article (doi:10.1007/s00330-010-1718-6) contains supplementary material, which is available to authorized users. PMID:20157814

  17. A mixed L2 norm regularized HRF estimation method for rapid event-related fMRI experiments.

    PubMed

    Lei, Yu; Tong, Li; Yan, Bin

    2013-01-01

    Brain state decoding or "mind reading" via multivoxel pattern analysis (MVPA) has become a popular focus of functional magnetic resonance imaging (fMRI) studies. In brain decoding, stimulus presentation rate is increased as fast as possible to collect many training samples and obtain an effective and reliable classifier or computational model. However, for extremely rapid event-related experiments, the blood-oxygen-level-dependent (BOLD) signals evoked by adjacent trials are heavily overlapped in the time domain. Thus, identifying trial-specific BOLD responses is difficult. In addition, voxel-specific hemodynamic response function (HRF), which is useful in MVPA, should be used in estimation to decrease the loss of weak information across voxels and obtain fine-grained spatial information. Regularization methods have been widely used to increase the efficiency of HRF estimates. In this study, we propose a regularization framework called mixed L2 norm regularization. This framework involves Tikhonov regularization and an additional L2 norm regularization term to calculate reliable HRF estimates. This technique improves the accuracy of HRF estimates and significantly increases the classification accuracy of the brain decoding task when applied to a rapid event-related four-category object classification experiment. At last, some essential issues such as the impact of low-frequency fluctuation (LFF) and the influence of smoothing are discussed for rapid event-related experiments.

  18. Methods and evaluations of MRI content-adaptive finite element mesh generation for bioelectromagnetic problems.

    PubMed

    Lee, W H; Kim, T-S; Cho, M H; Ahn, Y B; Lee, S Y

    2006-12-01

    In studying bioelectromagnetic problems, finite element analysis (FEA) offers several advantages over conventional methods such as the boundary element method. It allows truly volumetric analysis and incorporation of material properties such as anisotropic conductivity. For FEA, mesh generation is the first critical requirement and there exist many different approaches. However, conventional approaches offered by commercial packages and various algorithms do not generate content-adaptive meshes (cMeshes), resulting in numerous nodes and elements in modelling the conducting domain, and thereby increasing computational load and demand. In this work, we present efficient content-adaptive mesh generation schemes for complex biological volumes of MR images. The presented methodology is fully automatic and generates FE meshes that are adaptive to the geometrical contents of MR images, allowing optimal representation of conducting domain for FEA. We have also evaluated the effect of cMeshes on FEA in three dimensions by comparing the forward solutions from various cMesh head models to the solutions from the reference FE head model in which fine and equidistant FEs constitute the model. The results show that there is a significant gain in computation time with minor loss in numerical accuracy. We believe that cMeshes should be useful in the FEA of bioelectromagnetic problems.

  19. Gauging MRI

    NASA Astrophysics Data System (ADS)

    Herron, Ison; Goodman, Jeremy

    2009-11-01

    Axisymmetric stability of viscous resistive magnetized Couette flow is re-examined, with emphasis on flows that would be hydrodynamically stable according to Rayleigh's criterion: opposing gradients of angular velocity and specific angular momentum. A uniform axial magnetic field permeates the fluid. In this regime, magnetorotational instability (MRI) may occur. It is proved that MRI is suppressed, in fact no instability at all occurs, with insulating boundary conditions, when the magnetic resistivity is sufficiently large. This shows conclusively that small magnetic dissipation is a feature of this instability for all magnetic Prandtl numbers. A criterion is provided for the onset of MRI.

  20. Musculoskeletal MRI.

    PubMed

    Sage, Jaime E; Gavin, Patrick

    2016-05-01

    MRI has the unique ability to detect abnormal fluid content, and is therefore unparalleled in its role of detection, diagnosis, prognosis, treatment planning and follow-up evaluation of musculoskeletal disease. MRI in companion animals should be considered in the following circumstances: a definitive diagnosis cannot be made on radiographs; a patient is nonresponsive to medical or surgical therapy; prognostic information is desired; assessing surgical margins and traumatic and/or infectious joint and bone disease; ruling out subtle developmental or early aggressive bone lesions. The MRI features of common disorders affecting the shoulder, elbow, stifle, carpal, and tarsal joints are included in this chapter.

  1. Derivation and validation of simple anthropometric equations to predict adipose tissue mass and total fat mass with MRI as the reference method.

    PubMed

    Al-Gindan, Yasmin Y; Hankey, Catherine R; Govan, Lindsay; Gallagher, Dympna; Heymsfield, Steven B; Lean, Michael E J

    2015-12-14

    The reference organ-level body composition measurement method is MRI. Practical estimations of total adipose tissue mass (TATM), total adipose tissue fat mass (TATFM) and total body fat are valuable for epidemiology, but validated prediction equations based on MRI are not currently available. We aimed to derive and validate new anthropometric equations to estimate MRI-measured TATM/TATFM/total body fat and compare them with existing prediction equations using older methods. The derivation sample included 416 participants (222 women), aged between 18 and 88 years with BMI between 15·9 and 40·8 (kg/m2). The validation sample included 204 participants (110 women), aged between 18 and 86 years with BMI between 15·7 and 36·4 (kg/m2). Both samples included mixed ethnic/racial groups. All the participants underwent whole-body MRI to quantify TATM (dependent variable) and anthropometry (independent variables). Prediction equations developed using stepwise multiple regression were further investigated for agreement and bias before validation in separate data sets. Simplest equations with optimal R (2) and Bland-Altman plots demonstrated good agreement without bias in the validation analyses: men: TATM (kg)=0·198 weight (kg)+0·478 waist (cm)-0·147 height (cm)-12·8 (validation: R 2 0·79, CV=20 %, standard error of the estimate (SEE)=3·8 kg) and women: TATM (kg)=0·789 weight (kg)+0·0786 age (years)-0·342 height (cm)+24·5 (validation: R (2) 0·84, CV=13 %, SEE=3·0 kg). Published anthropometric prediction equations, based on MRI and computed tomographic scans, correlated strongly with MRI-measured TATM: (R (2) 0·70-0·82). Estimated TATFM correlated well with published prediction equations for total body fat based on underwater weighing (R (2) 0·70-0·80), with mean bias of 2·5-4·9 kg, correctable with log-transformation in most equations. In conclusion, new equations, using simple anthropometric measurements, estimated MRI-measured TATM with correlations and

  2. Derivation and validation of simple anthropometric equations to predict adipose tissue mass and total fat mass with MRI as the reference method.

    PubMed

    Al-Gindan, Yasmin Y; Hankey, Catherine R; Govan, Lindsay; Gallagher, Dympna; Heymsfield, Steven B; Lean, Michael E J

    2015-12-14

    The reference organ-level body composition measurement method is MRI. Practical estimations of total adipose tissue mass (TATM), total adipose tissue fat mass (TATFM) and total body fat are valuable for epidemiology, but validated prediction equations based on MRI are not currently available. We aimed to derive and validate new anthropometric equations to estimate MRI-measured TATM/TATFM/total body fat and compare them with existing prediction equations using older methods. The derivation sample included 416 participants (222 women), aged between 18 and 88 years with BMI between 15·9 and 40·8 (kg/m2). The validation sample included 204 participants (110 women), aged between 18 and 86 years with BMI between 15·7 and 36·4 (kg/m2). Both samples included mixed ethnic/racial groups. All the participants underwent whole-body MRI to quantify TATM (dependent variable) and anthropometry (independent variables). Prediction equations developed using stepwise multiple regression were further investigated for agreement and bias before validation in separate data sets. Simplest equations with optimal R (2) and Bland-Altman plots demonstrated good agreement without bias in the validation analyses: men: TATM (kg)=0·198 weight (kg)+0·478 waist (cm)-0·147 height (cm)-12·8 (validation: R 2 0·79, CV=20 %, standard error of the estimate (SEE)=3·8 kg) and women: TATM (kg)=0·789 weight (kg)+0·0786 age (years)-0·342 height (cm)+24·5 (validation: R (2) 0·84, CV=13 %, SEE=3·0 kg). Published anthropometric prediction equations, based on MRI and computed tomographic scans, correlated strongly with MRI-measured TATM: (R (2) 0·70-0·82). Estimated TATFM correlated well with published prediction equations for total body fat based on underwater weighing (R (2) 0·70-0·80), with mean bias of 2·5-4·9 kg, correctable with log-transformation in most equations. In conclusion, new equations, using simple anthropometric measurements, estimated MRI-measured TATM with correlations and

  3. A fast, model-independent method for cerebral cortical thickness estimation using MRI.

    PubMed

    Scott, M L J; Bromiley, P A; Thacker, N A; Hutchinson, C E; Jackson, A

    2009-04-01

    Several algorithms for measuring the cortical thickness in the human brain from MR image volumes have been described in the literature, the majority of which rely on fitting deformable models to the inner and outer cortical surfaces. However, the constraints applied during the model fitting process in order to enforce spherical topology and to fit the outer cortical surface in narrow sulci, where the cerebrospinal fluid (CSF) channel may be obscured by partial voluming, may introduce bias in some circumstances, and greatly increase the processor time required. In this paper we describe an alternative, voxel based technique that measures the cortical thickness using inversion recovery anatomical MR images. Grey matter, white matter and CSF are identified through segmentation, and edge detection is used to identify the boundaries between these tissues. The cortical thickness is then measured along the local 3D surface normal at every voxel on the inner cortical surface. The method was applied to 119 normal volunteers, and validated through extensive comparisons with published measurements of both cortical thickness and rate of thickness change with age. We conclude that the proposed technique is generally faster than deformable model-based alternatives, and free from the possibility of model bias, but suffers no reduction in accuracy. In particular, it will be applicable in data sets showing severe cortical atrophy, where thinning of the gyri leads to points of high curvature, and so the fitting of deformable models is problematic. PMID:19068276

  4. Method for MRI-guided conformal thermal therapy of prostate with planar transurethral ultrasound heating applicators

    NASA Astrophysics Data System (ADS)

    Chopra, Rajiv; Burtnyk, Mathieu; Haider, Masoom A.; Bronskill, Michael J.

    2005-11-01

    A method for conformal prostate thermal therapy using transurethral ultrasound heating applicators incorporating planar transducers is described. The capability to shape heating patterns to the geometry of the prostate gland from a single element in a multi-element heating applicator was evaluated using Bioheat transfer modelling. Eleven prostate geometries were obtained from patients who underwent MR imaging of the prostate gland prior to radical prostatectomy. Results indicate that ultrasound heating applicators incorporating multi-frequency planar transducers (4 × 20 mm, f = 4.7 MHz, 9.7 MHz) are capable of shaping thermal damage patterns to the geometry of individual prostates. A temperature feedback control algorithm has been developed to control the frequency, rotation rate and applied power level from transurethral heating applicators based on measurements of the boundary temperature during heating. The discrepancy between the thermal damage boundary and the target boundary was less than 5 mm, and the transition distance between coagulation and normal tissue was less than 1 cm. Treatment times for large prostate volumes were less than 50 min, and perfusion did not have significant impact on the control algorithm. Rectal cooling will play an important role in reducing undesired heating near the rectal wall. Experimental validation of the simulations in a tissue-mimicking gel phantom demonstrated good agreement between the predicted and generated patterns of thermal damage.

  5. Method for in situ characterization of radiofrequency heating in parallel transmit MRI.

    PubMed

    Alon, Leeor; Deniz, Cem Murat; Brown, Ryan; Sodickson, Daniel K; Zhu, Yudong

    2013-05-01

    In ultra-high-field magnetic resonance imaging, parallel radiofrequency (RF) transmission presents both opportunities and challenges for specific absorption rate management. On one hand, parallel transmission provides flexibility in tailoring electric fields in the body while facilitating magnetization profile control. On the other hand, it increases the complexity of energy deposition as well as possibly exacerbating local specific absorption rate by improper design or delivery of RF pulses. This study shows that the information needed to characterize RF heating in parallel transmission is contained within a local power correlation matrix. Building upon a calibration scheme involving a finite number of magnetic resonance thermometry measurements, this work establishes a way of estimating the local power correlation matrix. Determination of this matrix allows prediction of temperature change for an arbitrary parallel transmit RF pulse. In the case of a three transmit coil MR experiment in a phantom, determination and validation of the power correlation matrix were conducted in less than 200 min with induced temperature changes of <4°C. Further optimization and adaptation are possible, and simulations evaluating potential feasibility for in vivo use are presented. The method allows general characteristics indicative of RF coil/pulse safety determined in situ.

  6. Sparse Reconstruction Challenge for diffusion MRI: Validation on a physical phantom to determine which acquisition scheme and analysis method to use?

    PubMed

    Ning, Lipeng; Laun, Frederik; Gur, Yaniv; DiBella, Edward V R; Deslauriers-Gauthier, Samuel; Megherbi, Thinhinane; Ghosh, Aurobrata; Zucchelli, Mauro; Menegaz, Gloria; Fick, Rutger; St-Jean, Samuel; Paquette, Michael; Aranda, Ramon; Descoteaux, Maxime; Deriche, Rachid; O'Donnell, Lauren; Rathi, Yogesh

    2015-12-01

    Diffusion magnetic resonance imaging (dMRI) is the modality of choice for investigating in-vivo white matter connectivity and neural tissue architecture of the brain. The diffusion-weighted signal in dMRI reflects the diffusivity of water molecules in brain tissue and can be utilized to produce image-based biomarkers for clinical research. Due to the constraints on scanning time, a limited number of measurements can be acquired within a clinically feasible scan time. In order to reconstruct the dMRI signal from a discrete set of measurements, a large number of algorithms have been proposed in recent years in conjunction with varying sampling schemes, i.e., with varying b-values and gradient directions. Thus, it is imperative to compare the performance of these reconstruction methods on a single data set to provide appropriate guidelines to neuroscientists on making an informed decision while designing their acquisition protocols. For this purpose, the SPArse Reconstruction Challenge (SPARC) was held along with the workshop on Computational Diffusion MRI (at MICCAI 2014) to validate the performance of multiple reconstruction methods using data acquired from a physical phantom. A total of 16 reconstruction algorithms (9 teams) participated in this community challenge. The goal was to reconstruct single b-value and/or multiple b-value data from a sparse set of measurements. In particular, the aim was to determine an appropriate acquisition protocol (in terms of the number of measurements, b-values) and the analysis method to use for a neuroimaging study. The challenge did not delve on the accuracy of these methods in estimating model specific measures such as fractional anisotropy (FA) or mean diffusivity, but on the accuracy of these methods to fit the data. This paper presents several quantitative results pertaining to each reconstruction algorithm. The conclusions in this paper provide a valuable guideline for choosing a suitable algorithm and the corresponding

  7. Optogenetic Functional MRI

    PubMed Central

    Lin, Peter; Fang, Zhongnan; Liu, Jia; Lee, Jin Hyung

    2016-01-01

    The investigation of the functional connectivity of precise neural circuits across the entire intact brain can be achieved through optogenetic functional magnetic resonance imaging (ofMRI), which is a novel technique that combines the relatively high spatial resolution of high-field fMRI with the precision of optogenetic stimulation. Fiber optics that enable delivery of specific wavelengths of light deep into the brain in vivo are implanted into regions of interest in order to specifically stimulate targeted cell types that have been genetically induced to express light-sensitive trans-membrane conductance channels, called opsins. fMRI is used to provide a non-invasive method of determining the brain's global dynamic response to optogenetic stimulation of specific neural circuits through measurement of the blood-oxygen-level-dependent (BOLD) signal, which provides an indirect measurement of neuronal activity. This protocol describes the construction of fiber optic implants, the implantation surgeries, the imaging with photostimulation and the data analysis required to successfully perform ofMRI. In summary, the precise stimulation and whole-brain monitoring ability of ofMRI are crucial factors in making ofMRI a powerful tool for the study of the connectomics of the brain in both healthy and diseased states. PMID:27167840

  8. A robust method for suppressing motion-induced coil sensitivity variations during prospective correction of head motion in fMRI.

    PubMed

    Faraji-Dana, Zahra; Tam, Fred; Chen, J Jean; Graham, Simon J

    2016-10-01

    Prospective motion correction is a promising candidate solution to suppress the effects of head motion during fMRI, ideally allowing the imaging plane to remain fixed with respect to the moving head. Residual signal artifacts may remain, however, because head motion in relation to a fixed multi-channel receiver coil (with non-uniform sensitivity maps) can potentially introduce unwanted signal variations comparable to the weak fMRI BOLD signal (~1%-4% at 1.5-3.0T). The present work aimed to investigate the magnitude of these residual artifacts, and characterize the regime over which prospective motion correction benefits from adjusting sensitivity maps to reflect relative positional change between the head and the coil. Numerical simulations were used to inform human fMRI experiments. The simulations indicated that for axial imaging within a commonly used 12-channel head coil, 5° of head rotation in-plane produced artifact signal changes of ~3%. Subsequently, six young adults were imaged with and without overt head motions of approximately this extent, with and without prospective motion correction using the Prospective Acquisition CorrEction (PACE) method, and with and without sensitivity map adjustments. Sensitivity map adjustments combined with PACE strongly protected against the artifacts of interest, as indicated by comparing three metrics of data quality (number of activated voxels, Dice coefficient of activation overlap, temporal standard deviation of baseline fMRI timeseries data) across the different experimental conditions. It is concluded that head motion in relation to a fixed multi-channel coil can adversely affect fMRI with prospective motion correction, and that sensitivity map adjustment can mitigate this effect at 3.0T. PMID:27451407

  9. [Research on K-means clustering segmentation method for MRI brain image based on selecting multi-peaks in gray histogram].

    PubMed

    Chen, Zhaoxue; Yu, Haizhong; Chen, Hao

    2013-12-01

    To solve the problem of traditional K-means clustering in which initial clustering centers are selected randomly, we proposed a new K-means segmentation algorithm based on robustly selecting 'peaks' standing for White Matter, Gray Matter and Cerebrospinal Fluid in multi-peaks gray histogram of MRI brain image. The new algorithm takes gray value of selected histogram 'peaks' as the initial K-means clustering center and can segment the MRI brain image into three parts of tissue more effectively, accurately, steadily and successfully. Massive experiments have proved that the proposed algorithm can overcome many shortcomings caused by traditional K-means clustering method such as low efficiency, veracity, robustness and time consuming. The histogram 'peak' selecting idea of the proposed segmentootion method is of more universal availability.

  10. A new ex vivo method to evaluate the performance of candidate MRI contrast agents: a proof-of-concept study

    PubMed Central

    2014-01-01

    Background Magnetic resonance imaging (MRI) plays an important role in tumor detection/diagnosis. The use of exogenous contrast agents (CAs) helps to improve the discrimination between lesion and neighbouring tissue, but most of the currently available CAs are non-specific. Assessing the performance of new, selective CAs requires exhaustive assays and large amounts of material. Accordingly, in a preliminary screening of new CAs, it is important to choose candidate compounds with good potential for in vivo efficiency. This screening method should reproduce as close as possible the in vivo environment. In this sense, a fast and reliable method to select the best candidate CAs for in vivo studies would minimize time and investment cost, and would benefit the development of better CAs. Results The post-mortem ex vivo relative contrast enhancement (RCE) was evaluated as a method to screen different types of CAs, including paramagnetic and superparamagnetic agents. In detail, sugar/gadolinium-loaded gold nanoparticles (Gd-GNPs) and iron nanoparticles (SPIONs) were tested. Our results indicate that the post-mortem ex vivo RCE of evaluated CAs, did not correlate well with their respective in vitro relaxivities. The results obtained with different Gd-GNPs suggest that the linker length of the sugar conjugate could modulate the interactions with cellular receptors and therefore the relaxivity value. A paramagnetic CA (GNP (E_2)), which performed best among a series of Gd-GNPs, was evaluated both ex vivo and in vivo. The ex vivo RCE was slightly worst than gadoterate meglumine (201.9 ± 9.3% versus 237 ± 14%, respectively), while the in vivo RCE, measured at the time-to-maximum enhancement for both compounds, pointed to GNP E_2 being a better CA in vivo than gadoterate meglumine. This is suggested to be related to the nanoparticule characteristics of the evaluated GNP. Conclusion We have developed a simple, cost-effective relatively high-throughput method for

  11. Intraoperative MRI and functional mapping.

    PubMed

    Gasser, Thomas; Szelenyi, Andrea; Senft, Christian; Muragaki, Yoshihiro; Sandalcioglu, I Erol; Sure, Ulrich; Nimsky, Christopher; Seifert, Volker

    2011-01-01

    The integration of functional and anatomical data into neuronavigation is an established standard of care in many neurosurgical departments. Yet, this method has limitations as in most cases the data are acquired prior to surgery. Due to brain-shift the accurate presentation of functional as well as anatomical structures declines in the course of surgery. In consequence, the acquisition of information during surgery about the brain's current functional state is of specific interest. The advancement of imaging technologies (e.g. fMRI, MEG, Intraoperative Optical Intrinsic Signal Imaging--IOIS) and neurophysiological techniques and the advent of intraoperative MRI all had a major impact on neurosurgery. The combination of modalities such as neurophysiology and intraoperative MRI (ioMRI), as well as the acquisition of functional MRI during surgery (ifMRI) are in the focus of this work. Especially the technical aspects and safety issues are elucidated.

  12. Task-Related Edge Density (TED)—A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain

    PubMed Central

    Lohmann, Gabriele; Stelzer, Johannes; Zuber, Verena; Buschmann, Tilo; Margulies, Daniel; Bartels, Andreas; Scheffler, Klaus

    2016-01-01

    The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach “Task-related Edge Density” (TED). TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function. PMID:27341204

  13. Task-Related Edge Density (TED)-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.

    PubMed

    Lohmann, Gabriele; Stelzer, Johannes; Zuber, Verena; Buschmann, Tilo; Margulies, Daniel; Bartels, Andreas; Scheffler, Klaus

    2016-01-01

    The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identification in fMRI data of the human brain is notoriously difficult. Here we propose a new method of fMRI data analysis that tackles this problem by considering large-scale, task-related synchronisation networks. Networks consist of nodes and edges connecting them, where nodes correspond to voxels in fMRI data, and the weight of an edge is determined via task-related changes in dynamic synchronisation between their respective times series. Based on these definitions, we developed a new data analysis algorithm that identifies edges that show differing levels of synchrony between two distinct task conditions and that occur in dense packs with similar characteristics. Hence, we call this approach "Task-related Edge Density" (TED). TED proved to be a very strong marker for dynamic network formation that easily lends itself to statistical analysis using large scale statistical inference. A major advantage of TED compared to other methods is that it does not depend on any specific hemodynamic response model, and it also does not require a presegmentation of the data for dimensionality reduction as it can handle large networks consisting of tens of thousands of voxels. We applied TED to fMRI data of a fingertapping and an emotion processing task provided by the Human Connectome Project. TED revealed network-based involvement of a large number of brain areas that evaded detection using traditional GLM-based analysis. We show that our proposed method provides an entirely new window into the immense complexity of human brain function. PMID:27341204

  14. Polarized noble gas MRI

    SciTech Connect

    Brookeman, James R.; Mugler, John P. III; Lange, Eduard E. de; Knight-Scott, Jack; Maier, Therese; Bogorad, Paul; Driehuys, Bastiaan; Cates, Gordon; Happer, William; Daniel, Thomas M.; Truwit, Jonathon D.

    1998-01-20

    The development of convenient methods to polarize liter quantities of the noble gases helium-3 and xenon-129 has provided the opportunity for a new MRI method to visualize the internal air spaces of the human lung. These spaces are usually poorly seen with hydrogen-based MRI, because of the limited water content of the lung and the low thermal polarization of the water protons achieved in conventional magnets. In addition, xenon, which has a relatively high solubility and a sufficiently persistent polarization level in blood and biological tissue, offers the prospect of providing perfusion images of the lung, brain and other organs.

  15. Inferring the Dysconnection Syndrome in Schizophrenia: Interpretational Considerations on Methods for the Network Analyses of fMRI Data

    PubMed Central

    Silverstein, Brian H.; Bressler, Steven L.; Diwadkar, Vaibhav A.

    2016-01-01

    Schizophrenia has long been considered one of the most intractable psychiatric conditions. Its etiology is likely polygenic, and its symptoms are hypothesized to result from complex aberrations in network-level neuronal activity. While easily identifiable by psychiatrists based on clear behavioral signs, the biological substrate of the disease remains poorly understood. Here, we discuss current trends and key concepts in the theoretical framework surrounding schizophrenia and critically discuss network approaches applied to neuroimaging data that can illuminate the correlates of the illness. We first consider a theoretical framework encompassing basic principles of brain function ranging from neural units toward perspectives of network function. Next, we outline the strengths and limitations of several fMRI-based analytic methodologies for assessing in vivo brain network function, including undirected and directed functional connectivity and effective connectivity. The underlying assumptions of each approach for modeling fMRI data are treated in some quantitative detail, allowing for assessment of the utility of each for generating inferences about brain networks relevant to schizophrenia. fMRI and the analyses of fMRI signals provide a limited, yet vibrant platform from which to test specific hypotheses about brain network dysfunction in schizophrenia. Carefully considered and applied connectivity measures have the power to illuminate loss or change of function at the network level, thus providing insight into the underlying neurobiology which gives rise to the emergent symptoms seen in the altered cognition and behavior of schizophrenia patients. PMID:27536253

  16. Inferring the Dysconnection Syndrome in Schizophrenia: Interpretational Considerations on Methods for the Network Analyses of fMRI Data.

    PubMed

    Silverstein, Brian H; Bressler, Steven L; Diwadkar, Vaibhav A

    2016-01-01

    Schizophrenia has long been considered one of the most intractable psychiatric conditions. Its etiology is likely polygenic, and its symptoms are hypothesized to result from complex aberrations in network-level neuronal activity. While easily identifiable by psychiatrists based on clear behavioral signs, the biological substrate of the disease remains poorly understood. Here, we discuss current trends and key concepts in the theoretical framework surrounding schizophrenia and critically discuss network approaches applied to neuroimaging data that can illuminate the correlates of the illness. We first consider a theoretical framework encompassing basic principles of brain function ranging from neural units toward perspectives of network function. Next, we outline the strengths and limitations of several fMRI-based analytic methodologies for assessing in vivo brain network function, including undirected and directed functional connectivity and effective connectivity. The underlying assumptions of each approach for modeling fMRI data are treated in some quantitative detail, allowing for assessment of the utility of each for generating inferences about brain networks relevant to schizophrenia. fMRI and the analyses of fMRI signals provide a limited, yet vibrant platform from which to test specific hypotheses about brain network dysfunction in schizophrenia. Carefully considered and applied connectivity measures have the power to illuminate loss or change of function at the network level, thus providing insight into the underlying neurobiology which gives rise to the emergent symptoms seen in the altered cognition and behavior of schizophrenia patients. PMID:27536253

  17. Methods for Acquiring Structural MRI Data in Very Young Children with Autism without the Use of Sedation

    ERIC Educational Resources Information Center

    Nordahl, Christine Wu; Simon, Tony J.; Zierhut, Cynthia; Solomon, Marjorie; Rogers, Sally J.; Amaral, David G.

    2008-01-01

    We describe a protocol with which we achieved a 93% success rate in acquiring high quality MRI scans without the use of sedation in 2.5-4.5 year old children with autism, developmental delays, and typical development. Our main strategy was to conduct MRIs during natural nocturnal sleep in the evenings after the child's normal bedtime.…

  18. Construction and investigation of 3D vessels net of the brain according to MRI data using the method of variation of scanning plane

    NASA Astrophysics Data System (ADS)

    Cherevko, A. A.; Yankova, G. S.; Maltseva, S. V.; Parshin, D. V.; Akulov, A. E.; Khe, A. K.; Chupakhin, A. P.

    2016-06-01

    The blood realizes the transport of substances, which are necessary for livelihoods, throughout the body. The assumption about the relationship genotype and structure of vasculature (in particular of brain) is natural. In the paper we consider models of vessel net for two genetic lines of laboratory mice. Vascular net obtained as a result of preprocessing MRI data. MRI scanning is realized using the method of variation of slope of scanning plane, i.e. by several sets of parallel planes specified by different normal vectors. The following special processing allowed to construct models of vessel nets without fragmentation. The purpose of the work is to compare the vascular network models of two different genetic lines of laboratory mice.

  19. A Method for Automated Classification of Parkinson's Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI.

    PubMed

    Banerjee, Monami; Okun, Michael S; Vaillancourt, David E; Vemuri, Baba C

    2016-01-01

    Parkinson's disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future.

  20. A Method for Automated Classification of Parkinson’s Disease Diagnosis Using an Ensemble Average Propagator Template Brain Map Estimated from Diffusion MRI

    PubMed Central

    Banerjee, Monami; Okun, Michael S.; Vaillancourt, David E.; Vemuri, Baba C.

    2016-01-01

    Parkinson’s disease (PD) is a common and debilitating neurodegenerative disorder that affects patients in all countries and of all nationalities. Magnetic resonance imaging (MRI) is currently one of the most widely used diagnostic imaging techniques utilized for detection of neurologic diseases. Changes in structural biomarkers will likely play an important future role in assessing progression of many neurological diseases inclusive of PD. In this paper, we derived structural biomarkers from diffusion MRI (dMRI), a structural modality that allows for non-invasive inference of neuronal fiber connectivity patterns. The structural biomarker we use is the ensemble average propagator (EAP), a probability density function fully characterizing the diffusion locally at a voxel level. To assess changes with respect to a normal anatomy, we construct an unbiased template brain map from the EAP fields of a control population. Use of an EAP captures both orientation and shape information of the diffusion process at each voxel in the dMRI data, and this feature can be a powerful representation to achieve enhanced PD brain mapping. This template brain map construction method is applicable to small animal models as well as to human brains. The differences between the control template brain map and novel patient data can then be assessed via a nonrigid warping algorithm that transforms the novel data into correspondence with the template brain map, thereby capturing the amount of elastic deformation needed to achieve this correspondence. We present the use of a manifold-valued feature called the Cauchy deformation tensor (CDT), which facilitates morphometric analysis and automated classification of a PD versus a control population. Finally, we present preliminary results of automated discrimination between a group of 22 controls and 46 PD patients using CDT. This method may be possibly applied to larger population sizes and other parkinsonian syndromes in the near future. PMID

  1. Portable MRI

    SciTech Connect

    Espy, Michelle A.

    2012-06-29

    This project proposes to: (1) provide the power of MRI to situations where it presently isn't available; (2) perform the engineering required to move from lab to a functional prototype; and (3) leverage significant existing infrastructure and capability in ultra-low field MRI. The reasons for doing this: (1) MRI is the most powerful tool for imaging soft-tissue (e.g. brain); (2) Billions don't have access due to cost or safety issues; (3) metal will heat/move in high magnetic fields; (4) Millions of cases of traumatic brain injury in US alone; (5) even more of non-traumatic brain injury; (6) (e.g. stroke, infection, chemical exposure); (7) Need for early diagnostic; (8) 'Signature' wound of recent conflicts; (9) 22% of injuries; (10) Implications for post-traumatic stress disorder; and (11) chronic traumatic encephalopathy.

  2. MO-C-17A-02: A Novel Method for Evaluating Hepatic Stiffness Based On 4D-MRI and Deformable Image Registration

    SciTech Connect

    Cui, T; Liang, X; Czito, B; Palta, M; Bashir, M; Yin, F; Cai, J

    2014-06-15

    Purpose: Quantitative imaging of hepatic stiffness has significant potential in radiation therapy, ranging from treatment planning to response assessment. This study aims to develop a novel, noninvasive method to quantify liver stiffness with 3D strains liver maps using 4D-MRI and deformable image registration (DIR). Methods: Five patients with liver cancer were imaged with an institutionally developed 4D-MRI technique under an IRB-approved protocol. Displacement vector fields (DVFs) across the liver were generated via DIR of different phases of 4D-MRI. Strain tensor at each voxel of interest (VOI) was computed from the relative displacements between the VOI and each of the six adjacent voxels. Three principal strains (E{sub 1}, E{sub 2} and E{sub 3}) of the VOI were derived as the eigenvalue of the strain tensor, which represent the magnitudes of the maximum and minimum stretches. Strain tensors for two regions of interest (ROIs) were calculated and compared for each patient, one within the tumor (ROI{sub 1}) and the other in normal liver distant from the heart (ROI{sub 2}). Results: 3D strain maps were successfully generated fort each respiratory phase of 4D-MRI for all patients. Liver deformations induced by both respiration and cardiac motion were observed. Differences in strain values adjacent to the distant from the heart indicate significant deformation caused by cardiac expansion during diastole. The large E{sub 1}/E{sub 2} (∼2) and E{sub 1}/E{sub 2} (∼10) ratios reflect the predominance of liver deformation in the superior-inferior direction. The mean E{sub 1} in ROI{sub 1} (0.12±0.10) was smaller than in ROI{sub 2} (0.15±0.12), reflecting a higher degree of stiffness of the cirrhotic tumor. Conclusion: We have successfully developed a novel method for quantitatively evaluating regional hepatic stiffness based on DIR of 4D-MRI. Our initial findings indicate that liver strain is heterogeneous, and liver tumors may have lower principal strain values

  3. Feasibility of simultaneous whole-brain imaging on an integrated PET-MRI system using an enhanced 2-point Dixon attenuation correction method

    PubMed Central

    Anazodo, Udunna C.; Thiessen, Jonathan D.; Ssali, Tracy; Mandel, Jonathan; Günther, Matthias; Butler, John; Pavlosky, William; Prato, Frank S.; Thompson, R. Terry; St. Lawrence, Keith S.

    2015-01-01

    Purpose: To evaluate a potential approach for improved attenuation correction (AC) of PET in simultaneous PET and MRI brain imaging, a straightforward approach that adds bone information missing on Dixon AC was explored. Methods: Bone information derived from individual T1-weighted MRI data using segmentation tools in SPM8, were added to the standard Dixon AC map. Percent relative difference between PET reconstructed with Dixon+bone and with Dixon AC maps were compared across brain regions of 13 oncology patients. The clinical potential of the improved Dixon AC was investigated by comparing relative perfusion (rCBF) measured with arterial spin labeling to relative glucose uptake (rPETdxbone) measured simultaneously with 18F-flurodexoyglucose in several regions across the brain. Results: A gradual increase in PET signal from center to the edge of the brain was observed in PET reconstructed with Dixon+bone. A 5–20% reduction in regional PET signals were observed in data corrected with standard Dixon AC maps. These regional underestimations of PET were either reduced or removed when Dixon+bone AC was applied. The mean relative correlation coefficient between rCBF and rPETdxbone was r = 0.53 (p < 0.001). Marked regional variations in rCBF-to-rPET correlation were observed, with the highest associations in the caudate and cingulate and the lowest in limbic structures. All findings were well matched to observations from previous studies conducted with PET data reconstructed with computed tomography derived AC maps. Conclusion: Adding bone information derived from T1-weighted MRI to Dixon AC maps can improve underestimation of PET activity in hybrid PET-MRI neuroimaging. PMID:25601825

  4. A novel manipulation method of human body ownership using an fMRI-compatible master-slave system.

    PubMed

    Hara, Masayuki; Salomon, Roy; van der Zwaag, Wietske; Kober, Tobias; Rognini, Giulio; Nabae, Hiroyuki; Yamamoto, Akio; Blanke, Olaf; Higuchi, Toshiro

    2014-09-30

    Bodily self-consciousness has become an important topic in cognitive neuroscience aiming to understand how the brain creates a unified sensation of the self in a body. Specifically, full body illusion (FBI) in which changes in bodily self-consciousness are experimentally introduced by using visual-tactile stimulation has led to improve understanding of these mechanisms. This paper introduces a novel approach to the classic FBI paradigm using a robotic master-slave system which allows us to examine interactions between action and the sense of body ownership in behavioral and MRI experiments. In the proposed approach, the use of the robotic master-slave system enables unique stimulation in which experimental participants can administer tactile cues on their own back using active self-touch. This active self-touch has never been employed in FBI experiments and it allows to test the role of sensorimotor integration and agency (the feeling of control over our actions) in FBI paradigms. The objective of this study is to propose a robotic-haptic platform allowing a new FBI paradigm including the active self-touch in MRI environments. This paper, first, describes the design concept and the performance of the prototype device in the fMRI environment (for 3T and 7T MRI scanners). In addition, the prototype device is applied to a classic FBI experiment, and we verify that the use of the prototype device succeeded in inducing the FBI. These results indicate that the proposed approach has a potential to drive advances in our understanding of human body ownership and agency by allowing novel manipulation and paradigms.

  5. Infarct density distribution by MRI in the porcine model of acute and chronic myocardial infarction as a potential method transferable to the clinic.

    PubMed

    Varga-Szemes, Akos; Simor, Tamas; Lenkey, Zsofia; van der Geest, Rob J; Kirschner, Robert; Toth, Levente; Brott, Brigitta C; Elgavish, Ada; Elgavish, Gabriel A

    2014-06-01

    To study the feasibility of a myocardial infarct (MI) quantification method [signal intensity-based percent infarct mapping (SI-PIM)] that is able to evaluate not only the size, but also the density distribution of the MI. In 14 male swine, MI was generated by 90 min of closed-chest balloon occlusion followed by reperfusion. Seven (n = 7) or 56 (n = 7) days after reperfusion, Gd-DTPA-bolus and continuous-infusion enhanced late gadolinium enhancement (LGE) MRI, and R1-mapping were carried out and post mortem triphenyl-tetrazolium-chloride (TTC) staining was performed. MI was quantified using binary [2 or 5 standard deviation (SD)], SI-PIM and R1-PIM methods. Infarct fraction (IF), and infarct-involved voxel fraction (IIVF) were determined by each MRI method. Bias of each method was compared to the TTC technique. The accuracy of MI quantification did not depend on the method of contrast administration or the age of the MI. IFs obtained by either of the two PIM methods were statistically not different from the IFs derived from the TTC measurements at either MI age. IFs obtained from the binary 2SD method overestimated IF obtained from TTC. IIVF among the three different PIM methods did not vary, but with the binary methods the IIVF gradually decreased with increasing the threshold limit. The advantage of SI-PIM over the conventional binary method is the ability to represent not only IF but also the density distribution of the MI. Since the SI-PIM methods are based on a single LGE acquisition, the bolus-data-based SI-PIM method can effortlessly be incorporated into the clinical image post-processing procedure.

  6. Evaluation of the partial flip angle spin echo method to improve non-uniformity in T1-weighted imaging with the 3-tesla MRI

    NASA Astrophysics Data System (ADS)

    Watanabe, Youhei; Tsuzaka, Masatoshi; Ishibashi, Kazuto; Sakurai, Yasuo

    2008-03-01

    The higher signal-to-noise ratio (SNR) of 3-Tesla magnetic resonance imaging (3T MRI) contributes to an improvement in the spatial and temporal resolution. However, T1-weighted images of the brain obtained by the spin-echo (SE) method using 3T MRI are unsuitable for clinical use because of the inhomogeneity of the radio frequency (RF) field B1 non-uniformity. And it is clear by SE method. In addition, the prolongation of the longitudinal relaxation time (T1) of most tissues leads to a decrease in the T1 contrast. Therefore, many hospitals that utilize 3TMRI use the GRE method instead of the SE method in order to obtain an adequate T1 contrast, as can be obtained using FLASH (fast low angle shot), and high uniformity of images. Further, many studies have been performed to improve the non uniformity using techniques such as spatial presaturation. However, when filters are used, the high intensity of the influence in susceptible regions, signal deficits, and original contrast are lost, and a distortion can be clearly observed when the GRE method is used. Therefore, we obtained the T1-weighted images by using the partial flip angle SE method instead of the GRE method or SE method. We attempted to improve the image non-uniformity by using the partial flip angle SE method. Using this method, we could improve the image uniformity and also realize an adequate T1 contrast. As a result, the uniformity was found to improve by 6% and it became 82.6% at 110°. These results indicate that the use of the partial flip angle SE method is effective for obtaining adequate uniformity in the T1-weighted images of the brain.

  7. Optimizing preprocessing and analysis pipelines for single-subject fMRI. I. Standard temporal motion and physiological noise correction methods.

    PubMed

    Churchill, Nathan W; Oder, Anita; Abdi, Hervé; Tam, Fred; Lee, Wayne; Thomas, Christopher; Ween, Jon E; Graham, Simon J; Strother, Stephen C

    2012-03-01

    either weak or absent under fixed pipelines, which has implications for the overall interpretation of fMRI data, and the relative importance of preprocessing methods.

  8. Development and application of methods to quantify spatial and temporal hyperpolarized 3He MRI ventilation dynamics: preliminary results in chronic obstructive pulmonary disease

    NASA Astrophysics Data System (ADS)

    Kirby, Miranda; Wheatley, Andrew; McCormack, David G.; Parraga, Grace

    2010-03-01

    Hyperpolarized helium-3 (3He) magnetic resonance imaging (MRI) has emerged as a non-invasive research method for quantifying lung structural and functional changes, enabling direct visualization in vivo at high spatial and temporal resolution. Here we described the development of methods for quantifying ventilation dynamics in response to salbutamol in Chronic Obstructive Pulmonary Disease (COPD). Whole body 3.0 Tesla Excite 12.0 MRI system was used to obtain multi-slice coronal images acquired immediately after subjects inhaled hyperpolarized 3He gas. Ventilated volume (VV), ventilation defect volume (VDV) and thoracic cavity volume (TCV) were recorded following segmentation of 3He and 1H images respectively, and used to calculate percent ventilated volume (PVV) and ventilation defect percent (VDP). Manual segmentation and Otsu thresholding were significantly correlated for VV (r=.82, p=.001), VDV (r=.87 p=.0002), PVV (r=.85, p=.0005), and VDP (r=.85, p=.0005). The level of agreement between these segmentation methods was also evaluated using Bland-Altman analysis and this showed that manual segmentation was consistently higher for VV (Mean=.22 L, SD=.05) and consistently lower for VDV (Mean=-.13, SD=.05) measurements than Otsu thresholding. To automate the quantification of newly ventilated pixels (NVp) post-bronchodilator, we used translation, rotation, and scaling transformations to register pre-and post-salbutamol images. There was a significant correlation between NVp and VDV (r=-.94 p=.005) and between percent newly ventilated pixels (PNVp) and VDP (r=- .89, p=.02), but not for VV or PVV. Evaluation of 3He MRI ventilation dynamics using Otsu thresholding and landmark-based image registration provides a way to regionally quantify functional changes in COPD subjects after treatment with beta-agonist bronchodilators, a common COPD and asthma therapy.

  9. Application of advanced machine learning methods on resting-state fMRI network for identification of mild cognitive impairment and Alzheimer's disease.

    PubMed

    Khazaee, Ali; Ebrahimzadeh, Ata; Babajani-Feremi, Abbas

    2016-09-01

    The study of brain networks by resting-state functional magnetic resonance imaging (rs-fMRI) is a promising method for identifying patients with dementia from healthy controls (HC). Using graph theory, different aspects of the brain network can be efficiently characterized by calculating measures of integration and segregation. In this study, we combined a graph theoretical approach with advanced machine learning methods to study the brain network in 89 patients with mild cognitive impairment (MCI), 34 patients with Alzheimer's disease (AD), and 45 age-matched HC. The rs-fMRI connectivity matrix was constructed using a brain parcellation based on a 264 putative functional areas. Using the optimal features extracted from the graph measures, we were able to accurately classify three groups (i.e., HC, MCI, and AD) with accuracy of 88.4 %. We also investigated performance of our proposed method for a binary classification of a group (e.g., MCI) from two other groups (e.g., HC and AD). The classification accuracies for identifying HC from AD and MCI, AD from HC and MCI, and MCI from HC and AD, were 87.3, 97.5, and 72.0 %, respectively. In addition, results based on the parcellation of 264 regions were compared to that of the automated anatomical labeling atlas (AAL), consisted of 90 regions. The accuracy of classification of three groups using AAL was degraded to 83.2 %. Our results show that combining the graph measures with the machine learning approach, on the basis of the rs-fMRI connectivity analysis, may assist in diagnosis of AD and MCI.

  10. Automated fibroglandular tissue segmentation and volumetric density estimation in breast MRI using an atlas-aided fuzzy C-means method

    SciTech Connect

    Wu, Shandong; Weinstein, Susan P.; Conant, Emily F.; Kontos, Despina

    2013-12-15

    Purpose: Breast magnetic resonance imaging (MRI) plays an important role in the clinical management of breast cancer. Studies suggest that the relative amount of fibroglandular (i.e., dense) tissue in the breast as quantified in MR images can be predictive of the risk for developing breast cancer, especially for high-risk women. Automated segmentation of the fibroglandular tissue and volumetric density estimation in breast MRI could therefore be useful for breast cancer risk assessment. Methods: In this work the authors develop and validate a fully automated segmentation algorithm, namely, an atlas-aided fuzzy C-means (FCM-Atlas) method, to estimate the volumetric amount of fibroglandular tissue in breast MRI. The FCM-Atlas is a 2D segmentation method working on a slice-by-slice basis. FCM clustering is first applied to the intensity space of each 2D MR slice to produce an initial voxelwise likelihood map of fibroglandular tissue. Then a prior learned fibroglandular tissue likelihood atlas is incorporated to refine the initial FCM likelihood map to achieve enhanced segmentation, from which the absolute volume of the fibroglandular tissue (|FGT|) and the relative amount (i.e., percentage) of the |FGT| relative to the whole breast volume (FGT%) are computed. The authors' method is evaluated by a representative dataset of 60 3D bilateral breast MRI scans (120 breasts) that span the full breast density range of the American College of Radiology Breast Imaging Reporting and Data System. The automated segmentation is compared to manual segmentation obtained by two experienced breast imaging radiologists. Segmentation performance is assessed by linear regression, Pearson's correlation coefficients, Student's pairedt-test, and Dice's similarity coefficients (DSC). Results: The inter-reader correlation is 0.97 for FGT% and 0.95 for |FGT|. When compared to the average of the two readers’ manual segmentation, the proposed FCM-Atlas method achieves a correlation ofr = 0

  11. Analysis of dynamic cerebral contrast-enhanced perfusion MRI time-series based on unsupervised clustering methods

    NASA Astrophysics Data System (ADS)

    Lange, Oliver; Meyer-Baese, Anke; Wismuller, Axel; Hurdal, Monica

    2005-03-01

    We employ unsupervised clustering techniques for the analysis of dynamic contrast-enhanced perfusion MRI time-series in patients with and without stroke. "Neural gas" network, fuzzy clustering based on deterministic annealing, self-organizing maps, and fuzzy c-means clustering enable self-organized data-driven segmentation w.r.t.fine-grained differences of signal amplitude and dynamics, thus identifying asymmetries and local abnormalities of brain perfusion. We conclude that clustering is a useful extension to conventional perfusion parameter maps.

  12. Anatomo-clinical overlapping maps (AnaCOM): a new method to create anatomo-functional maps from neuropsychological tests and structural MRI scan of subjects with brain lesions

    NASA Astrophysics Data System (ADS)

    Kinkingnehun, Serge R. J.; du Boisgueheneuc, Foucaud; Golmard, Jean-Louis; Zhang, Sandy X.; Levy, Richard; Dubois, Bruno

    2004-04-01

    We have developed a new technique to analyze correlations between brain anatomy and its neurological functions. The technique is based on the anatomic MRI of patients with brain lesions who are administered neuropsychological tests. Brain lesions of the MRI scans are first manually segmented. The MRI volumes are then normalized to a reference map, using the segmented area as a mask. After normalization, the brain lesions of the MRI are segmented again in order to redefine the border of the lesions in the context of the normalized brain. Once the MRI is segmented, the patient's score on the neuropsychological test is assigned to each voxel in the lesioned area, while the rest of the voxels of the image are set to 0. Subsequently, the individual patient's MRI images are superimposed, and each voxel is reassigned the average score of the patients who have a lesion at that voxel. A threshold is applied to remove regions having less than three overlaps. This process leads to an anatomo-functional map that links brain areas to functional loss. Other maps can be created to aid in analyzing the functional maps, such as one that indicates the 95% confidence interval of the averaged scores for each area. This anatomo-clinical overlapping map (AnaCOM) method was used to obtain functional maps from patients with lesions in the superior frontal gyrus. By finding particular subregions more responsible for a particular deficit, this method can generate new hypotheses to be tested by conventional group methods.

  13. Integration of DCE-MRI and DW-MRI Quantitative Parameters for Breast Lesion Classification

    PubMed Central

    Fusco, Roberta; Sansone, Mario; Filice, Salvatore; Granata, Vincenza; Catalano, Orlando; Amato, Daniela Maria; Di Bonito, Maurizio; D'Aiuto, Massimiliano; Capasso, Immacolata; Rinaldo, Massimo; Petrillo, Antonella

    2015-01-01

    Objective. The purpose of our study was to evaluate the diagnostic value of an imaging protocol combining dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI) in patients with suspicious breast lesions. Materials and Methods. A total of 31 breast lesions (15 malignant and 16 benign proved by histological examination) in 26 female patients were included in this study. For both DCE-MRI and DW-MRI model free and model based parameters were computed pixel by pixel on manually segmented ROIs. Statistical procedures included conventional linear analysis and more advanced techniques for classification of lesions in benign and malignant. Results. Our findings indicated no strong correlation between DCE-MRI and DW-MRI parameters. Results of classification analysis show that combining of DCE parameters or DW-MRI parameter, in comparison of single feature, does not yield a dramatic improvement of sensitivity and specificity of the two techniques alone. The best performance was obtained considering a full combination of all features. Moreover, the classification results combining all features are dominated by DCE-MRI features alone. Conclusion. The combination of DWI and DCE-MRI does not show a potential to dramatically increase the sensitivity and specificity of breast MRI. DCE-MRI alone gave the same performance as in combination with DW-MRI. PMID:26339597

  14. Intraoperative, real-time, functional MRI.

    PubMed

    Gering, D T; Weber, D M

    1998-01-01

    Functional MRI (fMRI) methods have been demonstrated to noninvasively identify motor-sensory, visual, and other areas of eloquent cortex for guiding surgical intervention. Typically, fMRI data are acquired preoperatively during a conventional surgical planning MRI examination. Unlike direct cortical stimulation at the time of surgery, however, preoperative fMRI methods do not account for the potential movement of tissues (relative to the time of functional imaging) that may occur in the surgical suite as a direct result of the intervention. Recently, an MRI device has been demonstrated for use in the surgical suite that has the potential to reduce the extent of cortical exposure required for the intervention. However, the invasive requirements of cortical mapping may supersede the invasive requirements of the surgical intervention itself. Consequently, we demonstrate here a modification to the intraoperative MRI device that facilitates a noninvasive, real-time, functional MR examination in the surgical suite.

  15. A novel segmentation approach for implementation of MRAC in head PET/MRI employing Short-TE MRI and 2-point Dixon method in a fuzzy C-means framework

    NASA Astrophysics Data System (ADS)

    Khateri, Parisa; Rad, Hamidreza Saligheh; Jafari, Amir Homayoun; Ay, Mohammad Reza

    2014-01-01

    Quantitative PET image reconstruction requires an accurate map of attenuation coefficients of the tissue under investigation at 511 keV (μ-map), and in order to correct the emission data for attenuation. The use of MRI-based attenuation correction (MRAC) has recently received lots of attention in the scientific literature. One of the major difficulties facing MRAC has been observed in the areas where bone and air collide, e.g. ethmoidal sinuses in the head area. Bone is intrinsically not detectable by conventional MRI, making it difficult to distinguish air from bone. Therefore, development of more versatile MR sequences to label the bone structure, e.g. ultra-short echo-time (UTE) sequences, certainly plays a significant role in novel methodological developments. However, long acquisition time and complexity of UTE sequences limit its clinical applications. To overcome this problem, we developed a novel combination of Short-TE (ShTE) pulse sequence to detect bone signal with a 2-point Dixon technique for water-fat discrimination, along with a robust image segmentation method based on fuzzy clustering C-means (FCM) to segment the head area into four classes of air, bone, soft tissue and adipose tissue. The imaging protocol was set on a clinical 3 T Tim Trio and also 1.5 T Avanto (Siemens Medical Solution, Erlangen, Germany) employing a triple echo time pulse sequence in the head area. The acquisition parameters were as follows: TE1/TE2/TE3=0.98/4.925/6.155 ms, TR=8 ms, FA=25 on the 3 T system, and TE1/TE2/TE3=1.1/2.38/4.76 ms, TR=16 ms, FA=18 for the 1.5 T system. The second and third echo-times belonged to the Dixon decomposition to distinguish soft and adipose tissues. To quantify accuracy, sensitivity and specificity of the bone segmentation algorithm, resulting classes of MR-based segmented bone were compared with the manual segmented one by our expert neuro-radiologist. Results for both 3 T and 1.5 T systems show that bone segmentation applied in several

  16. Fiber estimation and tractography in diffusion MRI: development of simulated brain images and comparison of multi-fiber analysis methods at clinical b-values.

    PubMed

    Wilkins, Bryce; Lee, Namgyun; Gajawelli, Niharika; Law, Meng; Leporé, Natasha

    2015-04-01

    Advances in diffusion-weighted magnetic resonance imaging (DW-MRI) have led to many alternative diffusion sampling strategies and analysis methodologies. A common objective among methods is estimation of white matter fiber orientations within each voxel, as doing so permits in-vivo fiber-tracking and the ability to study brain connectivity and networks. Knowledge of how DW-MRI sampling schemes affect fiber estimation accuracy, tractography and the ability to recover complex white-matter pathways, differences between results due to choice of analysis method, and which method(s) perform optimally for specific data sets, all remain important problems, especially as tractography-based studies become common. In this work, we begin to address these concerns by developing sets of simulated diffusion-weighted brain images which we then use to quantitatively evaluate the performance of six DW-MRI analysis methods in terms of estimated fiber orientation accuracy, false-positive (spurious) and false-negative (missing) fiber rates, and fiber-tracking. The analysis methods studied are: 1) a two-compartment "ball and stick" model (BSM) (Behrens et al., 2003); 2) a non-negativity constrained spherical deconvolution (CSD) approach (Tournier et al., 2007); 3) analytical q-ball imaging (QBI) (Descoteaux et al., 2007); 4) q-ball imaging with Funk-Radon and Cosine Transform (FRACT) (Haldar and Leahy, 2013); 5) q-ball imaging within constant solid angle (CSA) (Aganj et al., 2010); and 6) a generalized Fourier transform approach known as generalized q-sampling imaging (GQI) (Yeh et al., 2010). We investigate these methods using 20, 30, 40, 60, 90 and 120 evenly distributed q-space samples of a single shell, and focus on a signal-to-noise ratio (SNR = 18) and diffusion-weighting (b = 1000 s/mm(2)) common to clinical studies. We found that the BSM and CSD methods consistently yielded the least fiber orientation error and simultaneously greatest detection rate of fibers. Fiber detection

  17. Fiber estimation and tractography in diffusion MRI: development of simulated brain images and comparison of multi-fiber analysis methods at clinical b-values.

    PubMed

    Wilkins, Bryce; Lee, Namgyun; Gajawelli, Niharika; Law, Meng; Leporé, Natasha

    2015-04-01

    Advances in diffusion-weighted magnetic resonance imaging (DW-MRI) have led to many alternative diffusion sampling strategies and analysis methodologies. A common objective among methods is estimation of white matter fiber orientations within each voxel, as doing so permits in-vivo fiber-tracking and the ability to study brain connectivity and networks. Knowledge of how DW-MRI sampling schemes affect fiber estimation accuracy, tractography and the ability to recover complex white-matter pathways, differences between results due to choice of analysis method, and which method(s) perform optimally for specific data sets, all remain important problems, especially as tractography-based studies become common. In this work, we begin to address these concerns by developing sets of simulated diffusion-weighted brain images which we then use to quantitatively evaluate the performance of six DW-MRI analysis methods in terms of estimated fiber orientation accuracy, false-positive (spurious) and false-negative (missing) fiber rates, and fiber-tracking. The analysis methods studied are: 1) a two-compartment "ball and stick" model (BSM) (Behrens et al., 2003); 2) a non-negativity constrained spherical deconvolution (CSD) approach (Tournier et al., 2007); 3) analytical q-ball imaging (QBI) (Descoteaux et al., 2007); 4) q-ball imaging with Funk-Radon and Cosine Transform (FRACT) (Haldar and Leahy, 2013); 5) q-ball imaging within constant solid angle (CSA) (Aganj et al., 2010); and 6) a generalized Fourier transform approach known as generalized q-sampling imaging (GQI) (Yeh et al., 2010). We investigate these methods using 20, 30, 40, 60, 90 and 120 evenly distributed q-space samples of a single shell, and focus on a signal-to-noise ratio (SNR = 18) and diffusion-weighting (b = 1000 s/mm(2)) common to clinical studies. We found that the BSM and CSD methods consistently yielded the least fiber orientation error and simultaneously greatest detection rate of fibers. Fiber detection

  18. Pelvis MRI scan

    MedlinePlus

    MRI - pelvis; MRI - hips; Pelvic MRI with prostate probe; Magnetic resonance imaging - pelvis ... care provider if you are afraid of close spaces (have claustrophobia). You may be given a medicine ...

  19. Breast MRI scan

    MedlinePlus

    MRI - breast; Magnetic resonance imaging - breast; Breast cancer - MRI; Breast cancer screening - MRI ... the same breast or the other breast after breast cancer has been diagnosed Distinguish between scar tissue and ...

  20. MRI of plants and foods

    NASA Astrophysics Data System (ADS)

    Van As, Henk; van Duynhoven, John

    2013-04-01

    The importance and prospects for MRI as applied to intact plants and to foods are presented in view of one of humanity's most pressing concerns, the sustainable and healthy feeding of a worldwide increasing population. Intact plants and foods have in common that their functionality is determined by complex multiple length scale architectures. Intact plants have an additional level of complexity since they are living systems which critically depend on transport and signalling processes between and within tissues and organs. The combination of recent cutting-edge technical advances and integration of MRI accessible parameters has the perspective to contribute to breakthroughs in understanding complex regulatory plant performance mechanisms. In food science and technology MRI allows for quantitative multi-length scale structural assessment of food systems, non-invasive monitoring of heat and mass transport during shelf-life and processing, and for a unique view on food properties under shear. These MRI applications are powerful enablers of rationally (re)designed food formulations and processes. Limitations and bottlenecks of the present plant and food MRI methods are mainly related to short T2 values and susceptibility artefacts originating from small air spaces in tissues/materials. We envisage cross-fertilisation of solutions to overcome these hurdles in MRI applications in plants and foods. For both application areas we witness a development where MRI is moving from highly specialised equipment to mobile and downscaled versions to be used by a broad user base in the field, greenhouse, food laboratory or factory.

  1. Power spectrum scale invariance quantifies limbic dysregulation in trait anxious adults using fMRI: adapting methods optimized for characterizing autonomic dysregulation to neural dynamic timeseries.

    PubMed Central

    Tolkunov, Denis; Rubin, Denis; Mujica-Parodi, LR

    2010-01-01

    In a well-regulated control system, excitatory and inhibitory components work closely together with minimum lag; in response to inputs of finite duration, outputs should show rapid rise and, following the input's termination, immediate return to baseline. The efficiency of this response can be quantified using the power spectrum density's scaling parameter β, a measure of self-similarity, applied to the first-derivative of the raw signal. In this study, we adapted power spectrum density methods, previously used to quantify autonomic dysregulation (heart rate variability), to neural time-series obtained via functional MRI. The negative feedback loop we investigated was the limbic system, using affect-valent faces as stimuli. We hypothesized that trait anxiety would be related to efficiency of regulation of limbic responses, as quantified by power law scaling of fMRI time series. Our results supported this hypothesis, showing moderate to strong correlations of β (r = 0.4–0.54) for the amygdala, orbitofrontal cortex, hippocampus, superior temporal gyrus, posterior insula, and anterior cingulate. Strong anticorrelations were also found between the amygdala's β and wake heart rate variability (r = −0.61), suggesting a robust relationship between dysregulated limbic outputs and their autonomic consequences. PMID:20025979

  2. An equivalent distributed magnetic current based FDTD method for the calculation of E-fields induced by gradient coils in MRI.

    PubMed

    Crozier, S; Liu, F; Wei, Q

    2004-01-01

    This paper evaluates a low-frequency FDTD method applied to the problem of induced E-fields/eddy currents in the human body resulting from the pulsed magnetic field gradients in MRI. In this algorithm, a distributed equivalent magnetic current (DEMC) is proposed as the electromagnetic source and is obtained by quasistatic calculation of the empty coil's vector potential or measurements therein. This technique circumvents the discretizing of complicated gradient coil geometries into a mesh of Yee cells, and thereby enables any type of gradient coil modeling or other complex low frequency sources. The proposed method has been verified against an example with an analytical solution. Results are presented showing the spatial distribution of gradient-induced electric fields in a multilayered spherical phantom model and a complete body model.

  3. MRI-aided tissues interface characterization: An accurate signal propagation time calculation method for UWB breast tumor imaging

    NASA Astrophysics Data System (ADS)

    Wang, Liang; Xiao, Xia; Kikkawa, Takamaro

    2016-12-01

    Radar-based ultrawideband (UWB) microwave imaging is expected to be a safe, low-cost tool for breast cancer detection. However, since radar wave travels at different speeds in different tissues, propagation time is hard to be estimated in heterogeneous breast. Wrongly estimated propagation time leads to error of tumor location in resulting image, aka imaging error. In this paper, we develop a magnetic resonance imaging-aided (MRI-aided) propagation time calculation technique which is independent from radar imaging system but can help decrease the imaging error. The technique can eliminate the influence of the rough interface between fat layer and gland layer in breast and get relative accurate thicknesses of two layers. The propagation time in each layer is calculated and summed. The summed propagation time is used in Confocal imaging algorithm to increase the accuracy of resulting image. 25 patients' breast models with glands of varying size are classified into four categories for imaging simulation tests. Imaging accuracy in terms of tumor location along x-direction has been improved for 21 among 25 cases, as a result, overall around 50% improvement compared to conventional UWB imaging.

  4. A New Method to Explore the Spectral Impact of the Piriform Fossae on the Singing Voice: Benchmarking Using MRI-Based 3D-Printed Vocal Tracts

    PubMed Central

    Delvaux, Bertrand; Howard, David

    2014-01-01

    The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4–5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output. PMID:25048199

  5. Three-Dimensional Carotid Plaque Progression Simulation Using Meshless Generalized Finite Difference Method Based on Multi-Year MRI Patient-Tracking Data.

    PubMed

    Yang, Chun; Tang, Dalin; Atluri, Satya

    2010-01-01

    Cardiovascular disease (CVD) is becoming the number one cause of death worldwide. Atherosclerotic plaque rupture and progression are closely related to most severe cardiovascular syndromes such as heart attack and stroke. Mechanisms governing plaque rupture and progression are not well understood. A computational procedure based on three-dimensional meshless generalized finite difference (MGFD) method and serial magnetic resonance imaging (MRI) data was introduced to quantify patient-specific carotid atherosclerotic plaque growth functions and simulate plaque progression. Participating patients were scanned three times (T1, T2, and T3, at intervals of about 18 months) to obtain plaque progression data. Vessel wall thickness (WT) changes were used as the measure for plaque progression. Since there was insufficient data with the current technology to quantify individual plaque component growth, the whole plaque was assumed to be uniform, homogeneous, isotropic, linear, and nearly incompressible. The linear elastic model was used. The 3D plaque model was discretized and solved using a meshless generalized finite difference (GFD) method. Four growth functions with different combinations of wall thickness, stress, and neighboring point terms were introduced to predict future plaque growth based on previous time point data. Starting from the T2 plaque geometry, plaque progression was simulated by solving the solid model and adjusting wall thickness using plaque growth functions iteratively until T3 is reached. Numerically simulated plaque progression agreed very well with the target T3 plaque geometry with errors ranging from 11.56%, 6.39%, 8.24%, to 4.45%, given by the four growth functions. We believe this is the first time 3D plaque progression simulation based on multi-year patient-tracking data was reported. Serial MRI-based progression simulation adds time dimension to plaque vulnerability assessment and will improve prediction accuracy for potential plaque rupture

  6. Cerebral cortex thickness in 15-year-old adolescents with low birth weight measured by an automated MRI-based method.

    PubMed

    Martinussen, M; Fischl, B; Larsson, H B; Skranes, J; Kulseng, S; Vangberg, T R; Vik, T; Brubakk, A-M; Haraldseth, O; Dale, A M

    2005-11-01

    Infants with low birth weight are at increased risk of perinatal brain injury. Disruption of normal cortical development may have consequences for later motor, behavioural and cognitive development. The aim of this study was to measure cerebral cortical thickness, area and volume with an automated MRI technique in 15-year-old adolescents who had low birth weight. Cerebral MRI for morphometric analysis was performed on 50 very low birth weight (VLBW, birth weight method of cortical surface models yielded measurements of cortical thickness and area for each subject's entire brain and computed cross-subject statistics based on cortical anatomy. The cortical surface models demonstrated regional thinning of the parietal, temporal and occipital lobes in the VLBW group, whereas regional thickening was demonstrated in the frontal and occipital lobes. The areas of change were greatest in those with the shortest gestational age at birth and lowest birth weight. Cortical surface area and cortical volume were lower in the VLBW than in the Control group. Within the VLBW group, there was an association between surface area and estimation of the intelligence quotient IQ (IQ(est)) and between cortical volume and IQ(est). Furthermore, cortical grey matter as a proportion of brain volume was significantly lower in the VLBW, but not in the SGA group compared with Controls. This observed reorganization of the developing brain offers a unique opportunity to investigate any relationship between changes in cortical anatomy and cognitive and social impairments, and the increase in psychiatric disorders that have been found in VLBW children and adolescents. PMID:16123146

  7. A study on a method to reduce the effect of the cross-talk artifact in a simultaneous, multiple-slice, plane, oblique MRI scan

    NASA Astrophysics Data System (ADS)

    Lee, Sun-Yeob; Cho, Jae-Hwan; Lee, Hae-Kag; Cho, Moo-Seong; Park, Cheol-Soo; Kim, Eng-Chan; Kim, Sung-Kyu; Dong, Kyung-Rae; Chung, Woon-Kwan; Shin, Jae-Woo; Kim, Young-Jae; Cho, Young-Kuk

    2012-09-01

    The aim of this study was to reduce the effect of cross-talk artifacts on the region of interest (ROI) and to improve the diagnostic value of an image by conducting an examination using the linear (series) method, rather than the interleave method, based on the time concept, which is a basic principle of MRI, with a focus on the T1-weighted image, which has a strong effect on the cross-talk artifact. A water phantom was placed in the center of a brain coil before using the interleave method and the linear method to obtain cross-sectional images. A sagittal oblique scan was conducted to ensure that the slice groups intersected one another. A reference image was also acquired at TR (time of repetition) = 500 msec. Subsequently, the TR was changed to 600 and 700 msec to conduct scans. The analysis method was to use the interleave method and the linear method to compare the effects of the cross-talk artifacts and the TR. As scanned images were suggested, the SNR (signal to noise ratio) for the ROI was measured. According to the study results, the effects of cross-talk artifacts were reduced more significantly in the image scanned using the linear method than in that using the interleave method. When the SNRs of the images scanned in the interleave method and the linear method were compared, the image scanned in the linear method showed higher SNRs for the anterior and the posterior parts at TR = 500, 600, and 700 msec. On the other hand, the image scanned in the interleave method showed an increase in the SNR for the middle part, where the cross-talk artifacts did not appear. This means that the cross-talk artifacts were reduced in the image scanned using the linear method, which resulted in an increase in the SNR. Overall, the SNRs of each image for the interleave method and the linear method were highest at TR = 700 msec. In conclusion, the linear method is selected to reduce the effects of cross-talk artifacts in a simultaneous and multiple slice plane oblique scan

  8. 3D Quantification of Wall Shear Stress and Oscillatory Shear Index Using a Finite-Element Method in 3D CINE PC-MRI Data of the Thoracic Aorta.

    PubMed

    Sotelo, Julio; Urbina, Jesus; Valverde, Israel; Tejos, Cristian; Irarrazaval, Pablo; Andia, Marcelo E; Uribe, Sergio; Hurtado, Daniel E

    2016-06-01

    Several 2D methods have been proposed to estimate WSS and OSI from PC-MRI, neglecting the longitudinal velocity gradients that typically arise in cardiovascular flow, particularly on vessel geometries whose cross section and centerline orientation strongly vary in the axial direction. Thus, the contribution of longitudinal velocity gradients remains understudied. In this work, we propose a 3D finite-element method for the quantification of WSS and OSI from 3D-CINE PC-MRI that accounts for both in-plane and longitudinal velocity gradients. We demonstrate the convergence and robustness of the method on cylindrical geometries using a synthetic phantom based on the Poiseuille flow equation. We also show that, in the presence of noise, the method is both stable and accurate. Using computational fluid dynamics simulations, we show that the proposed 3D method results in more accurate WSS estimates than those obtained from a 2D analysis not considering out-of-plane velocity gradients. Further, we conclude that for irregular geometries the accurate prediction of WSS requires the consideration of longitudinal gradients in the velocity field. Additionally, we compute 3D maps of WSS and OSI for 3D-CINE PC-MRI data sets from an aortic phantom and sixteen healthy volunteers and two patients. The OSI values show a greater dispersion than WSS, which is strongly dependent on the PC-MRI resolution. We envision that the proposed 3D method will improve the estimation of WSS and OSI from 3D-CINE PC-MRI images, allowing for more accurate estimates in vessels with pathologies that induce high longitudinal velocity gradients, such as coarctations and aneurisms.

  9. A model-constrained Monte Carlo method for blind arterial input function estimation in dynamic contrast-enhanced MRI: II. In vivo results

    NASA Astrophysics Data System (ADS)

    Schabel, Matthias C.; DiBella, Edward V. R.; Jensen, Randy L.; Salzman, Karen L.

    2010-08-01

    Accurate quantification of pharmacokinetic model parameters in tracer kinetic imaging experiments requires correspondingly accurate determination of the arterial input function (AIF). Despite significant effort expended on methods of directly measuring patient-specific AIFs in modalities as diverse as dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), dynamic positron emission tomography (PET), and perfusion computed tomography (CT), fundamental and technical difficulties have made consistent and reliable achievement of that goal elusive. Here, we validate a new algorithm for AIF determination, the Monte Carlo blind estimation (MCBE) method (which is described in detail and characterized by extensive simulations in a companion paper), by comparing AIFs measured in DCE-MRI studies of eight brain tumor patients with results of blind estimation. Blind AIFs calculated with the MCBE method using a pool of concentration-time curves from a region of normal brain tissue were found to be quite similar to the measured AIFs, with statistically significant decreases in fit residuals observed in six of eight patients. Biases between the blind and measured pharmacokinetic parameters were the dominant source of error. Averaged over all eight patients, the mean biases were +7% in K trans, 0% in kep, -11% in vp and +10% in ve. Corresponding uncertainties (median absolute deviation from the best fit line) were 0.0043 min-1 in K trans, 0.0491 min-1 in kep, 0.29% in vp and 0.45% in ve. The use of a published population-averaged AIF resulted in larger mean biases in three of the four parameters (-23% in K trans, -22% in kep, -63% in vp), with the bias in ve unchanged, and led to larger uncertainties in all four parameters (0.0083 min-1 in K trans, 0.1038 min-1 in kep, 0.31% in vp and 0.95% in ve). When blind AIFs were calculated from a region of tumor tissue, statistically significant decreases in fit residuals were observed in all eight patients despite larger

  10. MRI EVALUATION OF KNEE CARTILAGE

    PubMed Central

    Rodrigues, Marcelo Bordalo; Camanho, Gilberto Luís

    2015-01-01

    Through the ability of magnetic resonance imaging (MRI) to characterize soft tissue noninvasively, it has become an excellent method for evaluating cartilage. The development of new and faster methods allowed increased resolution and contrast in evaluating chondral structure, with greater diagnostic accuracy. In addition, physiological techniques for cartilage assessment that can detect early changes before the appearance of cracks and erosion have been developed. In this updating article, the various techniques for chondral assessment using knee MRI will be discussed and demonstrated. PMID:27022562

  11. Estimating Motion From MRI Data

    PubMed Central

    OZTURK, CENGIZHAN; DERBYSHIRE, J. ANDREW; MCVEIGH, ELLIOT R.

    2007-01-01

    Invited Paper Magnetic resonance imaging (MRI) is an ideal imaging modality to measure blood flow and tissue motion. It provides excellent contrast between soft tissues, and images can be acquired at positions and orientations freely defined by the user. From a temporal sequence of MR images, boundaries and edges of tissues can be tracked by image processing techniques. Additionally, MRI permits the source of the image signal to be manipulated. For example, temporary magnetic tags displaying a pattern of variable brightness may be placed in the object using MR saturation techniques, giving the user a known pattern to detect for motion tracking. The MRI signal is a modulated complex quantity, being derived from a rotating magnetic field in the form of an induced current. Well-defined patterns can also be introduced into the phase of the magnetization, and could be thought of as generalized tags. If the phase of each pixel is preserved during image reconstruction, relative phase shifts can be used to directly encode displacement, velocity and acceleration. New methods for modeling motion fields from MRI have now found application in cardiovascular and other soft tissue imaging. In this review, we shall describe the methods used for encoding, imaging, and modeling motion fields with MRI. PMID:18958181

  12. Dynamic keyhole: A novel method to improve MR images in the presence of respiratory motion for real-time MRI

    SciTech Connect

    Lee, Danny; Pollock, Sean; Whelan, Brendan; Keall, Paul; Kim, Taeho

    2014-07-15

    Purpose: In this work, the authors present a novel magnetic resonance imaging reconstruction method to improve the quality of MR images in the presence of respiratory motion for real-time thoracic image-guided radiotherapy. Methods: This new reconstruction method is called dynamic keyhole and utilizes a library of previously acquired, peripheral k-space datasets from the same (or similar) respiratory state in conjunction with central k-space datasets acquired in real-time. Internal or external respiratory signals are utilized to sort, match, and combine the two separate peripheral and central k-space datasets with respect to respiratory displacement, thereby reducing acquisition time and improving image quality without respiratory-related artifacts. In this study, the dynamic keyhole, conventional keyhole, and zero-filling methods were compared to full k-space acquisition (ground truth) for 60 coronal datasets acquired from 15 healthy human subjects. Results: For the same image-quality difference from the ground-truth image, the dynamic keyhole method reused 79% of the prior peripheral phase-encoding lines, while the conventional keyhole reused 73% and zero-filling 63% (p-value < 0.0001), corresponding to faster acquisition speed of dynamic keyhole for real-time imaging applications. Conclusions: This study demonstrates that the dynamic keyhole method is a promising technique for clinical applications such as image-guided radiotherapy requiring real-time MR monitoring of the thoracic region. Based on the results from this study, the dynamic keyhole method could increase the temporal resolution by a factor of five compared with full k-space methods.

  13. Computer-aided method for automated selection of optimal imaging plane for measurement of total cerebral blood flow by MRI

    NASA Astrophysics Data System (ADS)

    Teng, Pang-yu; Bagci, Ahmet Murat; Alperin, Noam

    2009-02-01

    A computer-aided method for finding an optimal imaging plane for simultaneous measurement of the arterial blood inflow through the 4 vessels leading blood to the brain by phase contrast magnetic resonance imaging is presented. The method performance is compared with manual selection by two observers. The skeletons of the 4 vessels for which centerlines are generated are first extracted. Then, a global direction of the relatively less curved internal carotid arteries is calculated to determine the main flow direction. This is then used as a reference direction to identify segments of the vertebral arteries that strongly deviates from the main flow direction. These segments are then used to identify anatomical landmarks for improved consistency of the imaging plane selection. An optimal imaging plane is then identified by finding a plane with the smallest error value, which is defined as the sum of the angles between the plane's normal and the vessel centerline's direction at the location of the intersections. Error values obtained using the automated and the manual methods were then compared using 9 magnetic resonance angiography (MRA) data sets. The automated method considerably outperformed the manual selection. The mean error value with the automated method was significantly lower than the manual method, 0.09+/-0.07 vs. 0.53+/-0.45, respectively (p<.0001, Student's t-test). Reproducibility of repeated measurements was analyzed using Bland and Altman's test, the mean 95% limits of agreements for the automated and manual method were 0.01~0.02 and 0.43~0.55 respectively.

  14. Validation of White-Matter Lesion Change Detection Methods on a Novel Publicly Available MRI Image Database.

    PubMed

    Lesjak, Žiga; Pernuš, Franjo; Likar, Boštjan; Špiclin, Žiga

    2016-10-01

    Changes of white-matter lesions (WMLs) are good predictors of the progression of neurodegenerative diseases like multiple sclerosis (MS). Based on longitudinal magnetic resonance (MR) imaging the changes can be monitored, while the need for their accurate and reliable quantification led to the development of several automated MR image analysis methods. However, an objective comparison of the methods is difficult, because publicly unavailable validation datasets with ground truth and different sets of performance metrics were used. In this study, we acquired longitudinal MR datasets of 20 MS patients, in which brain regions were extracted, spatially aligned and intensity normalized. Two expert raters then delineated and jointly revised the WML changes on subtracted baseline and follow-up MR images to obtain ground truth WML segmentations. The main contribution of this paper is an objective, quantitative and systematic evaluation of two unsupervised and one supervised intensity based change detection method on the publicly available datasets with ground truth segmentations, using common pre- and post-processing steps and common evaluation metrics. Besides, different combinations of the two main steps of the studied change detection methods, i.e. dissimilarity map construction and its segmentation, were tested to identify the best performing combination.

  15. Validation of White-Matter Lesion Change Detection Methods on a Novel Publicly Available MRI Image Database.

    PubMed

    Lesjak, Žiga; Pernuš, Franjo; Likar, Boštjan; Špiclin, Žiga

    2016-10-01

    Changes of white-matter lesions (WMLs) are good predictors of the progression of neurodegenerative diseases like multiple sclerosis (MS). Based on longitudinal magnetic resonance (MR) imaging the changes can be monitored, while the need for their accurate and reliable quantification led to the development of several automated MR image analysis methods. However, an objective comparison of the methods is difficult, because publicly unavailable validation datasets with ground truth and different sets of performance metrics were used. In this study, we acquired longitudinal MR datasets of 20 MS patients, in which brain regions were extracted, spatially aligned and intensity normalized. Two expert raters then delineated and jointly revised the WML changes on subtracted baseline and follow-up MR images to obtain ground truth WML segmentations. The main contribution of this paper is an objective, quantitative and systematic evaluation of two unsupervised and one supervised intensity based change detection method on the publicly available datasets with ground truth segmentations, using common pre- and post-processing steps and common evaluation metrics. Besides, different combinations of the two main steps of the studied change detection methods, i.e. dissimilarity map construction and its segmentation, were tested to identify the best performing combination. PMID:27207310

  16. A robust method to estimate the intracranial volume across MRI field strengths (1.5T and 3T).

    PubMed

    Keihaninejad, Shiva; Heckemann, Rolf A; Fagiolo, Gianlorenzo; Symms, Mark R; Hajnal, Joseph V; Hammers, Alexander

    2010-05-01

    As population-based studies may obtain images from scanners with different field strengths, a method to normalize regional brain volumes according to intracranial volume (ICV) independent of field strength is needed. We found systematic differences in ICV estimation, tested in a cohort of healthy subjects (n=5) that had been imaged using 1.5T and 3T scanners, and confirmed in two independent cohorts. This was related to systematic differences in the intensity of cerebrospinal fluid (CSF), with higher intensities for CSF located in the ventricles compared with CSF in the cisterns, at 3T versus 1.5T, which could not be removed with three different applied bias correction algorithms. We developed a method based on tissue probability maps in MNI (Montreal Neurological Institute) space and reverse normalization (reverse brain mask, RBM) and validated it against manual ICV measurements. We also compared it with alternative automated ICV estimation methods based on Statistical Parametric Mapping (SPM5) and Brain Extraction Tool (FSL). The proposed RBM method was equivalent to manual ICV normalization with a high intraclass correlation coefficient (ICC=0.99) and reliable across different field strengths. RBM achieved the best combination of precision and reliability in a group of healthy subjects, a group of patients with Alzheimer's disease (AD) and mild cognitive impairment (MCI) and can be used as a common normalization framework.

  17. A level set method for image segmentation in the presence of intensity inhomogeneities with application to MRI.

    PubMed

    Li, Chunming; Huang, Rui; Ding, Zhaohua; Gatenby, J Chris; Metaxas, Dimitris N; Gore, John C

    2011-07-01

    Intensity inhomogeneity often occurs in real-world images, which presents a considerable challenge in image segmentation. The most widely used image segmentation algorithms are region-based and typically rely on the homogeneity of the image intensities in the regions of interest, which often fail to provide accurate segmentation results due to the intensity inhomogeneity. This paper proposes a novel region-based method for image segmentation, which is able to deal with intensity inhomogeneities in the segmentation. First, based on the model of images with intensity inhomogeneities, we derive a local intensity clustering property of the image intensities, and define a local clustering criterion function for the image intensities in a neighborhood of each point. This local clustering criterion function is then integrated with respect to the neighborhood center to give a global criterion of image segmentation. In a level set formulation, this criterion defines an energy in terms of the level set functions that represent a partition of the image domain and a bias field that accounts for the intensity inhomogeneity of the image. Therefore, by minimizing this energy, our method is able to simultaneously segment the image and estimate the bias field, and the estimated bias field can be used for intensity inhomogeneity correction (or bias correction). Our method has been validated on synthetic images and real images of various modalities, with desirable performance in the presence of intensity inhomogeneities. Experiments show that our method is more robust to initialization, faster and more accurate than the well-known piecewise smooth model. As an application, our method has been used for segmentation and bias correction of magnetic resonance (MR) images with promising results. PMID:21518662

  18. A comparison between MRI, sonography and Functional Independence Score in Haemophilia methods in diagnosis, evaluation and classification of arthropathy in severe haemophilia A and B.

    PubMed

    Tasbihi, Mandana; Pishdad, Parisa; Haghpanah, Sezaneh; Ardeshiri, Rezvan; Tavoosi, Hakimeh; Karimi, Mehran

    2016-03-01

    Evaluation of joints in children with haemophilia is important in detecting abnormalities, staging their severity and following the effects of treatment. The aim of this study is to evaluate the correlation of FISH score (Functional Independence Score in Haemophilia) with the scores obtained by MRI and sonography for the diagnosis, evaluation and classification of arthropathy in severe haemophilia. In this cross-sectional study on 25 severe haemophilia patients, FISH, MRI and sonography procedures were performed in the elbow or knee joint. All patients' information, including age, type of haemophilia, affected joint, scores of MRI, sonography and FISH, dose of factor consumed, weight and prophylaxis protocol were collected and analysed. Among the 25 patients (age range of 11-70 years), 22 patients were haemophilia A and three patients were haemophilia B. Affected joints were right knee in 12 patients, left knee in nine and right elbow in four. There was only a statistically significant negative correlation between FISH and MRI Additive (A) scale (rs = -0.537, P = 0.006). Considering cartilage loss domain (related MRI A scale: 13-20), 20 patients (80%) were classified in this group with FISH scores ranged from 17 to 22. On the basis of our results, FISH scores in severe haemophilia patients were negatively correlated with MRI A scale. Also, it seems that a FISH score less than 22 could be considered as loss of cartilage; however, due to the small number of our patients, it needs further assessment in different populations.

  19. Getting an MRI

    MedlinePlus

    ... Help White House Lunch Recipes Getting an MRI (Video) KidsHealth > For Kids > Getting an MRI (Video) A A A en español Obtención de una resonancia magnética, RM (video) An MRI (magnetic resonance imaging) scan creates detailed ...

  20. A new method for the in vivo identification of mechanical properties in arteries from cine MRI images: theoretical framework and validation.

    PubMed

    Franquet, Alexandre; Avril, Stéphane; Le Riche, Rodolphe; Badel, Pierre; Schneider, Fabien C; Li, Zhi Yong; Boissier, Christian; Favre, Jean Pierre

    2013-08-01

    Quantifying the stiffness properties of soft tissues is essential for the diagnosis of many cardiovascular diseases such as atherosclerosis. In these pathologies it is widely agreed that the arterial wall stiffness is an indicator of vulnerability. The present paper focuses on the carotid artery and proposes a new inversion methodology for deriving the stiffness properties of the wall from cine-MRI (magnetic resonance imaging) data. We address this problem by setting-up a cost function defined as the distance between the modeled pixel signals and the measured ones. Minimizing this cost function yields the unknown stiffness properties of both the arterial wall and the surrounding tissues. The sensitivity of the identified properties to various sources of uncertainty is studied. Validation of the method is performed on a rubber phantom. The elastic modulus identified using the developed methodology lies within a mean error of 9.6%. It is then applied to two young healthy subjects as a proof of practical feasibility, with identified values of 625 kPa and 587 kPa for one of the carotid of each subject.

  1. A new method for the in vivo identification of mechanical properties in arteries from cine MRI images: theoretical framework and validation.

    PubMed

    Franquet, Alexandre; Avril, Stéphane; Le Riche, Rodolphe; Badel, Pierre; Schneider, Fabien C; Li, Zhi Yong; Boissier, Christian; Favre, Jean Pierre

    2013-08-01

    Quantifying the stiffness properties of soft tissues is essential for the diagnosis of many cardiovascular diseases such as atherosclerosis. In these pathologies it is widely agreed that the arterial wall stiffness is an indicator of vulnerability. The present paper focuses on the carotid artery and proposes a new inversion methodology for deriving the stiffness properties of the wall from cine-MRI (magnetic resonance imaging) data. We address this problem by setting-up a cost function defined as the distance between the modeled pixel signals and the measured ones. Minimizing this cost function yields the unknown stiffness properties of both the arterial wall and the surrounding tissues. The sensitivity of the identified properties to various sources of uncertainty is studied. Validation of the method is performed on a rubber phantom. The elastic modulus identified using the developed methodology lies within a mean error of 9.6%. It is then applied to two young healthy subjects as a proof of practical feasibility, with identified values of 625 kPa and 587 kPa for one of the carotid of each subject. PMID:23591477

  2. Fetal MRI: A pictorial essay.

    PubMed

    Rathee, Sapna; Joshi, Priscilla; Kelkar, Abhimanyu; Seth, Nagesh

    2016-01-01

    Ultrasonography (USG) is the primary method for antenatal fetal evaluation. However, fetal magnetic resonance imaging (MRI) has now become a valuable adjunct to USG in confirming/excluding suspected abnormalities and in the detection of additional abnormalities, thus changing the outcome of pregnancy and optimizing perinatal management. With the development of ultrafast sequences, fetal MRI has made remarkable progress in recent times. In this pictorial essay, we illustrate a spectrum of structural abnormalities affecting the central nervous system, thorax, genitourinary and gastrointestinal tract, as well as miscellaneous anomalies. Anomalies in twin gestations and placental abnormalities have also been included.

  3. Fetal MRI: A pictorial essay

    PubMed Central

    Rathee, Sapna; Joshi, Priscilla; Kelkar, Abhimanyu; Seth, Nagesh

    2016-01-01

    Ultrasonography (USG) is the primary method for antenatal fetal evaluation. However, fetal magnetic resonance imaging (MRI) has now become a valuable adjunct to USG in confirming/excluding suspected abnormalities and in the detection of additional abnormalities, thus changing the outcome of pregnancy and optimizing perinatal management. With the development of ultrafast sequences, fetal MRI has made remarkable progress in recent times. In this pictorial essay, we illustrate a spectrum of structural abnormalities affecting the central nervous system, thorax, genitourinary and gastrointestinal tract, as well as miscellaneous anomalies. Anomalies in twin gestations and placental abnormalities have also been included. PMID:27081224

  4. Gradient echo MRI

    PubMed Central

    Copenhaver, B R.; Shin, J; Warach, S; Butman, J A.; Saver, J L.; Kidwell, C S.

    2009-01-01

    Background: Recent studies have demonstrated that gradient echo (GRE) MRI sequences are as accurate as CT for the detection of intracerebral hemorrhage (ICH) in the context of acute stroke. However, many physicians who currently read acute stroke imaging studies may be unfamiliar with interpretation of GRE images. Methods: An NIH Web-based training program was developed including a pretest, tutorial, and posttest. Physicians involved in the care of acute stroke patients were encouraged to participate. The tutorial covered acute, chronic, and mimic hemorrhages as they appear on CT, diffusion-weighted imaging, and GRE sequences. Ability of users to identify ICH presence, type, and age on GRE was compared from the pretest to posttest timepoint. Results: A total of 104 users completed the tutorial. Specialties represented included general radiology (42%), general neurology (16%), neuroradiology (15%), stroke neurology (14%), emergency medicine (1%), and other (12%). Median overall score improved pretest to posttest from 66.7% to 83.3%, p < 0.001. Improvement by category was as follows: acute ICH, 66.7%–100%, p < 0.001; chronic ICH, 33.3%–66.7%, p < 0.001; ICH negatives/mimics, 100%–100%, p = 0.787. Sensitivity for identification of acute hemorrhage improved from 68.2% to 96.4%. Conclusions: Physicians involved in acute stroke care achieved significant improvement in gradient echo (GRE) hemorrhage interpretation after completing the NIH GRE MRI tutorial. This indicates that a Web-based tutorial may be a viable option for the widespread education of physicians to achieve an acceptable level of diagnostic accuracy at reading GRE MRI, thus enabling confident acute stroke treatment decisions. GLOSSARY AHA/ASA = American Heart Association/American Stroke Association; CME = continuing medical education; DWI = diffusion-weighted imaging; GRE = gradient echo; ICH = intracerebral hemorrhage; tPA = tissue plasminogen activator. PMID:19414724

  5. MRI endoscopy using intrinsically localized probes

    PubMed Central

    Sathyanarayana, Shashank; Bottomley, Paul A.

    2009-01-01

    Magnetic resonance imaging (MRI) is traditionally performed with fixed externally applied gradient magnetic fields and is hence intrinsically locked to the laboratory frame of reference (FoR). Here a method for high-resolution MRI that employs active, catheter-based, tiny internal probes that utilize the spatial properties of the probe itself for localization is proposed and demonstrated at 3 T. Because these properties are intrinsic to the probe, they move with it, transforming MRI from the laboratory FoR to the FoR of the device itself, analogous to an endoscope. The “MRI endoscope” can utilize loop coils and loopless antennas with modified sensitivity, in combination with adiabatic excitation by the device itself, to restrict the MRI sensitivity to a disk-shaped plane a few mm thick. Excitation with the MRI endoscope limits the eddy currents induced in the sample to an excited volume whose size is orders of magnitude below that excited by a conventional body MRI coil. Heat testing shows maximum local temperature increases of <1 °C during MRI, within regulatory guidelines. The method is demonstrated in a kiwifruit, in intact porcine and rabbit aortas, and in an atherosclerotic human iliac artery specimen, with in-plane resolution as small as 80 μm and 1.5–5 mm slice thickness. PMID:19378751

  6. Scaling index method: a novel nonlinear technique for the analysis of high-resolution MRI of human bones

    NASA Astrophysics Data System (ADS)

    Monetti, Roberto A.; Bohm, Holger; Muller, Dirk; Newitt, David; Majumdar, Sharmila; Rummeny, Ernst; Link, Thomas M.; Rath, Christoph

    2003-05-01

    The scaling index method (SIM) is a novel non-linear technique to extract structural information from arbitrary data sets. The tomographic images of a three dimensional object can be interpreted as a pixel distribution in a four dimensional space. The SIM provides a distribution of pointwise dimensions which characterizes the structural information of images. The SIM is applied to high resolution magnetic resonance images of human spinal and femoral bone specimens IN VITRO in order to derive a 3d non-linear texture measure which is compared to standard 2d morphometric parameters and bone mineral density in the prediction of biomechanical strength of trabecular bone. Our results show that structural non-linear parameters associated with the trabecular substructure of the bone can effectively predict the mechanical properties of trabecular bone in vitro. This indicates that the trabecular architecture contributes substantially to the biomechanical properties of the bone.

  7. 4D flow imaging with MRI

    PubMed Central

    Stankovic, Zoran; Allen, Bradley D.; Garcia, Julio; Jarvis, Kelly B.

    2014-01-01

    Magnetic resonance imaging (MRI) has become an important tool for the clinical evaluation of patients with cardiovascular disease. Since its introduction in the late 1980s, 2-dimensional phase contrast MRI (2D PC-MRI) has become a routine part of standard-of-care cardiac MRI for the assessment of regional blood flow in the heart and great vessels. More recently, time-resolved PC-MRI with velocity encoding along all three flow directions and three-dimensional (3D) anatomic coverage (also termed ‘4D flow MRI’) has been developed and applied for the evaluation of cardiovascular hemodynamics in multiple regions of the human body. 4D flow MRI allows for the comprehensive evaluation of complex blood flow patterns by 3D blood flow visualization and flexible retrospective quantification of flow parameters. Recent technical developments, including the utilization of advanced parallel imaging techniques such as k-t GRAPPA, have resulted in reasonable overall scan times, e.g., 8-12 minutes for 4D flow MRI of the aorta and 10-20 minutes for whole heart coverage. As a result, the application of 4D flow MRI in a clinical setting has become more feasible, as documented by an increased number of recent reports on the utility of the technique for the assessment of cardiac and vascular hemodynamics in patient studies. A number of studies have demonstrated the potential of 4D flow MRI to provide an improved assessment of hemodynamics which might aid in the diagnosis and therapeutic management of cardiovascular diseases. The purpose of this review is to describe the methods used for 4D flow MRI acquisition, post-processing and data analysis. In addition, the article provides an overview of the clinical applications of 4D flow MRI and includes a review of applications in the heart, thoracic aorta and hepatic system. PMID:24834414

  8. Penumbra detection using PWI/DWI mismatch MRI in a rat stroke model with and without comorbidity: comparison of methods

    PubMed Central

    Reid, Emma; Graham, Delyth; Lopez-Gonzalez, M Rosario; Holmes, William M; Macrae, I Mhairi; McCabe, Christopher

    2012-01-01

    Perfusion-diffusion (perfusion-weighted imaging (PWI)/diffusion-weighted imaging (DWI)) mismatch is used to identify penumbra in acute stroke. However, limitations in penumbra detection with mismatch are recognized, with a lack of consensus on thresholds, quantification and validation of mismatch. We determined perfusion and diffusion thresholds from final infarct in the clinically relevant spontaneously hypertensive stroke-prone (SHRSP) rat and its normotensive control strain, Wistar-Kyoto (WKY) and compared three methods for penumbra calculation. After permanent middle cerebral artery occlusion (MCAO) (WKY n=12, SHRSP n=15), diffusion-weighted (DWI) and perfusion-weighted (PWI) images were obtained for 4 hours post stroke and final infarct determined at 24 hours on T2 scans. The PWI/DWI mismatch was calculated from volumetric assessment (perfusion deficit volume minus apparent diffusion coefficient (ADC)-defined lesion volume) or spatial assessment of mismatch area on each coronal slice. The ADC-derived lesion growth provided the third, retrospective measure of penumbra. At 1 hour after MCAO, volumetric mismatch detected smaller volumes of penumbra in both strains (SHRSP: 31±50 mm3, WKY: 22±59 mm3, mean±s.d.) compared with spatial assessment (SHRSP: 36±15 mm3, WKY: 43±43 mm3) and ADC lesion expansion (SHRSP: 41±45 mm3, WKY: 65±41 mm3), although these differences were not statistically significant. Spatial assessment appears most informative, using both diffusion and perfusion data, eliminating the influence of negative mismatch and allowing the anatomical location of penumbra to be assessed at given time points after stroke. PMID:22669479

  9. High-performance computing MRI simulations.

    PubMed

    Stöcker, Tony; Vahedipour, Kaveh; Pflugfelder, Daniel; Shah, N Jon

    2010-07-01

    A new open-source software project is presented, JEMRIS, the Jülich Extensible MRI Simulator, which provides an MRI sequence development and simulation environment for the MRI community. The development was driven by the desire to achieve generality of simulated three-dimensional MRI experiments reflecting modern MRI systems hardware. The accompanying computational burden is overcome by means of parallel computing. Many aspects are covered that have not hitherto been simultaneously investigated in general MRI simulations such as parallel transmit and receive, important off-resonance effects, nonlinear gradients, and arbitrary spatiotemporal parameter variations at different levels. The latter can be used to simulate various types of motion, for instance. The JEMRIS user interface is very simple to use, but nevertheless it presents few limitations. MRI sequences with arbitrary waveforms and complex interdependent modules are modeled in a graphical user interface-based environment requiring no further programming. This manuscript describes the concepts, methods, and performance of the software. Examples of novel simulation results in active fields of MRI research are given.

  10. Reliability of Zygapophysial Joint Space Measurements Made from MRI Scans of Acute Low Back Pain Subjects: Comparison of Two Statistical Methods

    PubMed Central

    Cramer, Gregory D; Cantu, Joe A; Pocius, Judith D; Cambron, Jerrilyn A; McKinnis, Ray A

    2010-01-01

    Objective This purpose of this study was to assess the reliability of measurements made of the zygapophysial (Z) joint space from the MRI scans of subjects with acute low back pain (ALBP) using new equipment and 2 different methods of statistical analysis. If found reliable, the methods of Z joint measurement can be applied to scans taken before and after spinal manipulation in a larger study of ALBP subjects. Methods Three observers measured the central anterior-to-posterior distance of the left and right L4/L5 and L5/S1 Z joint space from 5 subject scans (20 digitizer measurements, rounded to 0.1mm) on two separate occasions separated by 4 weeks. Observers were blinded to each other and their previous work. Intra- and interobserver reliability was calculated by means of intra-class correlation coefficients (ICCs) and also by mean differences using the methods of Bland and Altman (1986). A mean difference of <±0.4 mm was considered clinically acceptable. Results ICCs showed intraobserver reliabilities of 0.95 (95%CI 0.87-0.98), 0.83 (0.62-0.92), and 0.92 (0.83-0.96) for each of the 3 observers; and interobserver reliabilities of 0.90 (0.82-0.95), 0.79 (0.61-0.90), and 0.84 (0.75-0.90) for the first and second measurements and overall reliability, respectively. The mean difference between the first and second measurements was -0.04 mm (±1.96 SD= -0.37 – 0.29), 0.23 (-0.48 – 0.94), 0.25 (-0.24 – 0.75), and 0.15 (-0.44 – 0.74) for each of the 3 observers and the overall agreement, respectively. Conclusions Both statistical methods were found to be useful and complementary and showed the measurements to be highly reliable. PMID:20350676

  11. Monodisperse magnetite (Fe3O4) nanoparticles modified with water soluble polymers for the diagnosis of breast cancer by MRI method

    NASA Astrophysics Data System (ADS)

    Rezayan, Ali Hossein; Mousavi, Majid; Kheirjou, Somayyeh; Amoabediny, Ghasem; Ardestani, Mehdi Shafiee; Mohammadnejad, Javad

    2016-12-01

    In this study, magnetic nanoparticles (MNPs) were synthesized via co-precipitation method. To enhance the biocompatibility and colloidal stability of the synthesized nanoparticles, they were modified with carboxyl functionalized PEG via dopamine (DPA) linker. Both modified and unmodified Fe3O4 nanoparticles exhibited super paramagnetic behavior (particle size below 20 nm). The saturation magnetization (Ms) of PEGdiacid-modified Fe3O4 was 45 emu/g, which was less than the unmodified Fe3O4 nanoparticles (70 emu/g). This difference indicated that PEGdiacid polymer was immobilized on the surface of Fe3O4 nanoparticles successfully. To evaluate the efficiency of the resulting nanoparticles as contrast agents for magnetic resonance imaging (MRI), different concentration of MNPs and different value of echo time TE were investigated. The results showed that by increasing the concentration of the nanoparticles, transverse relaxation time (T2) decreased, which subsequently resulted in MR signal enhancement. T2-weighted MR images of the different concentration of MNPs in different value of echo time TE indicated that MR signal intensity increased with increase in TE value up to 66 and then remained constant. The cytotoxicity effect of the modified and unmodified nanoparticles was evaluated in three different concentrations (12, 60 and 312 mg l-1) on MDA-MB-231 cancer cells for 24 and 48 h. In both tested time (24 and 48 h) for all three samples, the modified nanoparticles had long life time than unmodified nanoparticles. Cellular uptake of modified MNPs was 80% and reduced to 9% by the unmodified MNPs.

  12. Measuring vascular reactivity with breath-holds after stroke: a method to aid interpretation of group-level BOLD signal changes in longitudinal fMRI studies.

    PubMed

    Geranmayeh, Fatemeh; Wise, Richard J S; Leech, Robert; Murphy, Kevin

    2015-05-01

    Blood oxygenation level-dependent (BOLD) contrast functional magnetic resonance imaging (fMRI) is a widely used technique to map brain function, and to monitor its recovery after stroke. Since stroke has a vascular etiology, the neurovascular coupling between cerebral blood flow and neural activity may be altered, resulting in uncertainties when interpreting longitudinal BOLD signal changes. The purpose of this study was to demonstrate the feasibility of using a recently validated breath-hold task in patients with stroke, both to assess group level changes in cerebrovascular reactivity (CVR) and to determine if alterations in regional CVR over time will adversely affect interpretation of task-related BOLD signal changes. Three methods of analyzing the breath-hold data were evaluated. The CVR measures were compared over healthy tissue, infarcted tissue and the peri-infarct tissue, both sub-acutely (∼2 weeks) and chronically (∼4 months). In this cohort, a lack of CVR differences in healthy tissue between the patients and controls indicates that any group level BOLD signal change observed in these regions over time is unlikely to be related to vascular alterations. CVR was reduced in the peri-infarct tissue but remained unchanged over time. Therefore, although a lack of activation in this region compared with the controls may be confounded by a reduced CVR, longitudinal group-level BOLD changes may be more confidently attributed to neural activity changes in this cohort. By including this breath-hold-based CVR assessment protocol in future studies of stroke recovery, researchers can be more assured that longitudinal changes in BOLD signal reflect true alterations in neural activity.

  13. MRI brain imaging.

    PubMed

    Skinner, Sarah

    2013-11-01

    General practitioners (GPs) are expected to be allowed to request MRI scans for adults for selected clinically appropriate indications from November 2013 as part of the expansion of Medicare-funded MRI services announced by the Federal Government in 2011. This article aims to give a brief overview of MRI brain imaging relevant to GPs, which will facilitate explanation of scan findings and management planning with their patients. Basic imaging techniques, common findings and terminology are presented using some illustrative case examples.

  14. Influence of dental materials on dental MRI

    PubMed Central

    Tymofiyeva, O; Vaegler, S; Rottner, K; Boldt, J; Hopfgartner, AJ; Proff, PC; Richter, E-J; Jakob, PM

    2013-01-01

    Objectives: To investigate the potential influence of standard dental materials on dental MRI (dMRI) by estimating the magnetic susceptibility with the help of the MRI-based geometric distortion method and to classify the materials from the standpoint of dMRI. Methods: A series of standard dental materials was studied on a 1.5 T MRI system using spin echo and gradient echo pulse sequences and their magnetic susceptibility was estimated using the geometric method. Measurements on samples of dental materials were supported by in vivo examples obtained in dedicated dMRI procedures. Results: The tested materials showed a range of distortion degrees. The following materials were classified as fully compatible materials that can be present even in the tooth of interest: the resin-based sealer AH Plus® (Dentsply, Maillefer, Germany), glass ionomer cement, gutta-percha, zirconium dioxide and composites from one of the tested manufacturers. Interestingly, composites provided by the other manufacturer caused relatively strong distortions and were therefore classified as compatible I, along with amalgam, gold alloy, gold–ceramic crowns, titanium alloy and NiTi orthodontic wires. Materials, the magnetic susceptibility of which differed from that of water by more than 200 ppm, were classified as non-compatible materials that should not be present in the patient’s mouth for any dMRI applications. They included stainless steel orthodontic appliances and CoCr. Conclusions: A classification of the materials that complies with the standard grouping of materials according to their magnetic susceptibility was proposed and adopted for the purposes of dMRI. The proposed classification can serve as a guideline in future dMRI research. PMID:23610088

  15. MRI visualisation by digitally reconstructed radiographs

    NASA Astrophysics Data System (ADS)

    Serrurier, Antoine; Bönsch, Andrea; Lau, Robert; Deserno, Thomas M.

    2015-03-01

    Visualising volumetric medical images such as computed tomography and magnetic resonance imaging (MRI) on picture archiving and communication systems (PACS) clients is often achieved by image browsing in sagittal, coronal or axial views or three-dimensional (3D) rendering. This latter technique requires fine thresholding for MRI. On the other hand, computing virtual radiograph images, also referred to as digitally reconstructed radiographs (DRR), provides in a single two-dimensional (2D) image a complete overview of the 3D data. It appears therefore as a powerful alternative for MRI visualisation and preview in PACS. This study describes a method to compute DRR from T1-weighted MRI. After segmentation of the background, a histogram distribution analysis is performed and each foreground MRI voxel is labeled as one of three tissues: cortical bone, also known as principal absorber of the X-rays, muscle and fat. An intensity level is attributed to each voxel according to the Hounsfield scale, linearly related to the X-ray attenuation coefficient. Each DRR pixel is computed as the accumulation of the new intensities of the MRI dataset along the corresponding X-ray. The method has been tested on 16 T1-weighted MRI sets. Anterior-posterior and lateral DRR have been computed with reasonable qualities and avoiding any manual tissue segmentations. This proof-of-concept holds for research application for use in clinical PACS.

  16. Liver isolation in abdominal MRI.

    PubMed

    Rajasvaran, Logeswaran; Haw, Tan Wooi; Sarker, Shakowat Zaman

    2008-08-01

    This work presents a method for liver isolation in magnetic resonance imaging (MRI) abdomen images. It is based on a priori statistical information about the shape of the liver obtained from a training set using the segmentation approach. Morphological watershed algorithm is used as a key technique as it is a simple and intuitive method, producing a complete division of the image in separated regions even if the contrast is poor, and it is fast, with possibility for parallel implementation. To overcome the over-segmentation problem of the watershed process, image preprocessing and postprocessing are applied. Morphological smoothing, Gaussian smoothing, intensity thresholding, gradient computation and gradient thresholding are proposed for preprocessing with morphological and graph based region adjacent list constructed for region merging. A new integrated region similarity function is also defined for region merging control. The proposed method produces good isolation of liver in axial MRI images of the abdomen, as is shown in this paper.

  17. MRI-guided focused ultrasound treatments.

    PubMed

    Hynynen, Kullervo

    2010-02-01

    Focused ultrasound (FUS) allows noninvasive focal delivery of energy deep into soft tissues. The focused energy can be used to modify and eliminate tissue for therapeutic purposes while the energy delivery is targeted and monitored using magnetic resonance imaging (MRI). MRI compatible methods to deliver these exposures have undergone rapid development over the past 10 years such that clinical treatments are now routinely performed. This paper will review the current technical and clinical status of MRI-guided focused ultrasound therapy and discuss future research and development opportunities.

  18. Effects of high-impact training on bone and articular cartilage: 12-month randomized controlled quantitative MRI study.

    PubMed

    Multanen, Juhani; Nieminen, Miika T; Häkkinen, Arja; Kujala, Urho M; Jämsä, Timo; Kautiainen, Hannu; Lammentausta, Eveliina; Ahola, Riikka; Selänne, Harri; Ojala, Risto; Kiviranta, Ilkka; Heinonen, Ari

    2014-01-01

    Osteoarthritis and osteoporosis often coexist in postmenopausal women. The simultaneous effect of bone-favorable high-impact training on these diseases is not well understood and is a topic of controversy. We evaluated the effects of high-impact exercise on bone mineral content (BMC) and the estimated biochemical composition of knee cartilage in postmenopausal women with mild knee osteoarthritis. Eighty women aged 50 to 66 years with mild knee osteoarthritis were randomly assigned to undergo supervised progressive exercise three times a week for 12 months (n = 40) or to a nonintervention control group (n = 40). BMC of the femoral neck, trochanter, and lumbar spine was measured by dual-energy X-ray absorptiometry (DXA). The biochemical composition of cartilage was estimated using delayed gadolinium-enhanced magnetic resonance imaging (MRI) cartilage (dGEMRIC), sensitive to cartilage glycosaminoglycan content, and transverse relaxation time (T2) mapping that is sensitive to the properties of the collagen network. In addition, we evaluated clinically important symptoms and physical performance-related risk factors of falling: cardiorespiratory fitness, dynamic balance, maximal isometric knee extension and flexion forces, and leg power. Thirty-six trainees and 40 controls completed the study. The mean gain in femoral neck BMC in the exercise group was 0.6% (95% CI, -0.2% to 1.4%) and the mean loss in the control group was -1.2% (95% CI, -2.1% to -0.4%). The change in baseline, body mass, and adjusted body mass change in BMC between the groups was significant (p = 0.005), whereas no changes occurred in the biochemical composition of the cartilage, as investigated by MRI. Balance, muscle force, and cardiorespiratory fitness improved significantly more (3% to 11%) in the exercise group than in the control group. Progressively implemented high-impact training, which increased bone mass, did not affect the biochemical composition of cartilage and may be feasible

  19. Recommendations for Real-Time Speech MRI

    PubMed Central

    Lingala, Sajan Goud; Sutton, Brad P.; Miquel, Marc E.; Nayak, Krishna S.

    2016-01-01

    Real-time magnetic resonance imaging (RT-MRI) is being increasingly used for speech and vocal production research studies. Several imaging protocols have emerged based on advances in RT-MRI acquisition, reconstruction, and audio-processing methods. This review summarizes the state-of-the-art, discusses technical considerations, and provides specific guidance for new groups entering this field. We provide recommendations for performing RT-MRI of the upper airway. This is a consensus statement stemming from the ISMRM-endorsed Speech MRI summit held in Los Angeles, February 2014. A major unmet need identified at the summit was the need for consensus on protocols that can be easily adapted by researchers equipped with conventional MRI systems. To this end, we provide a discussion of tradeoffs in RT-MRI in terms of acquisition requirements, a priori assumptions, artifacts, computational load, and performance for different speech tasks. We provide four recommended protocols and identify appropriate acquisition and reconstruction tools. We list pointers to open-source software that facilitate implementation. We conclude by discussing current open challenges in the methodological aspects of RT-MRI of speech. PMID:26174802

  20. CEST MRI reporter genes.

    PubMed

    Liu, Guanshu; Bulte, Jeff W M; Gilad, Assaf A

    2011-01-01

    In recent years, several reporter genes have been developed that can serve as a beacon for non-invasive magnetic resonance imaging (MRI). Here, we provide a brief summary of recent advances in MRI reporter gene technology, as well as detailed "hands-on" protocols for cloning, expression, and imaging of reporter genes based on chemical exchange saturation transfer (CEST).

  1. Curved reformat of the paediatric brain MRI into a 'flat-earth map' - standardised method for demonstrating cortical surface atrophy resulting from hypoxic-ischaemic encephalopathy.

    PubMed

    Simpson, Ewan; Andronikou, Savvas; Vedajallam, Schadie; Chacko, Anith; Thai, Ngoc Jade

    2016-09-01

    Hypoxic-ischaemic encephalopathy is optimally imaged with brain MRI in the neonatal period. However neuroimaging is often also performed later in childhood (e.g., when parents seek compensation in cases of alleged birth asphyxia). We describe a standardised technique for creating two curved reconstructions of the cortical surface to show the characteristic surface changes of hypoxic-ischaemic encephalopathy in children imaged after the neonatal period. The technique was applied for 10 cases of hypoxic-ischaemic encephalopathy and also for age-matched healthy children to assess the visibility of characteristic features of hypoxic-ischaemic encephalopathy. In the abnormal brains, fissural or sulcal widening was seen in all cases and ulegyria was identifiable in 7/10. These images could be used as a visual aid for communicating MRI findings to clinicians and other interested parties. PMID:27337989

  2. Curved reformat of the paediatric brain MRI into a 'flat-earth map' - standardised method for demonstrating cortical surface atrophy resulting from hypoxic-ischaemic encephalopathy.

    PubMed

    Simpson, Ewan; Andronikou, Savvas; Vedajallam, Schadie; Chacko, Anith; Thai, Ngoc Jade

    2016-09-01

    Hypoxic-ischaemic encephalopathy is optimally imaged with brain MRI in the neonatal period. However neuroimaging is often also performed later in childhood (e.g., when parents seek compensation in cases of alleged birth asphyxia). We describe a standardised technique for creating two curved reconstructions of the cortical surface to show the characteristic surface changes of hypoxic-ischaemic encephalopathy in children imaged after the neonatal period. The technique was applied for 10 cases of hypoxic-ischaemic encephalopathy and also for age-matched healthy children to assess the visibility of characteristic features of hypoxic-ischaemic encephalopathy. In the abnormal brains, fissural or sulcal widening was seen in all cases and ulegyria was identifiable in 7/10. These images could be used as a visual aid for communicating MRI findings to clinicians and other interested parties.

  3. Correction of MRI-induced geometric distortions in whole-body small animal PET-MRI

    SciTech Connect

    Frohwein, Lynn J. Schäfers, Klaus P.; Hoerr, Verena; Faber, Cornelius

    2015-07-15

    Purpose: The fusion of positron emission tomography (PET) and magnetic resonance imaging (MRI) data can be a challenging task in whole-body PET-MRI. The quality of the registration between these two modalities in large field-of-views (FOV) is often degraded by geometric distortions of the MRI data. The distortions at the edges of large FOVs mainly originate from MRI gradient nonlinearities. This work describes a method to measure and correct for these kind of geometric distortions in small animal MRI scanners to improve the registration accuracy of PET and MRI data. Methods: The authors have developed a geometric phantom which allows the measurement of geometric distortions in all spatial axes via control points. These control points are detected semiautomatically in both PET and MRI data with a subpixel accuracy. The spatial transformation between PET and MRI data is determined with these control points via 3D thin-plate splines (3D TPS). The transformation derived from the 3D TPS is finally applied to real MRI mouse data, which were acquired with the same scan parameters used in the phantom data acquisitions. Additionally, the influence of the phantom material on the homogeneity of the magnetic field is determined via field mapping. Results: The spatial shift according to the magnetic field homogeneity caused by the phantom material was determined to a mean of 0.1 mm. The results of the correction show that distortion with a maximum error of 4 mm could be reduced to less than 1 mm with the proposed correction method. Furthermore, the control point-based registration of PET and MRI data showed improved congruence after correction. Conclusions: The developed phantom has been shown to have no considerable negative effect on the homogeneity of the magnetic field. The proposed method yields an appropriate correction of the measured MRI distortion and is able to improve the PET and MRI registration. Furthermore, the method is applicable to whole-body small animal

  4. Multi-parametric MRI-pathologic correlation of prostate cancer using tracked biopsies

    NASA Astrophysics Data System (ADS)

    Xu, Sheng; Turkbey, Baris; Kruecker, Jochen; Yan, Pingkun; Locklin, Julia; Pinto, Peter; Choyke, Peter; Wood, Bradford

    2010-02-01

    MRI is currently the most promising imaging modality for prostate cancer diagnosis due to its high resolution and multiparametric nature. However, currently there is no standard for integration of diagnostic information from different MRI sequences. We propose a method to increase the diagnostic accuracy of MRI by correlating biopsy specimens with four MRI sequences including T2 weighted MRI, Diffusion Weight Imaging, Dynamic Contrast Enhanced MRI and MRI spectroscopy. This method uses device tracking and image fusion to determine the specimen's position on MRI images. The proposed method is unbiased and cost effective. It does not substantially interfere with the standard biopsy workflow, allowing it to be easily accepted by physicians. A study of 41 patients was carried out to validate the approach. The performance of all four MRI sequences in various combinations is reported. Guidelines are given for multi-parametric imaging and tracked biopsy of prostate cancer.

  5. The PRESTO technique for fMRI.

    PubMed

    van Gelderen, P; Duyn, J H; Ramsey, N F; Liu, G; Moonen, C T W

    2012-08-15

    In the early days of BOLD fMRI, the acquisition of T(2)(*) weighted data was greatly facilitated by rapid scan techniques such as EPI. The latter, however, was only available on a few MRI systems that were equipped with specialized hardware that allowed rapid switching of the imaging gradients. For this reason, soon after the invention of fMRI, the scan technique PRESTO was developed to make rapid T(2)(*) weighted scanning available on standard clinical scanners. This method combined echo shifting, which allows for echo times longer than the sequence repetition time, with acquisition of multiple k-space lines per excitation. These two concepts were combined in order to achieve a method fast enough for fMRI, while maintaining a sufficiently long echo time for optimal contrast. PRESTO has been primarily used for 3D scanning, which minimized the contribution of large vessels due to inflow effects. Although PRESTO is still being used today, its appeal has lessened somewhat due to increased gradient performance of modern MRI scanners. Compared to 2D EPI, PRESTO may have somewhat reduced temporal stability, which is a disadvantage for fMRI that may not outweigh the advantage of reduced inflow effects provided by 3D scanning. In this overview, the history of the development of the PRESTO is presented, followed by a qualitative comparison with EPI. PMID:22245350

  6. Advanced flow MRI: emerging techniques and applications.

    PubMed

    Markl, M; Schnell, S; Wu, C; Bollache, E; Jarvis, K; Barker, A J; Robinson, J D; Rigsby, C K

    2016-08-01

    Magnetic resonance imaging (MRI) techniques provide non-invasive and non-ionising methods for the highly accurate anatomical depiction of the heart and vessels throughout the cardiac cycle. In addition, the intrinsic sensitivity of MRI to motion offers the unique ability to acquire spatially registered blood flow simultaneously with the morphological data, within a single measurement. In clinical routine, flow MRI is typically accomplished using methods that resolve two spatial dimensions in individual planes and encode the time-resolved velocity in one principal direction, typically oriented perpendicular to the two-dimensional (2D) section. This review describes recently developed advanced MRI flow techniques, which allow for more comprehensive evaluation of blood flow characteristics, such as real-time flow imaging, 2D multiple-venc phase contrast MRI, four-dimensional (4D) flow MRI, quantification of complex haemodynamic properties, and highly accelerated flow imaging. Emerging techniques and novel applications are explored. In addition, applications of these new techniques for the improved evaluation of cardiovascular (aorta, pulmonary arteries, congenital heart disease, atrial fibrillation, coronary arteries) as well as cerebrovascular disease (intra-cranial arteries and veins) are presented. PMID:26944696

  7. MRI morphometry in Alzheimer's disease.

    PubMed

    Matsuda, Hiroshi

    2016-09-01

    MRI based evaluation of brain atrophy is regarded as a valid method to stage the disease and to assess progression in Alzheimer's disease (AD). Volumetric software programs have made it possible to quantify gray matter in the human brain in an automated fashion. At present, voxel based morphometry (VBM) is easily applicable to the routine clinical procedure with a short execution time. The importance of the VBM approach is that it is not biased to one particular structure and is able to assess anatomical differences throughout the brain. Stand-alone VBM software running on Windows, Voxel-based Specific Regional analysis system for AD (VSRAD), has been widely used in the clinical diagnosis of AD in Japan. On the other hand, recent application of graph theory to MRI has made it possible to analyze changes in structural connectivity in AD.

  8. [MRI semiotics features of experimental acute intracerebral hematomas].

    PubMed

    Burenchev, D V; Skvortsova, V I; Tvorogova, T V; Guseva, O I; Gubskiĭ, L V; Kupriianov, D A; Pirogov, Iu A

    2009-01-01

    The aim of this study was to assess the possibility of revealing intracerebral hematomas (ICH), using MRI, within the first hours after onset and to determine their MRI semiotics features. Thirty animals with experimental ICH were studied. A method of two-stage introduction of autologous blood was used to develop ICH as human spontaneous intracranial hematomas. Within 3-5h after blood introduction to the rat brain. The control MRI was performed in the 3rd and 7th days after blood injections. ICH were definitely identified in the first MRI scans. The MRI semiotics features of acute ICH and their transformations were assessed. The high sensitivity of MRI to ICH as well as the uniform manifestations in all animals were shown. In conclusion, the method has high specificity for acute ICH detection.

  9. Leg MRI scan

    MedlinePlus

    ... resonance imaging) scan of the leg uses strong magnets to create pictures of the leg. This may ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  10. Shoulder MRI scan

    MedlinePlus

    ... an imaging test that uses energy from powerful magnets and to create pictures of the shoulder area. ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed in the room ...

  11. MRI (Magnetic Resonance Imaging)

    MedlinePlus

    ... some MRI exams, intravenous (IV) drugs, such as gadolinium-based contrast agents (GBCAs) are used to change the contrast of the MR image. Gadolinium-based contrast agents are rare earth metals that ...

  12. MRI of the Breast

    MedlinePlus

    ... as a supplemental tool to breast screening with mammography or ultrasound. It may be used to screen ... following diagnosis, or further evaluate abnormalities seen on mammography. Breast MRI does not use ionizing radiation, and ...

  13. Abdominal MRI scan

    MedlinePlus

    Nuclear magnetic resonance - abdomen; NMR - abdomen; Magnetic resonance imaging - abdomen; MRI of the abdomen ... used to look at: Blood flow in the abdomen Blood vessels in the abdomen The cause of ...

  14. MRI of the Chest

    MedlinePlus

    ... magnetic field of the MRI unit, metal and electronic items are not allowed in the exam room. ... tell the technologist if you have medical or electronic devices in your body. These objects may interfere ...

  15. Lumbar MRI scan

    MedlinePlus

    ... may need a lumbar MRI if you have: Low back pain that does not get better after treatment Leg ... spine Injury or trauma to the lower spine Low back pain and a history or signs of cancer Multiple ...

  16. Knee MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... health care provider before the test. The strong magnetic fields created during an MRI can cause heart pacemakers ...

  17. Cervical MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... tell your provider before the test. The strong magnetic fields created during an MRI can cause heart pacemakers ...

  18. Arm MRI scan

    MedlinePlus

    ... have been no reported side effects from the magnetic fields and radio waves. The most common type of ... tell your provider before the test The strong magnetic fields created during an MRI can cause heart pacemakers ...

  19. Tissue-Point Motion Tracking in the Tongue from Cine-MRI and Tagged-MRI

    PubMed Central

    Woo, Jonghye; Stone, Maureen; Suo, Yuanming; Murano, Emi Z.; Prince, Jerry L.

    2015-01-01

    Purpose Accurate tissue motion tracking within the tongue can help to diagnose and treat vocal tract related disorders, evaluate speech quality before and after surgery, and conduct various scientific studies. We have compared tissue tracking results from four widely used deformable registration (DR) methods applied to Cine-MRI with harmonic phase (HARP)-based tracking applied to tagged-MRI. Method Ten subjects repeated the words “a geese” multiple times while sagittal images of the head were collected at 26 Hz, first in a tagged-MRI data set, and then in a Cine-MRI data set. HARP tracked the motion of eight specified tissue points in the tagged data set. Four DR methods including diffeomorphic demons and free-form deformations based on cubic B-spline with three different similarity measures were used to track the same eight points in the Cine-MRI data set. Individual points were tracked and length changes of several muscles were calculated using the DR and HARP based tracking methods. Results Results showed that the DR tracking errors were non-systematic and varied in direction, amount, and timing across speakers and within speakers. Comparison of HARP and DR tracking with manual tracking showed better tracking results for HARP except at the tongue surface, where mistracking caused greater errors in HARP than DR. Conclusions Tissue point tracking using DR tracking methods contain non-systematic tracking errors within and across subjects, making it less successful than tagged-MRI tracking within the tongue. However, HARP sometimes mistracks points at the tongue surface of tagged MRI due to its limited bandpass filter and tag pattern fading, so that DR has better success measuring surface tissue points on Cine-MRI than HARP does. Therefore a hybrid method is being explored. PMID:24686470

  20. Diffusion MRI and its role in neuropsychology

    PubMed Central

    Mueller, Bryon A; Lim, Kelvin O; Hemmy, Laura; Camchong, Jazmin

    2015-01-01

    Diffusion Magnetic Resonance Imaging (dMRI) is a popular method used by neuroscientists to uncover unique information about the structural connections within the brain. dMRI is a non-invasive imaging methodology in which image contrast is based on the diffusion of water molecules in tissue. While applicable to many tissues in the body, this review focuses exclusively on the use of dMRI to examine white matter in the brain. In this review, we begin with a definition of diffusion and how diffusion is measured with MRI. Next we introduce the diffusion tensor model, the predominant model used in dMRI. We then describe acquisition issues related to acquisition parameters and scanner hardware and software. Sources of artifacts are then discussed, followed by a brief review of analysis approaches. We provide an overview of the limitations of the traditional diffusion tensor model, and highlight several more sophisticated non-tensor models that better describe the complex architecture of the brain’s white matter. We then touch on reliability and validity issues of diffusion measurements. Finally, we describe examples of ways in which dMRI has been applied to studies of brain disorders and how identified alterations relate to symptomatology and cognition. PMID:26255305

  1. Diffusion MRI and its Role in Neuropsychology.

    PubMed

    Mueller, Bryon A; Lim, Kelvin O; Hemmy, Laura; Camchong, Jazmin

    2015-09-01

    Diffusion Magnetic Resonance Imaging (dMRI) is a popular method used by neuroscientists to uncover unique information about the structural connections within the brain. dMRI is a non-invasive imaging methodology in which image contrast is based on the diffusion of water molecules in tissue. While applicable to many tissues in the body, this review focuses exclusively on the use of dMRI to examine white matter in the brain. In this review, we begin with a definition of diffusion and how diffusion is measured with MRI. Next we introduce the diffusion tensor model, the predominant model used in dMRI. We then describe acquisition issues related to acquisition parameters and scanner hardware and software. Sources of artifacts are then discussed, followed by a brief review of analysis approaches. We provide an overview of the limitations of the traditional diffusion tensor model, and highlight several more sophisticated non-tensor models that better describe the complex architecture of the brain's white matter. We then touch on reliability and validity issues of diffusion measurements. Finally, we describe examples of ways in which dMRI has been applied to studies of brain disorders and how identified alterations relate to symptomatology and cognition.

  2. Pediatric multifocal liver lesions evaluated by MRI

    PubMed Central

    Almotairi, Majed; Oudjhane, Kamaldine; Chavhan, Govind B

    2015-01-01

    Objective: The purpose of this study is to present our experience with MRI evaluation of multifocal liver lesions in children and describe the MRI characteristics of these lesions. Patients and Methods: A retrospective review of consecutive MRI exams performed for the evaluation of multiple liver lesions between 1 January 2007 and 31 December 2012 was done to note the number of lesions, the size of the largest lesion, MR signal characteristics, and background liver. Final diagnosis was assigned to each case based on pathology in the available cases and a combination of clinical features, imaging features, and follow-up in the remaining cases. Results: A total of 48 children (22 boys, 26 girls; age between 3 months and 18 years with average age 10.58 years and median age 11 years) were included in the study. Totally 51 lesion diagnoses were seen in 48 children that included 17 focal nodular hyperplasia (FNH), 8 hemangiomas, 7 metastases, 6 regenerative nodules, 3 adenomas, 3 abscesses, and one each of angiomyolipoma, epithelioid hemangioendothelioma, focal fatty infiltration, hepatocellular carcinoma, hepatic infarction, nodular regenerative hyperplasia, and hepatic cyst. Background liver was normal in 33, cirrhotic in 10, fatty in 3, and siderotic in 2 children. Most FNH, hemangiomas, and regenerative nodules showed characteristic MRI features, while metastases were variable in signal pattern. Conclusion: Many commonly seen multifocal liver lesions in children have characteristic MRI features. MRI can help to arrive at reasonable differential diagnoses for multifocal liver lesions in children and guide further investigation and management. PMID:26288526

  3. Quantitative MRI Assessment of Leukoencephalopathy

    PubMed Central

    Reddick, Wilburn E.; Glass, John O.; Langston, James W.; Helton, Kathleen J.

    2008-01-01

    Quantitative MRI assessment of leukoencephalopathy is difficult because the MRI properties of leukoencephalopathy significantly overlap those of normal tissue. This report describes the use of an automated procedure for longitudinal measurement of tissue volume and relaxation times to quantify leukoencephalopathy. Images derived by using this procedure in patients undergoing therapy for acute lymphoblastic leukemia (ALL) are presented. Five examinations from each of five volunteers (25 examinations) were used to test the reproducibility of quantitated baseline and subsequent, normal-appearing images; the coefficients of variation were less than 2% for gray and white matter. Regions of leukoencephalopathy in patients were assessed by comparison with manual segmentation. Two radiologists manually segmented images from 15 randomly chosen MRI examinations that exhibited leukoencephalopathy. Kappa analyses showed that the two radiologists’ interpretations were concordant (κ = 0.70) and that each radiologist’s interpretations agreed with the results of the automated procedure (κ = 0.57 and 0.55).The clinical application of this method was illustrated by analysis of images from sequential MR examinations of two patients who developed leukoencephalopathy during treatment for ALL. The ultimate goal is to use these quantitative MR imaging measures to better understand therapy-induced neurotoxicity, which can be limited or even reversed with some combination of therapy adjustments and pharmacological and neurobehavioral interventions. PMID:11979570

  4. Parallel MRI at microtesla fields.

    PubMed

    Zotev, Vadim S; Volegov, Petr L; Matlashov, Andrei N; Espy, Michelle A; Mosher, John C; Kraus, Robert H

    2008-06-01

    Parallel imaging techniques have been widely used in high-field magnetic resonance imaging (MRI). Multiple receiver coils have been shown to improve image quality and allow accelerated image acquisition. Magnetic resonance imaging at ultra-low fields (ULF MRI) is a new imaging approach that uses SQUID (superconducting quantum interference device) sensors to measure the spatially encoded precession of pre-polarized nuclear spin populations at microtesla-range measurement fields. In this work, parallel imaging at microtesla fields is systematically studied for the first time. A seven-channel SQUID system, designed for both ULF MRI and magnetoencephalography (MEG), is used to acquire 3D images of a human hand, as well as 2D images of a large water phantom. The imaging is performed at 46 mu T measurement field with pre-polarization at 40 mT. It is shown how the use of seven channels increases imaging field of view and improves signal-to-noise ratio for the hand images. A simple procedure for approximate correction of concomitant gradient artifacts is described. Noise propagation is analyzed experimentally, and the main source of correlated noise is identified. Accelerated imaging based on one-dimensional undersampling and 1D SENSE (sensitivity encoding) image reconstruction is studied in the case of the 2D phantom. Actual threefold imaging acceleration in comparison to single-average fully encoded Fourier imaging is demonstrated. These results show that parallel imaging methods are efficient in ULF MRI, and that imaging performance of SQUID-based instruments improves substantially as the number of channels is increased.

  5. Parallel MRI at microtesla fields

    NASA Astrophysics Data System (ADS)

    Zotev, Vadim S.; Volegov, Petr L.; Matlashov, Andrei N.; Espy, Michelle A.; Mosher, John C.; Kraus, Robert H.

    2008-06-01

    Parallel imaging techniques have been widely used in high-field magnetic resonance imaging (MRI). Multiple receiver coils have been shown to improve image quality and allow accelerated image acquisition. Magnetic resonance imaging at ultra-low fields (ULF MRI) is a new imaging approach that uses SQUID (superconducting quantum interference device) sensors to measure the spatially encoded precession of pre-polarized nuclear spin populations at microtesla-range measurement fields. In this work, parallel imaging at microtesla fields is systematically studied for the first time. A seven-channel SQUID system, designed for both ULF MRI and magnetoencephalography (MEG), is used to acquire 3D images of a human hand, as well as 2D images of a large water phantom. The imaging is performed at 46 μT measurement field with pre-polarization at 40 mT. It is shown how the use of seven channels increases imaging field of view and improves signal-to-noise ratio for the hand images. A simple procedure for approximate correction of concomitant gradient artifacts is described. Noise propagation is analyzed experimentally, and the main source of correlated noise is identified. Accelerated imaging based on one-dimensional undersampling and 1D SENSE (sensitivity encoding) image reconstruction is studied in the case of the 2D phantom. Actual threefold imaging acceleration in comparison to single-average fully encoded Fourier imaging is demonstrated. These results show that parallel imaging methods are efficient in ULF MRI, and that imaging performance of SQUID-based instruments improves substantially as the number of channels is increased.

  6. Hybrid-SPRITE MRI.

    PubMed

    Xiao, Dan; Balcom, Bruce J

    2013-10-01

    In a FID based frequency encoding MRI experiment the central part of k-space is not generally accessible due to the probe dead time. This portion of k-space is however crucial for image reconstruction. SPRITE (Single Point Ramped Imaging with T1 Enhancement), SPI with a linearly ramped phase encode gradient, has been employed to image short relaxation time systems for many years with great success. It is a robust imaging method in significant measure because it provides acquisition of high quality k-space origin data. We propose a new sampling scheme, termed hybrid-SPRITE, combining phase and frequency encoding to ensure high quality images with reduced acquisition times, reduced gradient duty cycle and increased sensitivity. In hybrid-SPRITE, numerous time domain points are collected to assist image reconstruction. An Inverse Non-uniform Discrete Fourier Transform (INDFT) is employed in 1D applications. A pseudo-polar grid is exploited in 2D hybrid-SPRITE for rapid and accurate image reconstruction. PMID:23916990

  7. MRI of uncommon lesions of the large bowel: a pictorial essay.

    PubMed

    Lee, Christine U; Glockner, James F

    2014-01-01

    This pictorial essay briefly discusses methods for optimizing bowel imaging with magnetic resonance imaging (MRI) and illustrates the MRI appearance of a variety of unusual lesions involving or related specifically to the large bowel.

  8. MRI of Uncommon Lesions of the Large Bowel: A Pictorial Essay

    PubMed Central

    Lee, Christine U; Glockner, James F

    2014-01-01

    This pictorial essay briefly discusses methods for optimizing bowel imaging with magnetic resonance imaging (MRI) and illustrates the MRI appearance of a variety of unusual lesions involving or related specifically to the large bowel. PMID:25806129

  9. Directly detected 55Mn MRI: Application to phantoms for human hyperpolarized 13C MRI development

    PubMed Central

    von Morze, Cornelius; Carvajal, Lucas; Reed, Galen D.; Swisher, Christine Leon; Tropp, James; Vigneron, Daniel B.

    2014-01-01

    In this work we demonstrate for the first time directly detected manganese-55 (55Mn) MRI using a clinical 3T MRI scanner designed for human hyperpolarized 13C clinical studies with no additional hardware modifications. Due to the similar frequency of the 55Mn and 13C resonances, the use of aqueous permanganate for large, signal-dense, and cost-effective “13C” MRI phantoms was investigated, addressing the clear need for new phantoms for these studies. Due to 100% natural abundance, higher intrinsic sensitivity, and favorable relaxation properties, 55Mn MRI of aqueous permanganate demonstrates dramatically increased sensitivity over typical 13C phantom MRI, at greatly reduced cost as compared with large 13C-enriched phantoms. A large sensitivity advantage (22-fold) was demonstrated. A cylindrical phantom (d= 8 cm) containing concentrated aqueous sodium permanganate (2.7M) was scanned rapidly by 55Mn MRI in a human head coil tuned for 13C, using a balanced SSFP acquisition. The requisite penetration of RF magnetic fields into concentrated permanganate was investigated by experiments and high frequency electromagnetic simulations, and found to be sufficient for 55Mn MRI with reasonably sized phantoms. A sub-second slice-selective acquisition yielded mean image SNR of ~60 at 0.5cm3 spatial resolution, distributed with minimum central signal ~40% of the maximum edge signal. We anticipate that permanganate phantoms will be very useful for testing HP 13C coils and methods designed for human studies. PMID:25179135

  10. The effects of pre-salting methods on salt and water distribution of heavily salted cod, as analyzed by (1)H and (23)Na MRI, (23)Na NMR, low-field NMR and physicochemical analysis.

    PubMed

    Gudjónsdóttir, María; Traoré, Amidou; Jónsson, Ásbjörn; Karlsdóttir, Magnea Gudrún; Arason, Sigurjón

    2015-12-01

    The effect of different pre-salting methods (brine injection with salt with/without polyphosphates, brining and pickling) on the water and salt distribution in dry salted Atlantic cod (Gadus morhua) fillets was studied with proton and sodium NMR and MRI methods, supported by physicochemical analysis of salt and water content as well as water holding capacity. The study indicated that double head brine injection with salt and phosphates lead to the least heterogeneous water distribution, while pickle salting had the least heterogeneous salt distribution. Fillets from all treatments contained spots with unsaturated brine, increasing the risk of microbial denaturation of the fillets during storage. Since a homogeneous water and salt distribution was not achieved with the studied pre-salting methods, further optimizations of the salting process, including the pre-salting and dry salting steps, must be made in the future. PMID:26041245

  11. "MRI Stealth" robot for prostate interventions.

    PubMed

    Stoianovici, Dan; Song, Danny; Petrisor, Doru; Ursu, Daniel; Mazilu, Dumitru; Muntener, Michael; Mutener, Michael; Schar, Michael; Patriciu, Alexandru

    2007-01-01

    The paper reports an important achievement in MRI instrumentation, a pneumatic, fully actuated robot located within the scanner alongside the patient and operating under remote control based on the images. Previous MRI robots commonly used piezoelectric actuation limiting their compatibility. Pneumatics is an ideal choice for MRI compatibility because it is decoupled from electromagnetism, but pneumatic actuators were hardly controllable. This achievement was possible due to a recent technology breakthrough, the invention of a new type of pneumatic motor, PneuStep 1, designed for the robot reported here with uncompromised MRI compatibility, high-precision, and medical safety. MrBot is one of the "MRI stealth" robots today (the second is described in this issue by Zangos et al.). Both of these systems are also multi-imager compatible, being able to operate with the imager of choice or cross-imaging modalities. For MRI compatibility the robot is exclusively constructed of nonmagnetic and dielectric materials such as plastics, ceramics, crystals, rubbers and is electricity free. Light-based encoding is used for feedback, so that all electric components are distally located outside the imager's room. MRI robots are modern, digital medical instruments in line with advanced imaging equipment and methods. These allow for accessing patients within closed bore scanners and performing interventions under direct (in scanner) imaging feedback. MRI robots could allow e.g. to biopsy small lesions imaged with cutting edge cancer imaging methods, or precisely deploy localized therapy at cancer foci. Our robot is the first to show the feasibility of fully automated in-scanner interventions. It is customized for the prostate and operates transperineally for needle interventions. It can accommodate various needle drivers for different percutaneous procedures such as biopsy, thermal ablations, or brachytherapy. The first needle driver is customized for fully automated low

  12. "MRI Stealth" robot for prostate interventions.

    PubMed

    Stoianovici, Dan; Song, Danny; Petrisor, Doru; Ursu, Daniel; Mazilu, Dumitru; Muntener, Michael; Mutener, Michael; Schar, Michael; Patriciu, Alexandru

    2007-01-01

    The paper reports an important achievement in MRI instrumentation, a pneumatic, fully actuated robot located within the scanner alongside the patient and operating under remote control based on the images. Previous MRI robots commonly used piezoelectric actuation limiting their compatibility. Pneumatics is an ideal choice for MRI compatibility because it is decoupled from electromagnetism, but pneumatic actuators were hardly controllable. This achievement was possible due to a recent technology breakthrough, the invention of a new type of pneumatic motor, PneuStep 1, designed for the robot reported here with uncompromised MRI compatibility, high-precision, and medical safety. MrBot is one of the "MRI stealth" robots today (the second is described in this issue by Zangos et al.). Both of these systems are also multi-imager compatible, being able to operate with the imager of choice or cross-imaging modalities. For MRI compatibility the robot is exclusively constructed of nonmagnetic and dielectric materials such as plastics, ceramics, crystals, rubbers and is electricity free. Light-based encoding is used for feedback, so that all electric components are distally located outside the imager's room. MRI robots are modern, digital medical instruments in line with advanced imaging equipment and methods. These allow for accessing patients within closed bore scanners and performing interventions under direct (in scanner) imaging feedback. MRI robots could allow e.g. to biopsy small lesions imaged with cutting edge cancer imaging methods, or precisely deploy localized therapy at cancer foci. Our robot is the first to show the feasibility of fully automated in-scanner interventions. It is customized for the prostate and operates transperineally for needle interventions. It can accommodate various needle drivers for different percutaneous procedures such as biopsy, thermal ablations, or brachytherapy. The first needle driver is customized for fully automated low

  13. Sodium MRI in human heart: a review.

    PubMed

    Bottomley, Paul A

    2016-02-01

    This paper offers a critical review of the properties, methods and potential clinical application of sodium ((23)Na) MRI in human heart. Because the tissue sodium concentration (TSC) in heart is about ~40 µmol/g wet weight, and the (23)Na gyromagnetic ratio and sensitivity are respectively about one-quarter and one-11th of that of hydrogen ((1)H), the signal-to-noise ratio of (23)Na MRI in the heart is about one-6000th of that of conventional cardiac (1)H MRI. In addition, as a quadrupolar nucleus, (23)Na exhibits ultra-short and multi-component relaxation behavior (T1 ~ 30 ms; T2 ~ 0.5-4 ms and 12-20 ms), which requires fast, specialized, ultra-short echo-time MRI sequences, especially for quantifying TSC. Cardiac (23)Na MRI studies from 1.5 to 7 T measure a volume-weighted sum of intra- and extra-cellular components present at cytosolic concentrations of 10-15 mM and 135-150 mM in healthy tissue, respectively, at a spatial resolution of about 0.1-1 ml in 10 min or so. Currently, intra- and extra-cellular sodium cannot be unambiguously resolved without the use of potentially toxic shift reagents. Nevertheless, increases in TSC attributable to an influx of intra-cellular sodium and/or increased extra-cellular volume have been demonstrated in human myocardial infarction consistent with prior animal studies, and arguably might also be seen in future studies of ischemia and cardiomyopathies--especially those involving defects in sodium transport. While technical implementation remains a hurdle, a central question for clinical use is whether cardiac (23)Na MRI can deliver useful information unobtainable by other more convenient methods, including (1)H MRI.

  14. APPLICATION OF LASERS AND LASER-OPTICAL METHODS IN LIFE SCIENCES Non-invasive, MRI-compatible fibreoptic device for functional near-IR reflectometry of human brain

    NASA Astrophysics Data System (ADS)

    Sorvoja H. S., S.; Myllylä, T. S.; Kirillin, M. Yu; Sergeeva, Ekaterina A.; Myllylä, Risto A.; Elseoud, A. A.; Nikkinen, J.; Tervonen, O.; Kiviniemi, V.

    2011-01-01

    A non-invasive device for measuring blood oxygen variations in human brain is designed, implemented, and tested for MRI compatibility. The device is based on principles of near-IR reflectometry; power LEDs serve as sources of probing radiation delivered to patient skin surface through optical fibres. Numerical Monte Carlo simulations of probing radiation propagation in a multilayer brain model are performed to evaluate signal levels at different source — detector separations at three operation wavelengths and an additional wavelength of 915 nm. It is shown that the device can be applied for brain activity studies using power LEDs operating at 830 and 915 nm, while employment of wavelength of 660 nm requires an increased probing power. Employment of the wavelength of 592 nm in the current configuration is unreasonable.

  15. Pharmacological MRI (phMRI) of the Human Central Nervous System.

    PubMed

    Lanfermann, H; Schindler, C; Jordan, J; Krug, N; Raab, P

    2015-10-01

    Pharmacological magnetic resonance imaging (phMRI) of the central nervous system (CNS) addresses the increasing demands in the biopharma industry for new methods that can accurately predict, as early as possible, whether novel CNS agents will be effective and safe. Imaging of physiological and molecular-level function can provide a more direct measure of a drug mechanism of action, enabling more predictive measures of drug activity. The availability of phMRI of the nervous system within the professional infrastructure of the Clinical Research Center (CRC) Hannover as proof of concept center ensures that advances in basic science progress swiftly into benefits for patients. Advanced standardized MRI techniques including quantitative MRI, kurtosis determination, functional MRI, and spectroscopic imaging of the entire brain are necessary for phMRI. As a result, MR scanners will evolve into high-precision measuring instruments for assessment of desirable and undesirable effects of drugs as the basic precondition for individually tailored therapy. The CRC's Imaging Unit with high-end large-scale equipment will allow the following unique opportunities: for example, identification of MR-based biomarkers to assess the effect of drugs (surrogate parameters), establishment of normal levels and reference ranges for MRI-based biomarkers, evaluation of the most relevant MRI sequences for drug monitoring in outpatient care. Another very important prerequisite for phMRI is the MHH Core Facility as the scientific and operational study unit of the CRC partner Hannover Medical School. This unit is responsible for the study coordination, conduction, complete study logistics, administration, and application of the quality assurance system based on required industry standards.

  16. Motion correction in MRI of the brain

    NASA Astrophysics Data System (ADS)

    Godenschweger, F.; Kägebein, U.; Stucht, D.; Yarach, U.; Sciarra, A.; Yakupov, R.; Lüsebrink, F.; Schulze, P.; Speck, O.

    2016-03-01

    Subject motion in MRI is a relevant problem in the daily clinical routine as well as in scientific studies. Since the beginning of clinical use of MRI, many research groups have developed methods to suppress or correct motion artefacts. This review focuses on rigid body motion correction of head and brain MRI and its application in diagnosis and research. It explains the sources and types of motion and related artefacts, classifies and describes existing techniques for motion detection, compensation and correction and lists established and experimental approaches. Retrospective motion correction modifies the MR image data during the reconstruction, while prospective motion correction performs an adaptive update of the data acquisition. Differences, benefits and drawbacks of different motion correction methods are discussed.

  17. Motion correction in MRI of the brain.

    PubMed

    Godenschweger, F; Kägebein, U; Stucht, D; Yarach, U; Sciarra, A; Yakupov, R; Lüsebrink, F; Schulze, P; Speck, O

    2016-03-01

    Subject motion in MRI is a relevant problem in the daily clinical routine as well as in scientific studies. Since the beginning of clinical use of MRI, many research groups have developed methods to suppress or correct motion artefacts. This review focuses on rigid body motion correction of head and brain MRI and its application in diagnosis and research. It explains the sources and types of motion and related artefacts, classifies and describes existing techniques for motion detection, compensation and correction and lists established and experimental approaches. Retrospective motion correction modifies the MR image data during the reconstruction, while prospective motion correction performs an adaptive update of the data acquisition. Differences, benefits and drawbacks of different motion correction methods are discussed.

  18. Dental MRI using wireless intraoral coils.

    PubMed

    Ludwig, Ute; Eisenbeiss, Anne-Katrin; Scheifele, Christian; Nelson, Katja; Bock, Michael; Hennig, Jürgen; von Elverfeldt, Dominik; Herdt, Olga; Flügge, Tabea; Hövener, Jan-Bernd

    2016-03-29

    Currently, the gold standard for dental imaging is projection radiography or cone-beam computed tomography (CBCT). These methods are fast and cost-efficient, but exhibit poor soft tissue contrast and expose the patient to ionizing radiation (X-rays). The need for an alternative imaging modality e.g. for soft tissue management has stimulated a rising interest in dental magnetic resonance imaging (MRI) which provides superior soft tissue contrast. Compared to X-ray imaging, however, so far the spatial resolution of MRI is lower and the scan time is longer. In this contribution, we describe wireless, inductively-coupled intraoral coils whose local sensitivity enables high resolution MRI of dental soft tissue. In comparison to CBCT, a similar image quality with complementary contrast was obtained ex vivo. In-vivo, a voxel size of the order of 250 ∙ 250 ∙ 500 μm(3) was achieved in 4 min only. Compared to dental MRI acquired with clinical equipment, the quality of the images was superior in the sensitive volume of the coils and is expected to improve the planning of interventions and monitoring thereafter. This method may enable a more accurate dental diagnosis and avoid unnecessary interventions, improving patient welfare and bringing MRI a step closer to becoming a radiation-free alternative for dental imaging.

  19. Dental MRI using wireless intraoral coils

    NASA Astrophysics Data System (ADS)

    Ludwig, Ute; Eisenbeiss, Anne-Katrin; Scheifele, Christian; Nelson, Katja; Bock, Michael; Hennig, Jürgen; von Elverfeldt, Dominik; Herdt, Olga; Flügge, Tabea; Hövener, Jan-Bernd

    2016-03-01

    Currently, the gold standard for dental imaging is projection radiography or cone-beam computed tomography (CBCT). These methods are fast and cost-efficient, but exhibit poor soft tissue contrast and expose the patient to ionizing radiation (X-rays). The need for an alternative imaging modality e.g. for soft tissue management has stimulated a rising interest in dental magnetic resonance imaging (MRI) which provides superior soft tissue contrast. Compared to X-ray imaging, however, so far the spatial resolution of MRI is lower and the scan time is longer. In this contribution, we describe wireless, inductively-coupled intraoral coils whose local sensitivity enables high resolution MRI of dental soft tissue. In comparison to CBCT, a similar image quality with complementary contrast was obtained ex vivo. In-vivo, a voxel size of the order of 250•250•500 μm3 was achieved in 4 min only. Compared to dental MRI acquired with clinical equipment, the quality of the images was superior in the sensitive volume of the coils and is expected to improve the planning of interventions and monitoring thereafter. This method may enable a more accurate dental diagnosis and avoid unnecessary interventions, improving patient welfare and bringing MRI a step closer to becoming a radiation-free alternative for dental imaging.

  20. Dental MRI using wireless intraoral coils

    PubMed Central

    Ludwig, Ute; Eisenbeiss, Anne-Katrin; Scheifele, Christian; Nelson, Katja; Bock, Michael; Hennig, Jürgen; von Elverfeldt, Dominik; Herdt, Olga; Flügge, Tabea; Hövener, Jan-Bernd

    2016-01-01

    Currently, the gold standard for dental imaging is projection radiography or cone-beam computed tomography (CBCT). These methods are fast and cost-efficient, but exhibit poor soft tissue contrast and expose the patient to ionizing radiation (X-rays). The need for an alternative imaging modality e.g. for soft tissue management has stimulated a rising interest in dental magnetic resonance imaging (MRI) which provides superior soft tissue contrast. Compared to X-ray imaging, however, so far the spatial resolution of MRI is lower and the scan time is longer. In this contribution, we describe wireless, inductively-coupled intraoral coils whose local sensitivity enables high resolution MRI of dental soft tissue. In comparison to CBCT, a similar image quality with complementary contrast was obtained ex vivo. In-vivo, a voxel size of the order of 250∙250∙500 μm3 was achieved in 4 min only. Compared to dental MRI acquired with clinical equipment, the quality of the images was superior in the sensitive volume of the coils and is expected to improve the planning of interventions and monitoring thereafter. This method may enable a more accurate dental diagnosis and avoid unnecessary interventions, improving patient welfare and bringing MRI a step closer to becoming a radiation-free alternative for dental imaging. PMID:27021387

  1. Functional Imaging: CT and MRI

    PubMed Central

    van Beek, Edwin JR; Hoffman, Eric A

    2008-01-01

    Synopsis Numerous imaging techniques permit evaluation of regional pulmonary function. Contrast-enhanced CT methods now allow assessment of vasculature and lung perfusion. Techniques using spirometric controlled MDCT allow for quantification of presence and distribution of parenchymal and airway pathology, Xenon gas can be employed to assess regional ventilation of the lungs and rapid bolus injections of iodinated contrast agent can provide quantitative measure of regional parenchymal perfusion. Advances in magnetic resonance imaging (MRI) of the lung include gadolinium-enhanced perfusion imaging and hyperpolarized helium imaging, which can allow imaging of pulmonary ventilation and .measurement of the size of emphysematous spaces. PMID:18267192

  2. [New opportunities, MRI biomarkers in the evaluation of gynaecological cancer].

    PubMed

    Horváth, Katalin; Gõdény, Mária

    2015-09-01

    The determination and classification of gynaecological tumour stage which is based on clinical and pathological examinations became more precise due to the development of imaging techniques. Recently new MRI methods are being introduced which serve functional, tissue-specific, molecular information; beyond the excellent anatomical and contrast resolution with the aid of high resolution morphological measurements as well as quantification can also be performed. Diffusion-weighted MRI (DW-MRI) is based on the mobility of water molecules and provides information about the cell density of a given tissue and the integrity of cell membranes. Quantification can also be performed using an apparent diffusion coefficient (ADC). DW-MRI is a useful tool in determining myometrium invasion in endometrium carcinomas especially if a tumour has the same signal intensity as the makromomyometrium on the T2-weighted images and the use of contrast agents are contraindicated. The extra-uterine tumour invasion, the peritoneal metastatic foci can be determined by DW-MRI as well. Lymph node status is the most important predictive factor regarding survival. Both CT and MRI have low sensitivity (70-80%) in revealing metastatic lymph nodes. DW-MRI is a promising method with a sensitivity of 87% and specificity of 80% in distinguishing benign and malignant lymph nodes. Dynamic contrastenhanced MRI (DCE-MRI), as a marker of angiogenesis, provides information about vascularisation at the tissue level. In endometrial carcinoma with application of T2-weighted sequence together with DCE-MRI in determining the stage MRI has the accuracy about 90%. DCE-MRI has proven to be useful for distinguishing benign from malignant ovarian tumours, for detecting tumour extension; it can help predict peritoneal carcinomatosis. It is proven by high-level evidence that multiparametric MRI (MP-MRI) is the most precise diagnostic tool in determining the status of cervical carcinoma, its accuracy being above 90%. In

  3. MRI of the brain (image)

    MedlinePlus

    An MRI (magnetic resonance imaging) of the brain creates a detailed image of the complex structures in the brain. An MRI can give a three-dimensional depiction of the brain, making location of problems such ...

  4. Compressed sensing MRI: a review of the clinical literature.

    PubMed

    Jaspan, Oren N; Fleysher, Roman; Lipton, Michael L

    2015-01-01

    MRI is one of the most dynamic and safe imaging techniques available in the clinic today. However, MRI acquisitions tend to be slow, limiting patient throughput and limiting potential indications for use while driving up costs. Compressed sensing (CS) is a method for accelerating MRI acquisition by acquiring less data through undersampling of k-space. This has the potential to mitigate the time-intensiveness of MRI. The limited body of research evaluating the effects of CS on MR images has been mostly positive with regards to its potential as a clinical tool. Studies have successfully accelerated MRI with this technology, with varying degrees of success. However, more must be performed before its diagnostic efficacy and benefits are clear. Studies involving a greater number radiologists and images must be completed, rating CS based on its diagnostic efficacy. Also, standardized methods for determining optimal imaging parameters must be developed. PMID:26402216

  5. MRI in decompression illness.

    PubMed

    Hierholzer, J; Tempka, A; Stroszczynski, C; Amodio, F; Hosten, N; Haas, J; Felix, R

    2000-05-01

    We report a case of decompression illness in which the patient developed paraparesis during scuba diving after rapid ascent. MRI of the spine revealed a focal intramedullary lesion consistent with the symptoms. The pathophysiological and radiological aspects of spinal decompression illness are discussed.

  6. Comprehensive MRI simulation methodology using a dedicated MRI scanner in radiation oncology for external beam radiation treatment planning

    SciTech Connect

    Paulson, Eric S.; Erickson, Beth; Schultz, Chris; Allen Li, X.

    2015-01-15

    Purpose: The use of magnetic resonance imaging (MRI) in radiation oncology is expanding rapidly, and more clinics are integrating MRI into their radiation therapy workflows. However, radiation therapy presents a new set of challenges and places additional constraints on MRI compared to diagnostic radiology that, if not properly addressed, can undermine the advantages MRI offers for radiation treatment planning (RTP). The authors introduce here strategies to manage several challenges of using MRI for virtual simulation in external beam RTP. Methods: A total of 810 clinical MRI simulation exams were performed using a dedicated MRI scanner for external beam RTP of brain, breast, cervix, head and neck, liver, pancreas, prostate, and sarcoma cancers. Patients were imaged in treatment position using MRI-optimal immobilization devices. Radiofrequency (RF) coil configurations and scan protocols were optimized based on RTP constraints. Off-resonance and gradient nonlinearity-induced geometric distortions were minimized or corrected prior to using images for RTP. A multidisciplinary MRI simulation guide, along with window width and level presets, was created to standardize use of MR images during RTP. A quality assurance program was implemented to maintain accuracy and repeatability of MRI simulation exams. Results: The combination of a large bore scanner, high field strength, and circumferentially wrapped, flexible phased array RF receive coils permitted acquisition of thin slice images with high contrast-to-noise ratio (CNR) and image intensity uniformity, while simultaneously accommodating patient setup and immobilization devices. Postprocessing corrections and alternative acquisition methods were required to reduce or correct off-resonance and gradient nonlinearity induced geometric distortions. Conclusions: The methodology described herein contains practical strategies the authors have implemented through lessons learned performing clinical MRI simulation exams. In

  7. Challenges for Molecular Neuroimaging with MRI

    PubMed Central

    Lelyveld, Victor S.; Atanasijevic, Tatjana; Jasanoff, Alan

    2010-01-01

    Magnetic resonance (MRI)-based molecular imaging methods are beginning to have impact in neuroscience. A growing number of molecular imaging agents have been synthesized and tested in vitro, but so far relatively few have been validated in the brains of live animals. Here, we discuss key challenges associated with expanding the repertoire of successful molecular neuroimaging approaches. The difficulty of delivering agents past the blood-brain barrier (BBB) is a particular obstacle to molecular imaging in the central nervous system. We review established and emerging techniques for trans-BBB delivery, including intracranial infusion, BBB disruption, and transporter-related methods. Improving the sensitivity with which MRI-based molecular agents can be detected is a second major challenge. Better sensitivity would in turn reduce the requirements for delivery and alleviate potential side effects. We discuss recent efforts to enhance relaxivity of conventional longitudinal relaxation time (T1) and transverse relaxation time (T2) MRI contrast agents, as well as strategies that involve amplifying molecular signals or reducing endogenous background influences. With ongoing refinement of imaging approaches and brain delivery methods, MRI-based techniques for molecular-level neuroscientific investigation will fall increasingly within reach. PMID:20808721

  8. Split gradient coils for simultaneous PET-MRI

    PubMed Central

    Poole, Michael; Bowtell, Richard; Green, Dan; Pittard, Simon; Lucas, Alun; Hawkes, Rob; Carpenter, Adrian

    2015-01-01

    Combining positron emission tomography (PET) and MRI necessarily involves an engineering tradeoff as the equipment needed for the two modalities vies for the space closest to the region where the signals originate. In one recently described scanner configuration for simultaneous positron emission tomography–MRI, the positron emission tomography detection scintillating crystals reside in an 80-mm gap between the 2 halves of a 1-T split-magnet cryostat. A novel set of gradient and shim coils has been specially designed for this split MRI scanner to include an 110-mm gap from which wires are excluded so as not to interfere with positron detection. An inverse boundary element method was necessarily employed to design the three orthogonal, shielded gradient coils and shielded Z0 shim coil. The coils have been constructed and tested in the hybrid positron emission tomography-MRI system and successfully used in simultaneous positron emission tomography-MRI experiments. PMID:19780167

  9. Massively Parallel MRI Detector Arrays

    PubMed Central

    Keil, Boris; Wald, Lawrence L

    2013-01-01

    Originally proposed as a method to increase sensitivity by extending the locally high-sensitivity of small surface coil elements to larger areas, the term parallel imaging now includes the use of array coils to perform image encoding. This methodology has impacted clinical imaging to the point where many examinations are performed with an array comprising multiple smaller surface coil elements as the detector of the MR signal. This article reviews the theoretical and experimental basis for the trend towards higher channel counts relying on insights gained from modeling and experimental studies as well as the theoretical analysis of the so-called “ultimate” SNR and g-factor. We also review the methods for optimally combining array data and changes in RF methodology needed to construct massively parallel MRI detector arrays and show some examples of state-of-the-art for highly accelerated imaging with the resulting highly parallel arrays. PMID:23453758

  10. SQUID-detected ultra-low field MRI

    NASA Astrophysics Data System (ADS)

    Espy, Michelle; Matlashov, Andrei; Volegov, Petr

    2013-04-01

    MRI remains the premier method for non-invasive imaging of soft-tissue. Since the first demonstration of ULF MRI the trend has been towards ever higher magnetic fields. This is because the signal, and efficiency of Faraday detectors, increases with ever higher magnetic fields and corresponding Larmor frequencies. Nevertheless, there are many compelling reasons to continue to explore MRI at much weaker magnetic fields, the so-called ultra-low field or (ULF) regime. In the past decade many excellent proof-of-concept demonstrations of ULF MRI have been made. These include combined MRI and magnetoencephalography, imaging in the presence of metal, unique tissue contrast, and implementation in situations where a high magnetic field is simply impractical. These demonstrations have routinely used pulsed pre-polarization (at magnetic fields from ∼10 to 100 mT) followed by read-out in a much weaker (1-100 μT) magnetic fields using the ultra-sensitive Superconducting Quantum Interference Device (SQUID) sensor. Even with pre-polarization and SQUID detection, ULF MRI suffers from many challenges associated with lower magnetization (i.e. signal) and inherently long acquisition times compared to conventional >1 T MRI. These are fundamental limitations imposed by the low measurement and gradient fields used. In this review article we discuss some of the techniques, potential applications, and inherent challenges of ULF MRI.

  11. NMR, MRI, and spectroscopic MRI in inhomogeneous fields

    DOEpatents

    Demas, Vasiliki; Pines, Alexander; Martin, Rachel W; Franck, John; Reimer, Jeffrey A

    2013-12-24

    A method for locally creating effectively homogeneous or "clean" magnetic field gradients (of high uniformity) for imaging (with NMR, MRI, or spectroscopic MRI) both in in-situ and ex-situ systems with high degrees of inhomogeneous field strength. THe method of imaging comprises: a) providing a functional approximation of an inhomogeneous static magnetic field strength B.sub.0({right arrow over (r)}) at a spatial position {right arrow over (r)}; b) providing a temporal functional approximation of {right arrow over (G)}.sub.shim(t) with i basis functions and j variables for each basis function, resulting in v.sub.ij variables; c) providing a measured value .OMEGA., which is an temporally accumulated dephasing due to the inhomogeneities of B.sub.0({right arrow over(r)}); and d) minimizing a difference in the local dephasing angle .phi.({right arrow over (r)},t)=.gamma..intg..sub.0.sup.t{square root over (|{right arrow over (B)}.sub.1({right arrow over (r)},t')|.sup.2+({right arrow over (r)}{right arrow over (G)}.sub.shimG.sub.shim(t')+.parallel.{right arrow over (B)}.sub.0({right arrow over (r)}).parallel..DELTA..omega.({right arrow over (r)},t'/.gamma/).sup.2)}dt'-.OMEGA. by varying the v.sub.ij variables to form a set of minimized v.sub.ij variables. The method requires calibration of the static fields prior to minimization, but may thereafter be implemented without such calibration, may be used in open or closed systems, and potentially portable systems.

  12. Eosinophilic granuloma: MRI manifestations.

    PubMed

    Beltran, J; Aparisi, F; Bonmati, L M; Rosenberg, Z S; Present, D; Steiner, G C

    1993-01-01

    The appearance on magnetic resonance imaging (MRI) of 16 cases of pathologically proven eosinophilic granuloma were reviewed retrospectively and correlated with the radiographic appearance of the lesion. The most common MR appearance (ten cases) was a focal lesion, surrounded by an extensive, ill-defined bone marrow and soft tissue reaction with low signal intensity on T1-weighted images and high signal intensity on T2-weighted images, considered to represent bone marrow and soft tissue edema (the flare phenomenon). The MRI manifestations of eosinophilic granuloma, especially during the early stages, are nonspecific, and may stimulate an aggressive lesion such as osteomyelitis or Ewings sarcoma, or other benign bone tumors such as osteoid osteoma or chondroblastoma. PMID:8480200

  13. MRI of the penis.

    PubMed

    Kirkham, A

    2012-11-01

    MRI of the penis is an expensive test that is not always superior to clinical examination or ultrasound. However, it shows many of the important structures, and in particular the combination of tumescence from intracavernosal alprostadil, and high-resolution T(2) sequences show the glans, corpora and the tunica albuginea well. In this paper we summarise the radiological anatomy and discuss the indications for MRI. For penile cancer, it may be useful in cases where the local stage is not apparent clinically. In priapism, it is an emerging technique for assessing corporal viability, and in fracture it can in most cases make the diagnosis and locate the injury. In some cases of penile fibrosis and Peyronie's disease, it may aid surgical planning, and in complex pelvic fracture may replace or augment conventional urethrography. It is an excellent investigation for the malfunctioning penile prosthesis.

  14. Superconducting magnets for MRI

    SciTech Connect

    Williams, J.E.

    1984-08-01

    Three types of magnets are currently used to provide the background field required for magnet resonance imaging (MRI). (i) Permanent magnets produce fields of up to 0.3 T in volumes sufficient for imaging the head or up to 0.15 T for whole body imaging. Cost and simplicity of operation are advantages, but relatively low field, weight (up to 100 tonnes) and, to a small extent, instability are limitations. (ii) Water-cooled magnets provide fields of up to 0.25 T in volumes suitable for whole body imaging, but at the expense of power (up to 150 kW for 0.25 T) and water-cooling. Thermal stability of the field requires the maintenance of constant temperature through periods both of use and of quiescence. (iii) Because of the limitations imposed by permanent and resistive magnets, particularly on field strength, the superconducting magnet is now most widely used to provide background fields of up to 2 T for whole body MRI. It requires very low operating power and that only for refrigeration. Because of the constant low temperature, 4.2 K, at which its stressed structure operates, its field is stable. The following review deals principally with superconducting magnets for MRI. However, the sections on field analysis apply to all types of magnet and the description of the source terms of circular coils and of the principals of design of solenoids apply equally to resistive solenoidal magnets.

  15. Anatomical MRI with an atomic magnetometer.

    PubMed

    Savukov, I; Karaulanov, T

    2013-06-01

    Ultra-low field (ULF) MRI is a promising method for inexpensive medical imaging with various additional advantages over conventional instruments such as low weight, low power, portability, absence of artifacts from metals, and high contrast. Anatomical ULF MRI has been successfully implemented with SQUIDs, but SQUIDs have the drawback of a cryogen requirement. Atomic magnetometers have sensitivity comparable to SQUIDs and can be in principle used for ULF MRI to replace SQUIDs. Unfortunately some problems exist due to the sensitivity of atomic magnetometers to a magnetic field and gradients. At low frequency, noise is also substantial and a shielded room is needed for improving sensitivity. In this paper, we show that at 85 kHz, the atomic magnetometer can be used to obtain anatomical images. This is the first demonstration of any use of atomic magnetometers for anatomical MRI. The demonstrated resolution is 1.1 mm×1.4 mm in about 6 min of acquisition with SNR of 10. Some applications of the method are discussed. We discuss several measures to increase the sensitivity to reach a resolution 1 mm×1 mm.

  16. Comparison of dual-echo DSC-MRI- and DCE-MRI-derived contrast agent kinetic parameters.

    PubMed

    Quarles, C Chad; Gore, John C; Xu, Lei; Yankeelov, Thomas E

    2012-09-01

    The application of dynamic susceptibility contrast (DSC) MRI methods to assess brain tumors is often confounded by the extravasation of contrast agent (CA). Disruption of the blood-brain barrier allows CA to leak out of the vasculature leading to additional T(1), T(2) and T(2) relaxation effects in the extravascular space, thereby affecting the signal intensity time course in a complex manner. The goal of this study was to validate a dual-echo DSC-MRI approach that separates and quantifies the T(1) and T(2) contributions to the acquired signal and enables the estimation of the volume transfer constant, K(trans), and the volume fraction of the extravascular extracellular space, v(e). To test the validity of this approach, DSC-MRI- and dynamic contrast enhanced (DCE) MRI-derived K(trans) and v(e) estimates were spatially compared in both 9L and C6 rat brain tumor models. A high degree of correlation (concordance correlation coefficients >0.83, Pearson's r>0.84) and agreement was found between the DSC-MRI- and DCE-MRI-derived measurements. These results indicate that dual-echo DSC-MRI can be used to simultaneously extract reliable DCE-MRI kinetic parameters in brain tumors in addition to conventional blood volume and blood flow metrics.

  17. An MRI-Compatible Robotic System With Hybrid Tracking for MRI-Guided Prostate Intervention

    PubMed Central

    Krieger, Axel; Iordachita, Iulian I.; Guion, Peter; Singh, Anurag K.; Kaushal, Aradhana; Ménard, Cynthia; Pinto, Peter A.; Camphausen, Kevin; Fichtinger, Gabor

    2012-01-01

    This paper reports the development, evaluation, and first clinical trials of the access to the prostate tissue (APT) II system—a scanner independent system for magnetic resonance imaging (MRI)-guided transrectal prostate interventions. The system utilizes novel manipulator mechanics employing a steerable needle channel and a novel six degree-of-freedom hybrid tracking method, comprising passive fiducial tracking for initial registration and subsequent incremental motion measurements. Targeting accuracy of the system in prostate phantom experiments and two clinical human-subject procedures is shown to compare favorably with existing systems using passive and active tracking methods. The portable design of the APT II system, using only standard MRI image sequences and minimal custom scanner interfacing, allows the system to be easily used on different MRI scanners. PMID:22009867

  18. A review of MRI evaluation of demyelination in cuprizone murine model

    SciTech Connect

    Krutenkova, E. Pan, E.; Khodanovich, M.

    2015-11-17

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  19. A review of MRI evaluation of demyelination in cuprizone murine model

    NASA Astrophysics Data System (ADS)

    Krutenkova, E.; Pan, E.; Khodanovich, M.

    2015-11-01

    The cuprizone mouse model of non-autoimmune demyelination reproduces some phenomena of multiple sclerosis and is appropriate for validation and specification of a new method of non-invasive diagnostics. In the review new data which are collected using the new MRI method are compared with one or more conventional MRI tools. Also the paper reviewed the validation of MRI approaches using histological or immunohistochemical methods. Luxol fast blue histological staining and myelin basic protein immunostaining is widespread. To improve the accuracy of non-invasive conventional MRI, multimodal scanning could be applied. The new quantitative MRI method of fast mapping of the macromolecular proton fraction is a reliable biomarker of myelin in the brain and can be used for research of demyelination in animals. To date, a validation of MPF method on the CPZ mouse model of demyelination is not performed, although this method is probably the best way to evaluate demyelination using MRI.

  20. MRI features of Binswanger’s disease predict prognosis and associated pathology

    PubMed Central

    Akiguchi, Ichiro; Budka, Herbert; Shirakashi, Yoshitomo; Woehrer, Adelheid; Watanabe, Toshiyuki; Shiino, Akihiko; Yamamoto, Yasumasa; Kawamoto, Yasuhiro; Krampla, Wolfgang; Jungwirth, Susanne; Fischer, Peter

    2014-01-01

    Objective To identify the prevalence of MRI features of Binswanger’s disease (BD), specifically MRI with diffuse white matter lesions and scattered multiple lacunes (BD-MRI), and to describe neurological features and pathological outcomes of a community-based cohort study. Methods Of 697 participants (all 75 years old), 503 completed neurological examinations at baseline and were followed-up every 30 months thereafter with MRIs, the mini-mental state examination (MMSE) and the Unified Parkinson Disease Rating Scale-Motor Section (UPDRSM). Data from participants with BD-MRI were compared with those from participants with predominant white matter lesions (WML-MRI), scattered multiple lacunes (ML-MRI), or normal MRIs. Results Fourteen BD-MRI patients (2.8%) were detected at baseline. The mean MMSE scores in the BD-MRI, WML-MRI, ML-MRI, and normal MRIs groups were 26.4, 28.2, 28.4, and 28.5, respectively, and the mean UPDRSM scores were 9.1, 1.3, 3.1, and 1.7, respectively. At the 30-month follow-up, mortality rates in the normal MRIs, WML-MRI and ML-MRI were 4%, 9.1%, and 22.2%, respectively, and follow-up MRIs were available for 80%, 82%, and 61% of the participants, respectively. In the BD-MRI, however, five patients were deceased, and only five follow-up individual MRIs were available (33.3%). Autopsies were performed on six of eight BD-MRI brains, and these brains fulfilled the pathological criteria for BD independent of Alzheimer disease pathology. All these six individuals also showed systemic atherosclerosis and renal arterio-arteriolosclerosis. Interpretation The BD-MRI participants had poor prognoses and showed pure BD pathology with advanced systemic vascular disease. BD-MRI appears to be a predictor of vascular neurocognitive impairment. PMID:25493272

  1. Biparametric versus multiparametric MRI in the diagnosis of prostate cancer

    PubMed Central

    Logager, Vibeke; Baslev, Ingerd; Møller, Jakob M; Hansen, Rasmus Hvass; Thomsen, Henrik S

    2016-01-01

    Background Since multiparametric magnetic resonance imaging (mp-MRI) of the prostate exceeds 30 min, minimizing the evaluation time of significant (Gleason scores > 6) prostate cancer (PCa) would be beneficial. A reduced protocol might be sufficient for the diagnosis. Purpose To study whether a short unenhanced biparametric MRI (bp-MRI) matches mp-MRI in detecting significant PCa. Material and Methods A total of 204 men (median age, 65 years; mean ± SD, 64.1; range 45–75 years; median serum PSA level, 14 ng/mL; range, 2.2–120 ng/mL; median prostate volume, 60 mL; range, 23–263 mL) fulfilled the criteria for being enrolled. They underwent mp-MRI and prostate biopsy from January through June 2014. Of the included patients, 9.3% underwent prostatectomy, 90.7% had TRUS-bx, and 10.8 had MRI-targeted TRUS-bx. Two radiologists separately assessed the mp-MRI examination (T2-weighted [T2W] imaging, diffusion-weighted imaging [DWI], apparent diffusion coefficient map [ADC-map] and dynamic contrast-enhanced imaging [DCE]). Two months later, the bp-MRI version (T2W imaging, DWI, and ADC-map) was evaluated. Results Reader 1: Assessing mp-MRI: 0 false negatives, sensitivity of 1, and specificity 0.04. Assessing bp-MRI: four false negatives, sensitivity of 0.94, and specificity 0.15. Reader 2: Assessing mp-MRI: five false negatives, sensitivity of 0.93, and specificity 0.16. Assessing bp-MRI: three false negatives, sensitivity of 0.96, and specificity 0.15. Intra-reader agreement Cohen’s Kappa (κ) was 0.87 for reader 1 (95% confidence interval [CI], 0.83–0.92) and 0.84 for reader 2 (95% CI 0.78–0.89). Conclusion Bp-MRI is as good as mp-MRI at detecting PCa. A large prospective study seems to be strongly warranted. PMID:27583170

  2. Extension of dVCA model and its application in estimating fMRI components

    NASA Astrophysics Data System (ADS)

    Zhang, Gaoyan; Zhang, Jiacai; Yao, Li; Zhao, Xiaojie

    2010-03-01

    General linear model (GLM) and independent component analysis (ICA) are widely used methods in the community of functional magnetic resonance imaging (fMRI) data analysis. GLM and ICA are all assuming that fMRI components are location locked. Here we extend the Differentially variable component analysis (dVCA) and introduce it into fMRI data to analyze the transient changes during fMRI experiments which are ignored in GLM and ICA. We apply the extended dVCA to model fMRI images as the linear combination of ongoing activity and multiple fMRI components. We test our extended dVCA method on simulated images that mimicked the fMRI slice images containing two components, and employ the iterative maximum a posteriori (MAP) solution succeed to estimate each component's time-invariant spatial patterns, and its time-variant amplitude scaling factors and location shifts. The extended dVCA algorithm also identify two fMRI components that reflect the fact of hemispheric asymmetry for motor area in another test with fMRI data acquired with the block design task of right/left hand finger tapping alternately. This work demonstrates that our extended dVCA method is robustness to detect the variability of the fMRI components that maybe existent during the fMRI experiments.

  3. Ferrite-enhanced MRI monitoring in hyperthermia.

    PubMed

    Reinl, Herbert M; Peller, Michael; Hagmann, Mark; Turner, Paul; Issels, Rolf D; Reiser, Maximilian

    2005-12-01

    In an MRI hyperthermia hybrid system, T1 changes are investigated for monitoring thermal therapy at 0.2 T. The water bolus, which is needed for power transmission and cooling of the skin, limits MR image quality by signal compression and artifacts. Superparamagnetic ferrofluid in different concentration was investigated with MR relaxometry and MRI methods. We found that using ferrofluid in a low concentration of 70-90 ppm magnetite the water signal can be suppressed without susceptibility artifacts. With our method of signal suppression, a significant improvement of spatial and temporal resolution is possible. The ferrofluid is stable and allows RF heating at 100 MHz. This method of signal extinction may also be useful for other experimental setups where suppression of water is necessary. PMID:16376187

  4. MRI in evaluation of perianal fistulae

    PubMed Central

    Sofic, Amela; Beslic, Serif; Sehovic, Nedzad; Caluk, Jasmin; Sofic, Damir

    2010-01-01

    Background Fistula is considered to be any abnormal passage which connects two epithelial surfaces. Parks’ fistulae classification demonstrates the biggest practical significance and divides fistulae into: intersphincteric, transsphincteric, suprasphincteric and extrasphincteric. Etiology of perianal fistulae is most commonly linked with the inflammation of anal glands in Crohn’s disease, tuberculosis, pelvic infections, pelvic malignant tumours, and with the radiotherapy. Diagnostic method options are: RTG fistulography, CT fistulography and magnetic resonance imaging (MRI) of pelvic organs. Patients and methods We have included 24 patients with perirectal fistulae in the prospective study. X-rays fistulography, CT fistulography, and then MRI of the pelvic cavity have been performed on all patients. Accuracy of each procedure in regards to the patients and the etiologic cause have been statistically determined. Results 29.16% of transphincteric fistulae have been found, followed by 25% of intersphincteric, 25% of recto-vaginal, 12.5% of extrasphincteric, and 8.33% of suprasphincteric. Abscess collections have been found in 16.6% patients. The most frequent etiologic cause of perianal fistulae was Crohn’s disease in 37.5%, where the accuracy of classification of MRI was 100%, CT was 11% and X-rays 0%. Ulcerous colitis was the second cause, with 20.9% where the accuracy of MRI was 100%, while CT was 80% and X-rays was 0%. All other etiologic causes of fistulae were found in 41.6% patients. Conclusions MRI is a reliable diagnostic modality in the classification of perirectal fistulae and can be an excellent diagnostic guide for successful surgical interventions with the aim to reduce the number of recurrences. Its advantage is that fistulae and abscess are visible without the need to apply any contrast medium. PMID:22933919

  5. Multiscan MRI-based virtual cystoscopy

    NASA Astrophysics Data System (ADS)

    Chen, Dongqing; Li, Bin; Huang, Wei; Liang, Zach

    2000-04-01

    Computed tomography (CT) based virtual cystoscopy (VC) has been studied as a potential tool for screening bladder cancer. It is accurate in localizing tumor of size larger than 1 cm and less expensive, as compared to fiberoptic cystoscopy. However, it is invasive and difficult to perform due to using Foley catheter for bladder insufflating with air. In a previous work, we investigated a magnetic resonance imaging (MRI) based VC scheme with urine as a natural contrast solution, in which a MRI acquisition protocol and an adaptive segmentation method were utilized. Both bladder lumen and wall were successfully delineated. To suppress motion artifact and insight pathological change on the bladder wall images, a multi-scan MRI scheme was presented in this study. One transverse and another coronal acquisitions of T1-weighted that cover the whole bladder were obtained twice, at one time the bladder is full of urine and at another time it is near the empty. Four bladder volumes extracted from those 4 datasets were registered first using a flexible three- dimensional (3D) registration algorithm. Then, associated 4 lumen surfaces were viewed simultaneously with the help of an interactive 3D visualization system. This MRI-based VC was tested on volunteers and demonstrated the feasibility to mass screening for bladder cancer.

  6. Diffusion-MRI in neurodegenerative disorders.

    PubMed

    Goveas, Joseph; O'Dwyer, Laurence; Mascalchi, Mario; Cosottini, Mirco; Diciotti, Stefano; De Santis, Silvia; Passamonti, Luca; Tessa, Carlo; Toschi, Nicola; Giannelli, Marco

    2015-09-01

    The ability to image the whole brain through ever more subtle and specific methods/contrasts has come to play a key role in understanding the basis of brain abnormalities in several diseases. In magnetic resonance imaging (MRI), "diffusion" (i.e. the random, thermally-induced displacements of water molecules over time) represents an extraordinarily sensitive contrast mechanism, and the exquisite structural detail it affords has proven useful in a vast number of clinical as well as research applications. Since diffusion-MRI is a truly quantitative imaging technique, the indices it provides can serve as potential imaging biomarkers which could allow early detection of pathological alterations as well as tracking and possibly predicting subtle changes in follow-up examinations and clinical trials. Accordingly, diffusion-MRI has proven useful in obtaining information to better understand the microstructural changes and neurophysiological mechanisms underlying various neurodegenerative disorders. In this review article, we summarize and explore the main applications, findings, perspectives as well as challenges and future research of diffusion-MRI in various neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, Huntington's disease and degenerative ataxias. PMID:25917917

  7. SU-E-J-239: IMRT Planning of Prostate Cancer for a MRI-Linac Based On MRI Only

    SciTech Connect

    Chen, X; Prior, P; Paulson, E; Lawton, C; Li, X

    2014-06-01

    Purpose: : To investigate dosimetric differences between MRI- and CT-based IMRT planning for prostate cancer, the impact of a magnetic field in a MRI-Linac, and to explore the feasibility of IMRT planning based on MRI alone. Methods: IMRT plans were generated based on CT and MRI images acquired on two representative prostate-cancer patients using clinical dose volume constraints. A research planning system (Monaco, Elekta), which employs a Monte Carlo dose engine and includes a perpendicular magnetic field of 1.5T from an MRI-Linac, was used. Bulk electron density assignments based on organ-specific values from ICRU 46 were used to convert MRI (T2) to pseudo CT. With the same beam configuration as in the original CT plan, 5 additional plans were generated based on CT or MRI, with or without optimization (i.e., just recalculation) and with or without the magnetic field. The plan quality in terms of commonly used dose volume (DV) parameters for all plans was compared. The statistical uncertainty on dose was < 1%. Results: For plans with the same contour set but without re-optimization, the DV parameters were different from those for the original CT plan, mostly less than 5% with a few exceptions. These differences were reduced to mostly less than 3% when the plans were re-optimized. For plans with contours from MRI, the differences in the DV parameters varied depending on the difference in the contours as compared to CT. For the optimized plans with contours from MR, the differences for PTV were less than 3%. Conclusion: The prostate IMRT plans based on MRI-only for a MR-Linac were practically similar as compared to the CT plan under the same beam and optimization configuration if the difference on the structure delineation is excluded, indicating the feasibility of using MRI-only for prostate IMRT.

  8. Functional connectomics from resting-state fMRI

    PubMed Central

    Smith, Stephen M; Vidaurre, Diego; Beckmann, Christian F; Glasser, Matthew F; Jenkinson, Mark; Miller, Karla L; Nichols, Thomas E; Robinson, Emma; Salimi-Khorshidi, Gholamreza; Woolrich, Mark W; Barch, Deanna M; Uğurbil, Kamil; Van Essen, David C

    2014-01-01

    Spontaneous fluctuations in activity in different parts of the brain can be used to study functional brain networks. We review the use of resting-state functional MRI for the purpose of mapping the macroscopic functional connectome. After describing MRI acquisition and image processing methods commonly used to generate data in a form amenable to connectomics network analysis, we discuss different approaches for estimating network structure from that data. Finally, we describe new possibilities resulting from the high-quality rfMRI data being generated by the Human Connectome Project, and highlight some upcoming challenges in functional connectomics. PMID:24238796

  9. Occupational exposure in MRI

    PubMed Central

    Mcrobbie, D W

    2012-01-01

    This article reviews occupational exposure in clinical MRI; it specifically considers units of exposure, basic physical interactions, health effects, guideline limits, dosimetry, results of exposure surveys, calculation of induced fields and the status of the European Physical Agents Directive. Electromagnetic field exposure in MRI from the static field B0, imaging gradients and radiofrequency transmission fields induces electric fields and currents in tissue, which are responsible for various acute sensory effects. The underlying theory and its application to the formulation of incident and induced field limits are presented. The recent International Commission on Non-Ionizing Radiation Protection (ICNIRP) Bundesministerium für Arbeit und Soziales and Institute of Electrical and Electronics Engineers limits for incident field exposure are interpreted in a manner applicable to MRI. Field measurements show that exposure from movement within the B0 fringe field can exceed ICNIRP reference levels within 0.5 m of the bore entrance. Rate of change of field dB/dt from the imaging gradients is unlikely to exceed the new limits, although incident field limits can be exceeded for radiofrequency (RF) exposure within 0.2–0.5 m of the bore entrance. Dosimetric surveys of routine clinical practice show that staff are exposed to peak values of 42±24% of B0, with time-averaged exposures of 5.2±2.8 mT for magnets in the range 0.6–4 T. Exposure to time-varying fields arising from movement within the B0 fringe resulted in peak dB/dt of approximately 2 T s−1. Modelling of induced electric fields from the imaging gradients shows that ICNIRP-induced field limits are unlikely to be exceeded in most situations; however, movement through the static field may still present a problem. The likely application of the limits is discussed with respect to the reformulation of the European Union (EU) directive and its possible implications for MRI. PMID:22457400

  10. Nanoformulations for molecular MRI

    PubMed Central

    Tu, Chuqiao; Louie, Angelique Y.

    2012-01-01

    Nanoscale contrast agents have shown the ability to increase the detection sensitivity of MRI by several orders of magnitude, endowing this traditionally macroscopic modality with the ability to observe unique molecular signatures. Herein, we describe three types of nanoparticulate contrast agents: iron oxide nanoparticles, gadolinium-based nanoparticles, and bio-essential manganese, cobalt, nickel, and copper ion-containing nanoformulations. Some of these agents have been approved for clinical use, but more are still under development for medical imaging. The advantages and disadvantages of each nanoformulation, in terms of intrinsic magnetism, ease of synthesis, and biodistribution, etc. are discussed. PMID:22488901

  11. Trust Region Methods for the Estimation of a Complex Exponential Decay Model in MRI With a Single-Shot or Multi-Shot Trajectory.

    PubMed

    Hu, Chenxi; Reeves, Stanley J

    2015-11-01

    Joint estimation of spin density R2* decay and OFF-resonance frequency maps is very useful in many magnetic resonance imaging applications. The standard multi-echo approach can achieve high accuracy but requires a long acquisition time for sampling multiple k-space frames. There are many approaches to accelerate the acquisition. Among them, single-shot or multi-shot trajectory-based sampling has recently drawn attention due to its fast data acquisition. However, this sampling strategy destroys the Fourier relationship between k-space and images, leading to a great challenge for the reconstruction. In this paper, we present two trust region methods based on two different linearization strategies for the nonlinear signal model. A trust region is defined as a local area in the variable space where a local linear approximation is trustable. In each iteration, the method minimizes a local approximation within a trust region so that the step size can be kept in a suitable scale. A continuation scheme is applied to reduce the regularization gradually over the parameter maps and facilitates convergence from poor initializations. The two trust region methods are compared with the two other previously proposed methods--the nonlinear conjugate gradients and the gradual refinement algorithm. Experiments based on various synthetic data and real phantom data show that the two trust region methods have a clear advantage in both speed and stability. PMID:26068316

  12. Biomimetic phantom for cardiac diffusion MRI

    PubMed Central

    Teh, Irvin; Zhou, Feng‐Lei; Hubbard Cristinacce, Penny L.; Parker, Geoffrey J.M.

    2015-01-01

    Purpose Diffusion magnetic resonance imaging (MRI) is increasingly used to characterize cardiac tissue microstructure, necessitating the use of physiologically relevant phantoms for methods development. Existing phantoms are generally simplistic and mostly simulate diffusion in the brain. Thus, there is a need for phantoms mimicking diffusion in cardiac tissue. Materials and Methods A biomimetic phantom composed of hollow microfibers generated using co‐electrospinning was developed to mimic myocardial diffusion properties and fiber and sheet orientations. Diffusion tensor imaging was carried out at monthly intervals over 4 months at 9.4T. 3D fiber tracking was performed using the phantom and compared with fiber tracking in an ex vivo rat heart. Results The mean apparent diffusion coefficient and fractional anisotropy of the phantom remained stable over the 4‐month period, with mean values of 7.53 ± 0.16 × 10‐4 mm2/s and 0.388 ± 0.007, respectively. Fiber tracking of the 1st and 3rd eigenvectors generated analogous results to the fiber and sheet‐normal direction respectively, found in the left ventricular myocardium. Conclusion A biomimetic phantom simulating diffusion in the heart was designed and built. This could aid development and validation of novel diffusion MRI methods for investigating cardiac microstructure, decrease the number of animals and patients needed for methods development, and improve quality control in longitudinal and multicenter cardiac diffusion MRI studies. J. MAGN. RESON. IMAGING 2016;43:594–600. PMID:26213152

  13. Neonatal cranial ultrasound versus MRI and neurodevelopmental outcome at school age in children born preterm

    PubMed Central

    Rademaker, K; Uiterwaal, C; Beek, F; van Haastert, I C; Lieftink, A; Groenendaal, F; Grobbee, D; de Vries, L S

    2005-01-01

    Aim: To examine the correlation between neonatal cranial ultrasound and school age magnetic resonance imaging (MRI) and neurodevelopmental outcome. Methods: In a prospective 2 year cohort study, 221 children (gestational age ⩽32 weeks and/or birth weight ⩽1500 g) participated at a median age of 8.1 years (inclusion percentage 78%). Conventional MRI, IQ (subtests of the WISC), and motor performance (Movement Assessment Battery for Children) at school age were primary outcome measurements. Results: Overall, there was poor correspondence between ultrasound group classifications and MRI group classifications, except for the severe group (over 70% agreement). There was only a 1% chance of the children with a normal cranial ultrasound having a major lesion on MRI. Mean IQ (standard deviation) was significantly lower in children with major ultrasound or MRI lesions, but was also lower in children with minor lesions on MRI compared to children with a normal MRI (91±16, 100±13, 104±13 for major lesions, minor lesions, and normal MRI, respectively). Median total impairment score (TIS) was significantly higher in children with major lesions on ultrasound or MRI as well as in children with minor lesions on MRI (TIS 4.0 and 6.25 for normal and minor lesions on MRI, respectively; p<0.0001). Conclusions: A normal neonatal cranial ultrasound excluded a severe lesion on MRI in 99% of cases. MRI correlated more strongly with mean IQ and median TIS than ultrasound. Subtle white matter lesions are better detected with MRI which could explain the stronger correlation of MRI with IQ and motor performance. PMID:15956095

  14. Nonaxisymmetric modes of MRI in dissipative Keplerian disks

    NASA Astrophysics Data System (ADS)

    Kitchatinov, L. L.; Rüdiger, G.

    2010-04-01

    Aims: Deviations from the axial symmetry are necessary to maintain self-sustained MRI-turbulence by a dynamo mechanism. We define the parameter region where the nonaxisymmetric MRI modes are excited and study their geometries and growth rates. Methods: The linear eigenvalue problem for global nonaxisymmetric modes of standard-MRI in Keplerian disks is solved numerically with allowance for finite diffusion. Results: For small magnetic Prandtl numbers the microscopic viscosity completely drops out of the analysis so that the stability maps and the growth rates expressed in terms of the magnetic Reynolds number Rm and the Lundquist number S do not depend on the magnetic Prandtl number Pm. The minimum magnetic field for the onset of nonaxisymmetric MRI grows with the rotation rate. For a given S all nonaxisymmetric modes disappear for a sufficiently large Rm. This is a consequence of the radial fine-structure of the nonaxisymmetric modes resulting from the winding effect of differential rotation. It is this fine-structure which also provides serious resolution problems for the numerical simulation of MRI at large Rm. Conclusions: For weak magnetic fields slightly above the critical value for the onset of MRI only axisymmetric modes are unstable. Nonaxisymmetric modes need stronger fields and not too large Rm. If Pm is small its real value does not play any role in MRI.

  15. Data Collection and Analysis Strategies for phMRI

    PubMed Central

    Mandeville, Joseph B.; Liu, Christina H.; Vanduffel, Wim; Marota, John J.A.; Jenkins, Bruce G.

    2014-01-01

    Although functional MRI traditionally has been applied mainly to study changes in task-induced brain function, evolving acquisition methodologies and improved knowledge of signal mechanisms have increased the utility of this method for studying responses to pharmacological stimuli, a technique often dubbed “phMRI”. The proliferation of higher magnetic field strengths and the use of exogenous contrast agent have boosted detection power, a critical factor for successful phMRI due to the restricted ability to average multiple stimuli within subjects. Receptor-based models of neurovascular coupling, including explicit pharmacological models incorporating receptor densities and affinities and data-driven models that incorporate weak biophysical constraints, have demonstrated compelling descriptions of phMRI signal induced by dopaminergic stimuli. This report describes phMRI acquisition and analysis methodologies, with an emphasis on data-driven analyses. As an example application, statistically efficient data-driven regressors were used to describe the biphasic response to the mu-opioid agonist remifentanil, and antagonism using dopaminergic and GABAergic ligands revealed modulation of the mesolimbic pathway. Results illustrate the power of phMRI as well as our incomplete understanding of mechanisms underlying the signal. Future directions are discussed for phMRI acquisitions in human studies, for evolving analysis methodologies, and for interpretative studies using the new generation of simultaneous PET/MRI scanners. PMID:24613447

  16. Target image search using fMRI signals

    NASA Astrophysics Data System (ADS)

    Xiong, Shi; Song, Sutao; Zhan, Yu; Zhang, Jiacai

    2014-03-01

    Recent neural signal decoding studies based on functional magnetic resonance imaging (fMRI) have identified the specific image presenting to the subject from a set of potential images, and some studies extend neural decoding into image reconstruction, i.e. image contents that the subject perceived were decoded from the fMRI signals recorded during the subject looking at images. In this paper, we decoded the target images using fMRI signals and described a target image searching method based on the relationship between target image stimuli and fMRI activity. We recorded fMRI data during a serial visual stimuli image presentation task, some of the stimuli images were target images and the rest images were non-target ones. Our fMRI data analysis results showed that in the serial visual presentation task, target images elicited a stereotypical response in the fMRI, which can be detected by multi-voxel pattern analysis (MVPA). Classifiers designed with support vector machine (SVM) used this response to decipher target images from non-target images. The leave-one-run-out cross-validation showed that we can pick out the target images with a possibility far above the chance level, which indicate that there's a neural signatures correlated with the target image recognition process in the human systems.

  17. Does MRI Increase the Diagnostic Confidence of Physicians in an Outpatient Memory Clinic

    PubMed Central

    Boelaarts, Leo; Scheltens, Philip; de Jonghe, Jos

    2016-01-01

    Background and Aim Data showing the usefulness of MRI to improve the accuracy of the diagnostic process in cognitive disorders were derived from studies in tertiary referral centers. MRI is widely used as a diagnostic tool in everyday practice, but it is unknown what the actual added value of MRI is. We studied the usefulness of MRI in the diagnostic process by measuring the change of confidence of the physician. Methods Physicians indicated confidence in their diagnosis before and after presentation of MR images using a visual analogue scale from 0-100%. Results Use of MRI increased the level of confidence by 3% in experienced clinicians and by 9% in inexperienced physicians. In 2/125 cases, MRI showed an unexpected finding. Conclusion MRI is a useful diagnostic tool in everyday practice of diagnosing cognitive disorders. PMID:27489558

  18. Microtesla MRI with dynamic nuclear polarization

    NASA Astrophysics Data System (ADS)

    Zotev, Vadim S.; Owens, Tuba; Matlashov, Andrei N.; Savukov, Igor M.; Gomez, John J.; Espy, Michelle A.

    2010-11-01

    Magnetic resonance imaging at microtesla fields is a promising imaging method that combines the pre-polarization technique and broadband signal reception by superconducting quantum interference device (SQUID) sensors to enable in vivo MRI at microtesla-range magnetic fields similar in strength to the Earth magnetic field. Despite significant advances in recent years, the potential of microtesla MRI for biomedical imaging is limited by its insufficient signal-to-noise ratio due to a relatively low sample polarization. Dynamic nuclear polarization (DNP) is a widely used approach that allows polarization enhancement by 2-4 orders of magnitude without an increase in the polarizing field strength. In this work, the first implementation of microtesla MRI with Overhauser DNP and SQUID signal detection is described. The first measurements of carbon-13 NMR spectra at microtesla fields are also reported. The experiments were performed at the measurement field of 96 μT, corresponding to Larmor frequency of 4 kHz for protons and 1 kHz for carbon-13. The Overhauser DNP was carried out at 3.5-5.7 mT fields using rf irradiation at 120 MHz. Objects for imaging included water phantoms and a cactus plant. Aqueous solutions of metabolically relevant sodium bicarbonate, pyruvate, alanine, and lactate, labeled with carbon-13, were used for NMR studies. All the samples were doped with TEMPO free radicals. The Overhauser DNP enabled nuclear polarization enhancement by factor as large as -95 for protons and as large as -200 for carbon-13, corresponding to thermal polarizations at 0.33 T and 1.1 T fields, respectively. These results demonstrate that SQUID-based microtesla MRI can be naturally combined with Overhauser DNP in one system, and that its signal-to-noise performance is greatly improved in this case. They also suggest that microtesla MRI can become an efficient tool for in vivo imaging of hyperpolarized carbon-13, produced by low-temperature dissolution DNP.

  19. Hyperoxia and Functional MRI.

    PubMed

    Bulte, Daniel

    2016-01-01

    Oxygen plays a fundamental role in functional magnetic resonance imaging (FMRI). Blood oxygenation level-dependent (BOLD) imaging is the foundation stone of all FMRI and is still the essential workhorse of the vast majority of FMRI procedures. Hemoglobin may provide the magnetic properties that allow the technique to work, but it is oxygen that allows the contrast to effectively be switched on or off, and it is oxygen that we are interested in tracking in order to observe the oxygen metabolism changes. In general the changes in venous oxygen saturation are observed in order to infer changes in the correlated mechanisms, which can include changes in cerebral blood flow, metabolism, and the fraction of inspired oxygen. By independently manipulating the fraction of inspired oxygen it is possible to alter the amount of dissolved oxygen in the plasma, the venous saturation, or even the blood flow. The effects that these changes have on the observed MRI signal can be either a help or a hindrance depending on how well the changes induced are understood. The administration of supplemental inspired oxygen is in a unique position to provide a flexible, noninvasive, inexpensive, patient-friendly addition to the MRI toolkit to enable investigations to look beyond statistics and regions of interest, and actually produce calibrated, targeted measurements of blood flow, metabolism or pathology. PMID:27343097

  20. Automatic Brachytherapy Seed Placement Under MRI Guidance

    PubMed Central

    Patriciu, Alexandru; Petrisor, Doru; Muntener, Michael; Mazilu, Dumitru; Schär, Michael; Stoianovici, Dan

    2011-01-01

    The paper presents a robotic method of performing low dose rate prostate brachytherapy under magnetic resonance imaging (MRI) guidance. The design and operation of a fully automated MR compatible seed injector is presented. This is used with the MrBot robot for transperineal percutaneous prostate access. A new image-registration marker and algorithms are also presented. The system is integrated and tested with a 3T MRI scanner. Tests compare three different registration methods, assess the precision of performing automated seed deployment, and use the seeds to assess the accuracy of needle targeting under image guidance. Under the ideal conditions of the in vitro experiments, results show outstanding image-guided needle and seed placement accuracy. PMID:17694871

  1. Intra voxel analysis in MRI

    NASA Astrophysics Data System (ADS)

    Ambrosanio, Michele; Baselice, Fabio; Ferraioli, Giampaolo; Pascazio, Vito

    2014-03-01

    A new application of Compressive Sensing (CS) in Magnetic Resonance Imaging (MRI) field is presented. In particular, first results of the Intra Voxel Analysis (IVA) technique are reported. The idea is to exploit CS peculiarities in order to distinguish different contributions inside the same resolution cell, instead of reconstructing images from not fully sampled k-space acquisition. Applied to MRI field, this means the possibility of estimating the presence of different tissues inside the same voxel, i.e. in one pixel of the obtained image. In other words, the method is the first attempt, as far as we know, of achieving Spectroscopy-like results starting from each pixel of MR images. In particular, tissues are distinguished each others by evaluating their spin-spin relaxation times. Within this manuscript, first results on clinical dataset, in particular a phantom made by aqueous solution and oil and an occipital brain lesion corresponding to a metastatic breast cancer nodule, are reported. Considering the phantom dataset, in particular focusing on the slice where the separation between water and oil occurs, the methodology is able to distinguish the two components with different spin-spin relaxation times. With respect to clinical dataset,focusing on a voxel of the lesion area, the approach is able to detect the presence of two tissues, namely the healthy and the cancer related ones, while in other location outside the lesion only the healthy tissue is detected. Of course, these are the first results of the proposed methodology, further studies on different types of clinical datasets are required in order to widely validate the approach. Although few datasets have been considered, results seem both interesting and promising.

  2. Dynamic MRI of small electrical activity.

    PubMed

    Song, Allen W; Truong, Trong-Kha; Woldorff, Marty

    2009-01-01

    Neuroscience methods entailing in vivo measurements of brain activity have greatly contributed to our understanding of brain function for the past decades, from the invasive early studies in animals using single-cell electrical recordings, to the noninvasive techniques in humans of scalp-recorded electroencephalography (EEG) and magnetoencephalography (MEG), positron emission tomography (PET), and, most recently, blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI). A central objective of these techniques is to measure neuronal activities with high spatial and temporal resolution. Each of these methods, however, has substantial limitations in this regard. Single-cell recording is invasive and only typically records cellular activity in a single location; EEG/MEG cannot generally provide accurate and unambiguous delineations of neuronal activation spatially; and the most sophisticated BOLD-based fMRI methods are still fundamentally limited by their dependence on the very slow hemodynamic responses upon which they are based. Even the latest neuroimaging methodology (e.g., multimodal EEG/fMRI) does not yet unambiguously provide accurate localization of neuronal activation spatially and temporally. There is hence a need to further develop noninvasive imaging methods that can directly image neuroelectric activity and thus truly achieve a high temporal resolution and spatial specificity in humans. Here, we discuss the theory, implementation, and potential utility of an MRI technique termed Lorentz effect imaging (LEI) that can detect spatially incoherent yet temporally synchronized, minute electrical activities in the neural amplitude range (microamperes) when they occur in a strong magnetic field. Moreover, we demonstrate with our preliminary results in phantoms and in vivo, the feasibility of imaging such activities with a temporal resolution on the order of milliseconds.

  3. Independent component analysis of instantaneous power-based fMRI.

    PubMed

    Zhong, Yuan; Zheng, Gang; Liu, Yijun; Lu, Guangming

    2014-01-01

    In functional magnetic resonance imaging (fMRI) studies using spatial independent component analysis (sICA) method, a model of "latent variables" is often employed, which is based on the assumption that fMRI data are linear mixtures of statistically independent signals. However, actual fMRI signals are nonlinear and do not automatically meet with the requirement of sICA. To provide a better solution to this problem, we proposed a novel approach termed instantaneous power based fMRI (ip-fMRI) for regularization of fMRI data. Given that the instantaneous power of fMRI signals is a scalar value, it should be a linear mixture that naturally satisfies the "latent variables" model. Based on our simulated data, the curves of accuracy and resulting receiver-operating characteristic curves indicate that the proposed approach is superior to the traditional fMRI in terms of accuracy and specificity by using sICA. Experimental results from human subjects have shown that spatial components of a hand movement task-induced activation reveal a brain network more specific to motor function by ip-fMRI than that by the traditional fMRI. We conclude that ICA decomposition of ip-fMRI may be used to localize energy signal changes in the brain and may have a potential to be applied to detection of brain activity.

  4. Independent Component Analysis of Instantaneous Power-Based fMRI

    PubMed Central

    Liu, Yijun; Lu, Guangming

    2014-01-01

    In functional magnetic resonance imaging (fMRI) studies using spatial independent component analysis (sICA) method, a model of “latent variables” is often employed, which is based on the assumption that fMRI data are linear mixtures of statistically independent signals. However, actual fMRI signals are nonlinear and do not automatically meet with the requirement of sICA. To provide a better solution to this problem, we proposed a novel approach termed instantaneous power based fMRI (ip-fMRI) for regularization of fMRI data. Given that the instantaneous power of fMRI signals is a scalar value, it should be a linear mixture that naturally satisfies the “latent variables” model. Based on our simulated data, the curves of accuracy and resulting receiver-operating characteristic curves indicate that the proposed approach is superior to the traditional fMRI in terms of accuracy and specificity by using sICA. Experimental results from human subjects have shown that spatial components of a hand movement task-induced activation reveal a brain network more specific to motor function by ip-fMRI than that by the traditional fMRI. We conclude that ICA decomposition of ip-fMRI may be used to localize energy signal changes in the brain and may have a potential to be applied to detection of brain activity. PMID:24738008

  5. The physics of functional magnetic resonance imaging (fMRI)

    NASA Astrophysics Data System (ADS)

    Buxton, Richard B.

    2013-09-01

    Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology.

  6. The physics of functional magnetic resonance imaging (fMRI)

    PubMed Central

    Buxton, Richard B

    2015-01-01

    Functional magnetic resonance imaging (fMRI) is a methodology for detecting dynamic patterns of activity in the working human brain. Although the initial discoveries that led to fMRI are only about 20 years old, this new field has revolutionized the study of brain function. The ability to detect changes in brain activity has a biophysical basis in the magnetic properties of deoxyhemoglobin, and a physiological basis in the way blood flow increases more than oxygen metabolism when local neural activity increases. These effects translate to a subtle increase in the local magnetic resonance signal, the blood oxygenation level dependent (BOLD) effect, when neural activity increases. With current techniques, this pattern of activation can be measured with resolution approaching 1 mm3 spatially and 1 s temporally. This review focuses on the physical basis of the BOLD effect, the imaging methods used to measure it, the possible origins of the physiological effects that produce a mismatch of blood flow and oxygen metabolism during neural activation, and the mathematical models that have been developed to understand the measured signals. An overarching theme is the growing field of quantitative fMRI, in which other MRI methods are combined with BOLD methods and analyzed within a theoretical modeling framework to derive quantitative estimates of oxygen metabolism and other physiological variables. That goal is the current challenge for fMRI: to move fMRI from a mapping tool to a quantitative probe of brain physiology. PMID:24006360

  7. SU-F-BRF-10: Deformable MRI to CT Validation Employing Same Day Planning MRI for Surrogate Analysis

    SciTech Connect

    Padgett, K; Stoyanova, R; Johnson, P; Dogan, N; Pollack, A; Piper, J; Javorek, A

    2014-06-15

    Purpose: To compare rigid and deformable registrations of the prostate in the multi-modality setting (diagnostic-MRI to planning-CT) by utilizing a planning-MRI as a surrogate. The surrogate allows for the direct quantitative analysis which can be difficult in the multi-modality domain where intensity mapping differs. Methods: For ten subjects, T2 fast-spin-echo images were acquired at two different time points, the first several weeks prior to planning (diagnostic-MRI) and the second on the same day in which the planning CT was collected (planning-MRI). Significant effort in patient positioning and bowel/bladder preparation was undertaken to minimize distortion of the prostate in all datasets. The diagnostic-MRI was deformed to the planning-CT utilizing a commercially available deformable registration algorithm synthesized from local registrations. The deformed MRI was then rigidly aligned to the planning MRI which was used as the surrogate for the planning-CT. Agreement between the two MRI datasets was scored using intensity based metrics including Pearson correlation and normalized mutual information, NMI. A local analysis was performed by looking only within the prostate, proximal seminal vesicles, penile bulb and combined areas. A similar method was used to assess a rigid registration between the diagnostic-MRI and planning-CT. Results: Utilizing the NMI, the deformable registrations were superior to the rigid registrations in 9 of 10 cases demonstrating a 15.94% improvement (p-value < 0.001) within the combined area. The Pearson correlation showed similar results with the deformable registration superior in the same number of cases and demonstrating a 6.97% improvement (p-value <0.011). Conclusion: Validating deformable multi-modality registrations using spatial intensity based metrics is difficult due to the inherent differences in intensity mapping. This population provides an ideal testing ground for MRI to CT deformable registrations by obviating the need

  8. Real time dynamic MRI by exploiting spatial and temporal sparsity.

    PubMed

    Chen, Chen; Li, Yeqing; Axel, Leon; Huang, Junzhou

    2016-05-01

    Online imaging requires that the reconstruction of current frame only depends on the previous frames, and real time imaging is the desired case. In this work, we propose a novel scheme for real time dynamic magnetic resonance imaging (dMRI) reconstruction. Different from previous methods, the reconstructions of the second frame to the last frame are independent in our scheme, which only require the first frame as the reference image. Therefore, this scheme can be naturally implemented in parallel. After the first frame is reconstructed, all the later frames can be processed as soon as the k-space data are acquired. As an extension of the conventional spatial total variation, a new online model called dynamic total variation is used to exploit the sparsity on both spatial and temporal domains in dMRI. In real time dMRI, each frame is required to be reconstructed very fast. We then design a novel reweighted least squares algorithm to solve the challenging problem. Motivated by the special structure of partial Fourier transform in sparse MRI, this algorithm is accelerated by the preconditioned conjugate gradient descent method. The proposed method is compared with 4 state-of-the-art online and offline methods on two in-vivo cardiac dMRI datasets. The experimental results show that our method significantly outperforms previous online methods, and is comparable to the offline methods in terms of reconstruction accuracy. PMID:26578303

  9. Magnetostimulation in MRI.

    PubMed

    Irnich, W; Schmitt, F

    1995-05-01

    In national and international bodies, there is active discussion of appropriate safety regulations of levels of magnetic field strength in MRI. Present limits are usually expressed in terms of the switching rate dB/dt, but the validity of this is open to debate. Application of the fundamental law of electrostimulation is well-established, both on theoretical and experimental grounds. Application of this law, in combination with Maxwell's law, yields a very simple equation that we call the fundamental law of magnetostimulation. This law has the hyperbolic form of a strength-duration curve and allows an estimation of the lowest possible value of the magnetic flux density capable of stimulating nerves and muscles. Calculations prove that the threshold for heart excitation is much higher than those for nerve and muscle stimulations. Experimental results from us and other authors confirm the correctness of the derived laws for magnetostimulation. In light of these findings, proposed safety limits should be reconsidered. PMID:7596265

  10. An RF dosimeter for independent SAR measurement in MRI scanners

    SciTech Connect

    Qian, Di; Bottomley, Paul A.; El-Sharkawy, AbdEl-Monem M.; Edelstein, William A.

    2013-12-15

    Purpose: The monitoring and management of radio frequency (RF) exposure is critical for ensuring magnetic resonance imaging (MRI) safety. Commercial MRI scanners can overestimate specific absorption rates (SAR) and improperly restrict clinical MRI scans or the application of new MRI sequences, while underestimation of SAR can lead to tissue heating and thermal injury. Accurate scanner-independent RF dosimetry is essential for measuring actual exposure when SAR is critical for ensuring regulatory compliance and MRI safety, for establishing RF exposure while evaluating interventional leads and devices, and for routine MRI quality assessment by medical physicists. However, at present there are no scanner-independent SAR dosimeters. Methods: An SAR dosimeter with an RF transducer comprises two orthogonal, rectangular copper loops and a spherical MRI phantom. The transducer is placed in the magnet bore and calibrated to approximate the resistive loading of the scanner's whole-body birdcage RF coil for human subjects in Philips, GE and Siemens 3 tesla (3T) MRI scanners. The transducer loop reactances are adjusted to minimize interference with the transmit RF field (B{sub 1}) at the MRI frequency. Power from the RF transducer is sampled with a high dynamic range power monitor and recorded on a computer. The deposited power is calibrated and tested on eight different MRI scanners. Whole-body absorbed power vs weight and body mass index (BMI) is measured directly on 26 subjects. Results: A single linear calibration curve sufficed for RF dosimetry at 127.8 MHz on three different Philips and three GE 3T MRI scanners. An RF dosimeter operating at 123.2 MHz on two Siemens 3T scanners required a separate transducer and a slightly different calibration curve. Measurement accuracy was ∼3%. With the torso landmarked at the xiphoid, human adult whole‑body absorbed power varied approximately linearly with patient weight and BMI. This indicates that whole-body torso SAR is on

  11. fMRI adaptation revisited.

    PubMed

    Larsson, Jonas; Solomon, Samuel G; Kohn, Adam

    2016-07-01

    Adaptation has been widely used in functional magnetic imaging (fMRI) studies to infer neuronal response properties in human cortex. fMRI adaptation has been criticized because of the complex relationship between fMRI adaptation effects and the multiple neuronal effects that could underlie them. Many of the longstanding concerns about fMRI adaptation have received empirical support from neurophysiological studies over the last decade. We review these studies here, and also consider neuroimaging studies that have investigated how fMRI adaptation effects are influenced by high-level perceptual processes. The results of these studies further emphasize the need to interpret fMRI adaptation results with caution, but they also provide helpful guidance for more accurate interpretation and better experimental design. In addition, we argue that rather than being used as a proxy for measurements of neuronal stimulus selectivity, fMRI adaptation may be most useful for studying population-level adaptation effects across cortical processing hierarchies.

  12. Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain

    SciTech Connect

    Andreasen, Daniel; Van Leemput, Koen; Hansen, Rasmus H.; Andersen, Jon A. L.; Edmund, Jens M.

    2015-04-15

    Purpose: In radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, the information on electron density must be derived from the MRI scan by creating a so-called pseudo computed tomography (pCT). This is a nontrivial task, since the voxel-intensities in an MRI scan are not uniquely related to electron density. To solve the task, voxel-based or atlas-based models have typically been used. The voxel-based models require a specialized dual ultrashort echo time MRI sequence for bone visualization and the atlas-based models require deformable registrations of conventional MRI scans. In this study, we investigate the potential of a patch-based method for creating a pCT based on conventional T{sub 1}-weighted MRI scans without using deformable registrations. We compare this method against two state-of-the-art methods within the voxel-based and atlas-based categories. Methods: The data consisted of CT and MRI scans of five cranial RT patients. To compare the performance of the different methods, a nested cross validation was done to find optimal model parameters for all the methods. Voxel-wise and geometric evaluations of the pCTs were done. Furthermore, a radiologic evaluation based on water equivalent path lengths was carried out, comparing the upper hemisphere of the head in the pCT and the real CT. Finally, the dosimetric accuracy was tested and compared for a photon treatment plan. Results: The pCTs produced with the patch-based method had the best voxel-wise, geometric, and radiologic agreement with the real CT, closely followed by the atlas-based method. In terms of the dosimetric accuracy, the patch-based method had average deviations of less than 0.5% in measures related to target coverage. Conclusions: We showed that a patch-based method could generate an accurate pCT based on conventional T{sub 1}-weighted MRI sequences and without deformable registrations. In our evaluations, the method performed better than existing voxel-based and

  13. Prostate MRI – an update for the referring urologist

    PubMed Central

    Jakuciński, Maciej; Królicki, Leszek

    2016-01-01

    Introduction Prostate MRI is a new and important tool which has a role in prostate cancer guidelines worldwide. The amount of articles published and studies currently taking place on the subject requires urologists to understand how the examination is performed and its possible applications. This article explains prostate MRI and standardized reporting schemes, as well as its applications according to patients’ staging and history. Material and methods The use of prostate MRI prior to biopsy, MRI-guided biopsy and its use in active surveillance, surgery staging and planning, as well as in cases with biochemical recurrence are discussed. Results The application of prostate MRI are not limited to initial diagnosis, but also has a developing role in biopsy and planning further treatment. Recently, its diagnostic applications have been included in EAU prostate cancer guidelines and new applications are in development. Conclusions Practicing urologists are seeing an emerging role of MRI in prostate cancer. Its current and future applications may have an impact on patient care, which mandates healthcare professionals to be vigilant about the method's new developments. PMID:27551553

  14. Tissue characterization in cerebral ischemia using multiparameter MRI

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Hammoud, Rabih; Jacobs, Michael A.; Patel, Suresh C.; Mitsias, Panayiotis D.; Pasnoor, Mamatha; Knight, Robert; Zheng, Zhang G.; Lu, Mei; Chopp, Michael

    2001-05-01

    After pre-processing and segmentation, the proposed method scores tissue regions between 1 and N. Score 1 is assigned to normal white matter and score N to CSF. Lesion zones are assigned a score based on their relative levels of similarities to white matter and CSF. To evaluate the method, 15 rats were imaged by a 7T MRI system at one of the three time points (acute, sub-acute, chronic) after MCA occlusion. Then, they were sacrificed and their brains were sliced and prepared for histological studies. MRI of 2 or 3 slices of each rat brain, using 2 DWI (b equals 400, b equals 800), 1 PDWI, 1 T2WI, and 1 T1WI, was used and an MRI score between 1 and 100 (N equals 100) was found for each region. Segmented regions were mapped onto the histology images and were scored by an experienced pathologist, from 1 to 10. MRI scores were validated using histology scores. To this end, correlation coefficients between the two scores (MRI and histology) were found. The results showed excellent correlations between MRI and histology scores at different time points.

  15. Analytic heuristics for a fast DSC-MRI

    NASA Astrophysics Data System (ADS)

    Virgulin, M.; Castellaro, M.; Marcuzzi, F.; Grisan, E.

    2014-03-01

    Hemodynamics of the human brain may be studied with Dynamic Susceptibility Contrast MRI (DSC-MRI) imaging. The sequence of volumes obtained exhibits a strong spatiotemporal correlation, that can be exploited to predict which measurements will bring mostly the new information contained in the next frames. In general, the sampling speed is an important issue in many applications of the MRI, so that the focus of many current researches is to study methods to reduce the number of measurement samples needed for each frame without degrading the image quality. For the DSC-MRI, the frequency under-sampling of single frame can be exploited to make more frequent space or time acquisitions, thus increasing the time resolution and allowing the analysis of fast dynamics not yet observed. Generally (and also for MRI), the recovery of sparse signals has been achieved by Compressed Sensing (CS) techniques, which are based on statistical properties rather than deterministic ones.. By studying analytically the compound Fourier+Wavelet transform, involved in the processes of reconstruction and sparsification of MR images, we propose a deterministic technique for a rapid-MRI, exploiting the relations between the wavelet sparse representation of the recovered and the frequency samples. We give results on real images and on artificial phantoms with added noise, showing the superiority of the methods both with respect to classical Iterative Hard Thresholding (IHT) and to Location Constraint Approximate Message Passing (LCAMP) reconstruction algorithms.

  16. Fetal MRI: A Technical Update with Educational Aspirations

    PubMed Central

    Gholipour, Ali; Estroff, Judith A.; Barnewolt, Carol E.; Robertson, Richard L.; Grant, P. Ellen; Gagoski, Borjan; Warfield, Simon K.; Afacan, Onur; Connolly, Susan A.; Neil, Jeffrey J.; Wolfberg, Adam; Mulkern, Robert V.

    2015-01-01

    Fetal magnetic resonance imaging (MRI) examinations have become well-established procedures at many institutions and can serve as useful adjuncts to ultrasound (US) exams when diagnostic doubts remain after US. Due to fetal motion, however, fetal MRI exams are challenging and require the MR scanner to be used in a somewhat different mode than that employed for more routine clinical studies. Herein we review the techniques most commonly used, and those that are available, for fetal MRI with an emphasis on the physics of the techniques and how to deploy them to improve success rates for fetal MRI exams. By far the most common technique employed is single-shot T2-weighted imaging due to its excellent tissue contrast and relative immunity to fetal motion. Despite the significant challenges involved, however, many of the other techniques commonly employed in conventional neuro- and body MRI such as T1 and T2*-weighted imaging, diffusion and perfusion weighted imaging, as well as spectroscopic methods remain of interest for fetal MR applications. An effort to understand the strengths and limitations of these basic methods within the context of fetal MRI is made in order to optimize their use and facilitate implementation of technical improvements for the further development of fetal MR imaging, both in acquisition and post-processing strategies. PMID:26225129

  17. Tissue Tracking: Applications for Brain MRI Classification

    PubMed Central

    Melonakos, John; Gao, Yi; Tannenbaum, Allen

    2013-01-01

    Bayesian classification methods have been extensively used in a variety of image processing applications, including medical image analysis. The basic procedure is to combine data-driven knowledge in the likelihood terms with clinical knowledge in the prior terms to classify an image into a pre-determined number of classes. In many applications, it is difficult to construct meaningful priors and, hence, homogeneous priors are assumed. In this paper, we show how expectation-maximization weights and neighboring posterior probabilities may be combined to make intuitive use of the Bayesian priors. Drawing upon insights from computer vision tracking algorithms, we cast the problem in a tissue tracking framework. We show results of our algorithm on the classification of gray and white matter along with surrounding cerebral spinal fluid in brain MRI scans. We show results of our algorithm on 20 brain MRI datasets along with validation against expert manual segmentations. PMID:24392193

  18. Tissue tracking: applications for brain MRI classification

    NASA Astrophysics Data System (ADS)

    Melonakos, John; Gao, Yi; Tannenbaum, Allen

    2007-03-01

    Bayesian classification methods have been extensively used in a variety of image processing applications, including medical image analysis. The basic procedure is to combine data-driven knowledge in the likelihood terms with clinical knowledge in the prior terms to classify an image into a pre-determined number of classes. In many applications, it is difficult to construct meaningful priors and, hence, homogeneous priors are assumed. In this paper, we show how expectation-maximization weights and neighboring posterior probabilities may be combined to make intuitive use of the Bayesian priors. Drawing upon insights from computer vision tracking algorithms, we cast the problem in a tissue tracking framework. We show results of our algorithm on the classification of gray and white matter along with surrounding cerebral spinal fluid in brain MRI scans. We show results of our algorithm on 20 brain MRI datasets along with validation against expert manual segmentations.

  19. Improving tumour heterogeneity MRI assessment with histograms

    PubMed Central

    Just, N

    2014-01-01

    By definition, tumours are heterogeneous. They are defined by marked differences in cells, microenvironmental factors (oxygenation levels, pH, VEGF, VPF and TGF-α) metabolism, vasculature, structure and function that in turn translate into heterogeneous drug delivery and therapeutic outcome. Ways to estimate quantitatively tumour heterogeneity can improve drug discovery, treatment planning and therapeutic responses. It is therefore of paramount importance to have reliable and reproducible biomarkers of cancerous lesions' heterogeneity. During the past decade, the number of studies using histogram approaches increased drastically with various magnetic resonance imaging (MRI) techniques (DCE-MRI, DWI, SWI etc.) although information on tumour heterogeneity remains poorly exploited. This fact can be attributed to a poor knowledge of the available metrics and of their specific meaning as well as to the lack of literature references to standardised histogram methods with which surrogate markers of heterogeneity can be compared. This review highlights the current knowledge and critical advances needed to investigate and quantify tumour heterogeneity. The key role of imaging techniques and in particular the key role of MRI for an accurate investigation of tumour heterogeneity is reviewed with a particular emphasis on histogram approaches and derived methods. PMID:25268373

  20. Measuring glomerular number from kidney MRI images

    NASA Astrophysics Data System (ADS)

    Thiagarajan, Jayaraman J.; Natesan Ramamurthy, Karthikeyan; Kanberoglu, Berkay; Frakes, David; Bennett, Kevin; Spanias, Andreas

    2016-03-01

    Measuring the glomerular number in the entire, intact kidney using non-destructive techniques is of immense importance in studying several renal and systemic diseases. Commonly used approaches either require destruction of the entire kidney or perform extrapolation from measurements obtained from a few isolated sections. A recent magnetic resonance imaging (MRI) method, based on the injection of a contrast agent (cationic ferritin), has been used to effectively identify glomerular regions in the kidney. In this work, we propose a robust, accurate, and low-complexity method for estimating the number of glomeruli from such kidney MRI images. The proposed technique has a training phase and a low-complexity testing phase. In the training phase, organ segmentation is performed on a few expert-marked training images, and glomerular and non-glomerular image patches are extracted. Using non-local sparse coding to compute similarity and dissimilarity graphs between the patches, the subspace in which the glomerular regions can be discriminated from the rest are estimated. For novel test images, the image patches extracted after pre-processing are embedded using the discriminative subspace projections. The testing phase is of low computational complexity since it involves only matrix multiplications, clustering, and simple morphological operations. Preliminary results with MRI data obtained from five kidneys of rats show that the proposed non-invasive, low-complexity approach performs comparably to conventional approaches such as acid maceration and stereology.

  1. Evaluating joint-space narrowing and cartilage loss in rheumatoid arthritis by using MRI

    PubMed Central

    2012-01-01

    Introduction Magnetic resonance imaging (MRI) has been shown to be superior to radiography (XR) for assessing synovitis, osteitis, and bone erosion in rheumatoid arthritis (RA), particularly in clinical trials. However, relatively little has been reported on the ability of MRI to evaluate articular cartilage loss, or joint-space narrowing (JSN), in the hands and wrists. In a previous study, we adapted the nine-point Genant-modified Sharp XR-JSN score for use with MRI (MRI-JSN). In this study, we compare MRI-JSN with XR-JSN by using images from two multicenter clinical trials. Methods Baseline XR and 1.5-Tesla MR images of one hand and wrist from each of 47 subjects with RA enrolled in one of two multicenter clinical trials were evaluated by using the XR-JSN and MRI-JSN methods by a single radiologist experienced in the two methods. Radiographs and MR images were read independently on different occasions. Results In total, 575 of 611 joints were compared (one metacarpophalangeal joint of the thumb and 35 proximal interphalangeal joints were outside the MRI field of view and could not be assessed). The 22 (47%) subjects showed JSN with both XR and MRI, and 25 (53%) subjects showed no JSN with either method. No subject showed JSN with only one or the other method. MRI showed high agreement with XR (intraclass correlation coefficient = 0.83). Sensitivity of MRI for JSN, by using XR as the gold standard, was 0.94; specificity was 0.91; accuracy was 0.91; positive predictive value was 0.64; and negative predictive value was 0.99. Conclusions This validation exercise suggests that MRI JSN scoring may offer a viable alternative to XR JSN scoring in multicenter clinical trials of RA. However, the relative longitudinal sensitivity of MRI to change and the ability to discriminate therapeutic effect on JSN were not evaluated in this study. PMID:22647501

  2. Quantitative Histological Validation of Diffusion MRI Fiber Orientation Distributions in the Rat Brain

    PubMed Central

    de Crespigny, Alex; Bolstad, Ingeborg; D'Arceuil, Helen; Bjaalie, Jan G.; Dale, Anders M.

    2010-01-01

    Diffusion MRI (dMRI) is widely used to measure microstructural features of brain white matter, but commonly used dMRI measures have limited capacity to resolve the orientation structure of complex fiber architectures. While several promising new approaches have been proposed, direct quantitative validation of these methods against relevant histological architectures remains missing. In this study, we quantitatively compare neuronal fiber orientation distributions (FODs) derived from ex vivo dMRI data against histological measurements of rat brain myeloarchitecture using manual recordings of individual myelin stained fiber orientations. We show that accurate FOD estimates can be obtained from dMRI data, even in regions with complex architectures of crossing fibers with an intrinsic orientation error of approximately 5–6 degrees in these regions. The reported findings have implications for both clinical and research studies based on dMRI FOD measures, and provide an important biological benchmark for improved FOD reconstruction and fiber tracking methods. PMID:20062822

  3. Three-dimensional MRI-linac intra-fraction guidance using multiple orthogonal cine-MRI planes

    NASA Astrophysics Data System (ADS)

    Bjerre, Troels; Crijns, Sjoerd; Rosenschöld, Per Munck af; Aznar, Marianne; Specht, Lena; Larsen, Rasmus; Keall, Paul

    2013-07-01

    The introduction of integrated MRI-radiation therapy systems will offer live intra-fraction imaging. We propose a feasible low-latency multi-plane MRI-linac guidance strategy. In this work we demonstrate how interleaved acquired, orthogonal cine-MRI planes can be used for low-latency tracking of the 3D trajectory of a soft-tissue target structure. The proposed strategy relies on acquiring a pre-treatment 3D breath-hold scan, extracting a 3D target template and performing template matching between this 3D template and pairs of orthogonal 2D cine-MRI planes intersecting the target motion path. For a 60 s free-breathing series of orthogonal cine-MRI planes, we demonstrate that the method was capable of accurately tracking the respiration related 3D motion of the left kidney. Quantitative evaluation of the method using a dataset designed for this purpose revealed a translational error of 1.15 mm for a translation of 39.9 mm. We have demonstrated how interleaved acquired, orthogonal cine-MRI planes can be used for online tracking of soft-tissue target volumes.

  4. Three-dimensional MRI-linac intra-fraction guidance using multiple orthogonal cine-MRI planes.

    PubMed

    Bjerre, Troels; Crijns, Sjoerd; af Rosenschöld, Per Munck; Aznar, Marianne; Specht, Lena; Larsen, Rasmus; Keall, Paul

    2013-07-21

    The introduction of integrated MRI-radiation therapy systems will offer live intra-fraction imaging. We propose a feasible low-latency multi-plane MRI-linac guidance strategy. In this work we demonstrate how interleaved acquired, orthogonal cine-MRI planes can be used for low-latency tracking of the 3D trajectory of a soft-tissue target structure. The proposed strategy relies on acquiring a pre-treatment 3D breath-hold scan, extracting a 3D target template and performing template matching between this 3D template and pairs of orthogonal 2D cine-MRI planes intersecting the target motion path. For a 60 s free-breathing series of orthogonal cine-MRI planes, we demonstrate that the method was capable of accurately tracking the respiration related 3D motion of the left kidney. Quantitative evaluation of the method using a dataset designed for this purpose revealed a translational error of 1.15 mm for a translation of 39.9 mm. We have demonstrated how interleaved acquired, orthogonal cine-MRI planes can be used for online tracking of soft-tissue target volumes. PMID:23807514

  5. On the feasibility of concurrent human TMS-EEG-fMRI measurements.

    PubMed

    Peters, Judith C; Reithler, Joel; Schuhmann, Teresa; de Graaf, Tom; Uludag, Kâmil; Goebel, Rainer; Sack, Alexander T

    2013-02-01

    Simultaneously combining the complementary assets of EEG, functional MRI (fMRI), and transcranial magnetic stimulation (TMS) within one experimental session provides synergetic results, offering insights into brain function that go beyond the scope of each method when used in isolation. The steady increase of concurrent EEG-fMRI, TMS-EEG, and TMS-fMRI studies further underlines the added value of such multimodal imaging approaches. Whereas concurrent EEG-fMRI enables monitoring of brain-wide network dynamics with high temporal and spatial resolution, the combination with TMS provides insights in causal interactions within these networks. Thus the simultaneous use of all three methods would allow studying fast, spatially accurate, and distributed causal interactions in the perturbed system and its functional relevance for intact behavior. Concurrent EEG-fMRI, TMS-EEG, and TMS-fMRI experiments are already technically challenging, and the three-way combination of TMS-EEG-fMRI might yield additional difficulties in terms of hardware strain or signal quality. The present study explored the feasibility of concurrent TMS-EEG-fMRI studies by performing safety and quality assurance tests based on phantom and human data combining existing commercially available hardware. Results revealed that combined TMS-EEG-fMRI measurements were technically feasible, safe in terms of induced temperature changes, allowed functional MRI acquisition with comparable image quality as during concurrent EEG-fMRI or TMS-fMRI, and provided artifact-free EEG before and from 300 ms after TMS pulse application. Based on these empirical findings, we discuss the conceptual benefits of this novel complementary approach to investigate the working human brain and list a number of precautions and caveats to be heeded when setting up such multimodal imaging facilities with current hardware.

  6. Metalloprotein-based MRI probes

    PubMed Central

    Matsumoto, Yuri; Jasanoff, Alan

    2013-01-01

    Metalloproteins have long been recognized as key determinants of endogenous contrast in magnetic resonance imaging (MRI) of biological subjects. More recently, both natural and engineered metalloproteins have been harnessed as biotechnological tools to probe gene expression, enzyme activity, and analyte concentrations by MRI. Metalloprotein MRI probes are paramagnetic and function by analogous mechanisms to conventional gadolinium or iron oxide-based MRI contrast agents. Compared with synthetic agents, metalloproteins typically offer worse sensitivity, but the possibilities of using protein engineering and targeted gene expression approaches in conjunction with metalloprotein contrast agents are powerful and sometimes definitive strengths. This review summarizes theoretical and practical aspects of metalloprotein-based contrast agents, and discusses progress in the exploitation of these proteins for molecular imaging applications. PMID:23376346

  7. Metalloprotein-based MRI probes.

    PubMed

    Matsumoto, Yuri; Jasanoff, Alan

    2013-04-17

    Metalloproteins have long been recognized as key determinants of endogenous contrast in magnetic resonance imaging (MRI) of biological subjects. More recently, both natural and engineered metalloproteins have been harnessed as biotechnological tools to probe gene expression, enzyme activity, and analyte concentrations by MRI. Metalloprotein MRI probes are paramagnetic and function by analogous mechanisms to conventional gadolinium or iron oxide-based MRI contrast agents. Compared with synthetic agents, metalloproteins typically offer worse sensitivity, but the possibilities of using protein engineering and targeted gene expression approaches in conjunction with metalloprotein contrast agents are powerful and sometimes definitive strengths. This review summarizes theoretical and practical aspects of metalloprotein-based contrast agents, and discusses progress in the exploitation of these proteins for molecular imaging applications.

  8. Practical Applications of in Vivo and ex Vivo MRI in Toxicologic Pathology Using a Novel High-performance Compact MRI System.

    PubMed

    Tempel-Brami, Catherine; Schiffenbauer, Yael S; Nyska, Abraham; Ezov, Nati; Spector, Itai; Abramovitch, Rinat; Maronpot, Robert R

    2015-07-01

    Magnetic resonance imaging (MRI) is widely used in preclinical research and drug development and is a powerful noninvasive method for assessment of phenotypes and therapeutic efficacy in murine models of disease. In vivo MRI provides an opportunity for longitudinal evaluation of tissue changes and phenotypic expression in experimental animal models. Ex vivo MRI of fixed samples permits a thorough examination of multiple digital slices while leaving the specimen intact for subsequent conventional hematoxylin and eosin (H&E) histology. With the advent of new compact MRI systems that are designed to operate in most conventional labs without the cost, complexity, and infrastructure needs of conventional MRI systems, the possibility of MRI becoming a practical modality is now viable. The purpose of this study was to investigate the capabilities of a new compact, high-performance MRI platform (M2™; Aspect Imaging, Israel) as it relates to preclinical toxicology studies. This overview will provide examples of major organ system pathologies with an emphasis on how compact MRI can serve as an important adjunct to conventional pathology by nondestructively providing 3-dimensional (3-D) digital data sets, detailed morphological insights, and quantitative information. Comparative data using compact MRI for both in vivo and ex vivo are provided as well as validation using conventional H&E.

  9. Performance Comparison of 1.5 T Endorectal Coil MRI with Non-Endorectal Coil 3.0 T MRI in Patients with Prostate Cancer

    PubMed Central

    Shah, Zarine K.; Elias, Saba N.; Abaza, Ronney; Zynger, Debra L.; DeRenne, Lawrence A.; Knopp, Michael V.; Guo, Beibei; Schurr, Ryan; Heymsfield, Steven B.; Jia, Guang

    2015-01-01

    Rationale and Objectives To compare prostate morphology, image quality, and diagnostic performance of 1.5 T endorectal coil MRI and 3.0 T non-endorectal coil MRI in patients with prostate cancer. Materials and Methods MR images obtained of 83 patients with prostate cancer using 1.5 T MRI systems with an endorectal coil were compared to images collected from 83 patients with a 3.0 T MRI system. Prostate diameters were measured and image quality was evaluated by one ABR-certified radiologist (Reader 1) and one ABR-certified diagnostic medical physicist (Reader 2). The likelihood of the peripheral zone cancer presence in each sextant and local extent were rated and compared with histopathologic findings. Results Prostate anterior-posterior diameter measured by both readers was significantly shorter with 1.5 T endorectal MRI than with 3.0 T MRI. The overall image quality score difference was significant only for Reader 1. Both readers found that the two MRI systems provided similar diagnostic accuracy in cancer localization, extraprostatic extension, and seminal vesicle involvement. Conclusion Non-endorectal coil 3.0 T MRI provides prostate images that are natural in shape and that have comparable image quality to those obtained at 1.5 T with an endorectal coil, but not superior diagnostic performance. These findings suggest an opportunity exists for improving technical aspects of 3.0 T prostate MRI. PMID:25579637

  10. MRI and intraocular tamponade media.

    PubMed

    Manfrè, L; Fabbri, G; Avitabile, T; Biondi, P; Reibaldi, A; Pero, G

    1993-01-01

    Thirteen patients who underwent surgery for retinal detachment and injection of intraocular tamponade media (silicone oil, fluorosilicone oil, or perfluorocarbon liquid) underwent magnetic resonance imaging (MRI), using spin-echo T1- and T2-weighted images. The ophthalmic tamponade media showed different signal intensity, according to their chemical structure. Unlike ophthalmoscopy or ultrasonography, MRI showed no oil-related artefact, making possible recognition of recurrent retinal detachment.

  11. High temporal resolution functional MRI with partial separability model.

    PubMed

    Ngo, Giang-Chau; Holtrop, Joseph L; Fu, Maojing; Lam, Fan; Sutton, Bradley P

    2015-01-01

    Even though the hemodynamic response is a slow phenomenon, high temporal resolution in functional fMRI can enable better differentiation between the signal of interest and physiological noise or increase the statistical power of functional studies. To increase the temporal resolution, several methods have been developed to decrease the repetition time, TR, such as simultaneous multi-slice imaging and MR encephalography approaches. In this work, a method using a fast acquisition and a partial separability model is presented to achieve a multi-slice fMRI protocol at a temporal resolution of 75 ms. The method is demonstrated on a visual block task. PMID:26738022

  12. Magnetization transfer prepared gradient echo MRI for CEST imaging.

    PubMed

    Dai, Zhuozhi; Ji, Jim; Xiao, Gang; Yan, Gen; Li, Shengkai; Zhang, Guishan; Lin, Yan; Shen, Zhiwei; Wu, Renhua

    2014-01-01

    Chemical exchange saturation transfer (CEST) is an emerging MRI contrast mechanism that is capable of noninvasively imaging dilute CEST agents and local properties such as pH and temperature, augmenting the routine MRI methods. However, the routine CEST MRI includes a long RF saturation pulse followed by fast image readout, which is associated with high specific absorption rate and limited spatial resolution. In addition, echo planar imaging (EPI)-based fast image readout is prone to image distortion, particularly severe at high field. To address these limitations, we evaluated magnetization transfer (MT) prepared gradient echo (GRE) MRI for CEST imaging. We proved the feasibility using numerical simulations and experiments in vitro and in vivo. Then we optimized the sequence by serially evaluating the effects of the number of saturation steps, MT saturation power (B1), GRE readout flip angle (FA), and repetition time (TR) upon the CEST MRI, and further demonstrated the endogenous amide proton CEST imaging in rats brains (n = 5) that underwent permanent middle cerebral artery occlusion. The CEST images can identify ischemic lesions in the first 3 hours after occlusion. In summary, our study demonstrated that the readily available MT-prepared GRE MRI, if optimized, is CEST-sensitive and remains promising for translational CEST imaging. PMID:25384020

  13. Clinical Correlation between Perverted Nystagmus and Brain MRI Abnormal Findings

    PubMed Central

    Han, Won-Gue; Yoon, Hee-Chul; Kim, Tae-Min; Rah, Yoon Chan

    2016-01-01

    Background and Objectives To analyze the clinical correlation between perverted nystagmus and brain magnetic resonance imaging (MRI) abnormal findings and to evaluate whether perverted nystagmus is clinically significant results of brain abnormal lesions or not. Subjects and Methods We performed medical charts review from January 2008 to July 2014, retrospectively. Patients who were suspected central originated vertigo at Frenzel goggles test were included among patients who visited our hospital. To investigate the correlation with nystagmus suspected central originated vertigo and brain MRI abnormal findings, we confirmed whether performing brain MRI or not. Then we exclude that patients not performed brain MRI. Results The number of patients with perverted nystagmus was 15, upbeating was 1 and down-beating was 14. Among these patients, 5 patients have brain MRI abnormal findings. However, 2 patients with MRI abnormal findings were not associated correctly with perverted nystagmus and only 3 patients with perverted nystagmus were considered central originated vertigo and further evaluation and treatment was performed by the department of neurology. Conclusions Perverted nystagmus was considered to the abnormalities at brain lesions, especially cerebellum, but neurologic symptoms and further evaluation were needed for exact diagnosis of central originated vertigo.

  14. Clinical Correlation between Perverted Nystagmus and Brain MRI Abnormal Findings

    PubMed Central

    Han, Won-Gue; Yoon, Hee-Chul; Kim, Tae-Min; Rah, Yoon Chan

    2016-01-01

    Background and Objectives To analyze the clinical correlation between perverted nystagmus and brain magnetic resonance imaging (MRI) abnormal findings and to evaluate whether perverted nystagmus is clinically significant results of brain abnormal lesions or not. Subjects and Methods We performed medical charts review from January 2008 to July 2014, retrospectively. Patients who were suspected central originated vertigo at Frenzel goggles test were included among patients who visited our hospital. To investigate the correlation with nystagmus suspected central originated vertigo and brain MRI abnormal findings, we confirmed whether performing brain MRI or not. Then we exclude that patients not performed brain MRI. Results The number of patients with perverted nystagmus was 15, upbeating was 1 and down-beating was 14. Among these patients, 5 patients have brain MRI abnormal findings. However, 2 patients with MRI abnormal findings were not associated correctly with perverted nystagmus and only 3 patients with perverted nystagmus were considered central originated vertigo and further evaluation and treatment was performed by the department of neurology. Conclusions Perverted nystagmus was considered to the abnormalities at brain lesions, especially cerebellum, but neurologic symptoms and further evaluation were needed for exact diagnosis of central originated vertigo. PMID:27626081

  15. Liver response to hemorrhagic shock and subsequent resuscitation: MRI analysis.

    PubMed

    Matot, Idit; Cohen, Keren; Pappo, Orit; Barash, Hila; Abramovitch, Rinat

    2008-01-01

    The liver is a target for injury in low flow states. Markers of liver injury are either invasive or not rapidly responding. Magnetic resonance imaging (MRI) may offer a noninvasive alternative to evaluate liver injury due to reduced perfusion. Recently, we reported an MRI method (functional MRI [fMRI]) that enables us to follow liver perfusion by changing the enrichment of inspired gas (air, air-5% carbon dioxide, 95% oxygen-5% carbon dioxide). Rats were subjected to hemorrhagic shock (HS) (bleeding to a MAP of 25 mmHg) and randomized to no resuscitation or resuscitation with Ringer lactate (RL) or adrenaline infusion targeted to a MAP of 50 mmHg or baseline. Significantly decreased fMRI responses to hyperoxia and hypercapnia were observed immediately after HS. Liver enzymes levels, liver histology, and apoptosis assessments were normal immediately after hemorrhage, however, showed significant changes after 6 h. Functional MRI revealed that adrenaline, but not RL infusion, significantly (P < 0.01) improved liver perfusion. Similarly, liver injury, as assessed by liver enzyme levels, liver histology, and apoptosis, was attenuated to a greater extent with adrenaline resuscitation. No significant differences in liver perfusion and injury were noted between resuscitation to low (50 mmHg) versus high (baseline) MAP. This study shows that fMRI enables early assessment of changes in liver perfusion, resulting in liver injury or recovery, and therefore, it may be considered as a noninvasive, rapidly responding tool for following liver outcome subsequent to hemorrhage and resuscitation. Using fMRI, we showed that adrenaline may be preferable to RL as an initial measure to attenuate liver injury after HS.

  16. THE IMPACT OF BREAST MRI ON SURGICAL DECISION-MAKING: ARE PATIENTS AT RISK FOR MASTECTOMY?

    PubMed Central

    Pettit, Kelli; Swatske, Mary Ellen; Gao, Feng; Salavaggione, Lorena; Gillanders, William E.; Aft, Rebecca L.; Monsees, Barbara S.; Eberlein, Timothy J.; Margenthaler, Julie A.

    2014-01-01

    Background and Objectives The goal of the current study was to determine whether MRI impacts multidisciplinary treatment planning and if it leads to increased mastectomy rates. Methods A retrospective review was conducted of 441 patients treated for breast cancer between January 2005 and May 2008 who underwent breast MRI. Data included number of additional findings and their imaging and pathologic work-up. This was analyzed to determine impact of MRI on treatment planning. Results Of 441 patients, 45% had ≥1 additional finding on MRI. Of 410 patients with complete records, 29% had changes in the treatment plan, including 36 patients who were initially considered for breast conservation but proceeded directly to mastectomy based on MRI findings of suspected multicentricity. Twenty-three of those patients did not have a biopsy of the MRI lesion, with 87% having unicentric disease on final pathology. Overall, the mastectomy rate was 44%, which was significantly increased compared to patients not undergoing MRI (32%, p<0.05). Conclusions Breast MRI alters the treatment planning for many patients with newly-diagnosed breast cancer. Mastectomy rates are increased when MRI results alone direct surgical planning. Biopsy of MRI-identified lesions should be performed to avoid over-treatment. PMID:19757442

  17. DT-MRI segmentation using graph cuts

    NASA Astrophysics Data System (ADS)

    Weldeselassie, Yonas T.; Hamarneh, Ghassan

    2007-03-01

    An important problem in medical image analysis is the segmentation of anatomical regions of interest. Once regions of interest are segmented, one can extract shape, appearance, and structural features that can be analyzed for disease diagnosis or treatment evaluation. Diffusion tensor magnetic resonance imaging (DT-MRI) is a relatively new medical imaging modality that captures unique water diffusion properties and fiber orientation information of the imaged tissues. In this paper, we extend the interactive multidimensional graph cuts segmentation technique to operate on DT-MRI data by utilizing latest advances in tensor calculus and diffusion tensor dissimilarity metrics. The user interactively selects certain tensors as object ("obj") or background ("bkg") to provide hard constraints for the segmentation. Additional soft constraints incorporate information about both regional tissue diffusion as well as boundaries between tissues of different diffusion properties. Graph cuts are used to find globally optimal segmentation of the underlying 3D DT-MR image among all segmentations satisfying the constraints. We develop a graph structure from the underlying DT-MR image with the tensor voxels corresponding to the graph vertices and with graph edge weights computed using either Log-Euclidean or the J-divergence tensor dissimilarity metric. The topology of our segmentation is unrestricted and both obj and bkg segments may consist of several isolated parts. We test our method on synthetic DT data and apply it to real 2D and 3D MRI, providing segmentations of the corpus callosum in the brain and the ventricles of the heart.

  18. The relevance of MRI for patient modeling in head and neck hyperthermia treatment planning: A comparison of CT and CT-MRI based tissue segmentation on simulated temperature

    SciTech Connect

    Verhaart, René F. Paulides, Margarethus M.; Fortunati, Valerio; Walsum, Theo van; Veenland, Jifke F.; Lugt, Aad van der

    2014-12-15

    Purpose: In current clinical practice, head and neck (H and N) hyperthermia treatment planning (HTP) is solely based on computed tomography (CT) images. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast over CT. The purpose of the authors’ study is to investigate the relevance of using MRI in addition to CT for patient modeling in H and N HTP. Methods: CT and MRI scans were acquired for 11 patients in an immobilization mask. Three observers manually segmented on CT, MRI T1 weighted (MRI-T1w), and MRI T2 weighted (MRI-T2w) images the following thermo-sensitive tissues: cerebrum, cerebellum, brainstem, myelum, sclera, lens, vitreous humor, and the optical nerve. For these tissues that are used for patient modeling in H and N HTP, the interobserver variation of manual tissue segmentation in CT and MRI was quantified with the mean surface distance (MSD). Next, the authors compared the impact of CT and CT and MRI based patient models on the predicted temperatures. For each tissue, the modality was selected that led to the lowest observer variation and inserted this in the combined CT and MRI based patient model (CT and MRI), after a deformable image registration. In addition, a patient model with a detailed segmentation of brain tissues (including white matter, gray matter, and cerebrospinal fluid) was created (CT and MRI{sub db}). To quantify the relevance of MRI based segmentation for H and N HTP, the authors compared the predicted maximum temperatures in the segmented tissues (T{sub max}) and the corresponding specific absorption rate (SAR) of the patient models based on (1) CT, (2) CT and MRI, and (3) CT and MRI{sub db}. Results: In MRI, a similar or reduced interobserver variation was found compared to CT (maximum of median MSD in CT: 0.93 mm, MRI-T1w: 0.72 mm, MRI-T2w: 0.66 mm). Only for the optical nerve the interobserver variation is significantly lower in CT compared to MRI (median MSD in CT: 0.58 mm, MRI-T1w: 1.27 mm, MRI-T2w: 1.40 mm

  19. Regularization of parallel MRI reconstruction using in vivo coil sensitivities

    NASA Astrophysics Data System (ADS)

    Duan, Qi; Otazo, Ricardo; Xu, Jian; Sodickson, Daniel K.

    2009-02-01

    Parallel MRI can achieve increased spatiotemporal resolution in MRI by simultaneously sampling reduced k-space data with multiple receiver coils. One requirement that different parallel MRI techniques have in common is the need to determine spatial sensitivity information for the coil array. This is often done by smoothing the raw sensitivities obtained from low-resolution calibration images, for example via polynomial fitting. However, this sensitivity post-processing can be both time-consuming and error-prone. Another important factor in Parallel MRI is noise amplification in the reconstruction, which is due to non-unity transformations in the image reconstruction associated with spatially correlated coil sensitivity profiles. Generally, regularization approaches, such as Tikhonov and SVD-based methods, are applied to reduce SNR loss, at the price of introducing residual aliasing. In this work, we present a regularization approach using in vivo coil sensitivities in parallel MRI to overcome these potential errors into the reconstruction. The mathematical background of the proposed method is explained, and the technique is demonstrated with phantom images. The effectiveness of the proposed method is then illustrated clinically in a whole-heart 3D cardiac MR acquisition within a single breath-hold. The proposed method can not only overcome the sensitivity calibration problem, but also suppress a substantial portion of reconstruction-related noise without noticeable introduction of residual aliasing artifacts.

  20. Pushing spatial and temporal resolution for functional and diffusion MRI in the Human Connectome Project

    PubMed Central

    Uğurbil, Kamil; Xu, Junqian; Auerbach, Edward J.; Moeller, Steen; Vu, An; Duarte-Carvajalino, Julio M.; Lenglet, Christophe; Wu, Xiaoping; Schmitter, Sebastian; Van de Moortele, Pierre Francois; Strupp, John; Sapiro, Guillermo; De Martino, Federico; Wang, Dingxin; Harel, Noam; Garwood, Michael; Chen, Liyong; Feinberg, David A.; Smith, Stephen M.; Miller, Karla L.; Sotiropoulos, Stamatios N; Jbabdi, Saad; Andersson, Jesper L; Behrens, Timothy EJ; Glasser, Matthew F.; Van Essen, David; Yacoub, Essa

    2013-01-01

    The human connectome project (HCP) relies primarily on three complementary magnetic resonance (MR) methods. These are: 1) resting state functional MR imaging (rfMRI) which uses correlations in the temporal fluctuations in an fMRI time series to deduce ‘functional connectivity’; 2) diffusion imaging (dMRI), which provides the input for tractography algorithms used for the reconstruction of the complex axonal fiber architecture; and 3) task based fMRI (tfMRI), which is employed to identify functional parcellation in the human brain in order to assist analyses of data obtained with the first two methods. We describe technical improvements and optimization of these methods as well as instrumental choices that impact speed of acquisition of fMRI and dMRI images at 3 Tesla, leading to whole brain coverage with 2 mm isotropic resolution in 0.7 second for fMRI, and 1.25 mm isotropic resolution dMRI data for tractography analysis with three-fold reduction in total data acquisition time. Ongoing technical developments and optimization for acquisition of similar data at 7 Tesla magnetic field are also presented, targeting higher resolution, specificity of functional imaging signals, mitigation of the inhomogeneous radio frequency (RF) fields and power deposition. Results demonstrate that overall, these approaches represent a significant advance in MR imaging of the human brain to investigate brain function and structure. PMID:23702417

  1. Gradient-Modulated PETRA MRI

    PubMed Central

    Kobayashi, Naoharu; Goerke, Ute; Wang, Luning; Ellermann, Jutta; Metzger, Gregory J.; Garwood, Michael

    2015-01-01

    Image blurring due to off-resonance and fast T2* signal decay is a common issue in radial ultrashort echo time MRI sequences. One solution is to use a higher readout bandwidth, but this may be impractical for some techniques like pointwise encoding time reduction with radial acquisition (PETRA), which is a hybrid method of zero echo time and single point imaging techniques. Specifically, PETRA has severe specific absorption rate (SAR) and radiofrequency (RF) pulse peak power limitations when using higher bandwidths in human measurements. In this study, we introduce gradient modulation (GM) to PETRA to reduce image blurring artifacts while keeping SAR and RF peak power low. Tolerance of GM-PETRA to image blurring was evaluated in simulations and experiments by comparing with the conventional PETRA technique. We performed inner ear imaging of a healthy subject at 7T. GM-PETRA showed significantly less image blurring due to off-resonance and fast T2* signal decay compared to PETRA. In in vivo imaging, GM-PETRA nicely captured complex structures of the inner ear such as the cochlea and semicircular canals. Gradient modulation can improve the PETRA image quality and mitigate SAR and RF peak power limitations without special hardware modification in clinical scanners. PMID:26771005

  2. Evaluation of highly accelerated real-time cardiac cine MRI in tachycardia.

    PubMed

    Bassett, Elwin C; Kholmovski, Eugene G; Wilson, Brent D; DiBella, Edward V R; Dosdall, Derek J; Ranjan, Ravi; McGann, Christopher J; Kim, Daniel

    2014-02-01

    Electrocardiogram (ECG)-gated breath-hold cine MRI is considered to be the gold standard test for the assessment of cardiac function. However, it may fail in patients with arrhythmia, impaired breath-hold capacity and poor ECG gating. Although ungated real-time cine MRI may mitigate these problems, commercially available real-time cine MRI pulse sequences using parallel imaging typically yield relatively poor spatiotemporal resolution because of their low image acquisition efficiency. As an extension of our previous work, the purpose of this study was to evaluate the diagnostic quality and accuracy of eight-fold-accelerated real-time cine MRI with compressed sensing (CS) for the quantification of cardiac function in tachycardia, where it is challenging for real-time cine MRI to provide sufficient spatiotemporal resolution. We evaluated the performances of eight-fold-accelerated cine MRI with CS, three-fold-accelerated real-time cine MRI with temporal generalized autocalibrating partially parallel acquisitions (TGRAPPA) and ECG-gated breath-hold cine MRI in 21 large animals with tachycardia (mean heart rate, 104 beats per minute) at 3T. For each cine MRI method, two expert readers evaluated the diagnostic quality in four categories (image quality, temporal fidelity of wall motion, artifacts and apparent noise) using a Likert scale (1-5, worst to best). One reader evaluated the left ventricular functional parameters. The diagnostic quality scores were significantly different between the three cine pulse sequences, except for the artifact level between CS and TGRAPPA real-time cine MRI. Both ECG-gated breath-hold cine MRI and eight-fold accelerated real-time cine MRI yielded all four scores of ≥ 3.0 (acceptable), whereas three-fold-accelerated real-time cine MRI yielded all scores below 3.0, except for artifact (3.0). The left ventricular ejection fraction (LVEF) measurements agreed better between ECG-gated cine MRI and eight-fold-accelerated real-time cine MRI

  3. Improving Bladder Cancer Imaging Using 3T Functional Dynamic Contrast-Enhanced MRI

    PubMed Central

    Nguyen, Huyen T.; Pohar, Kamal S.; Jia, Guang; Shah, Zarine K.; Mortazavi, Amir; Zynger, Debra L.; Wei, Lai; Clark, Daniel; Yang, Xiangyu; Knopp, Michael V.

    2015-01-01

    Objectives To assess the capability of T2-weighted MRI (T2W-MRI) and the additional diagnostic value of Dynamic Contrast-Enhanced MRI (DCE-MRI) using multi-transmit 3T in the localization of bladder cancer. Materials and Methods This prospective study was approved by the local Institutional Review Board. Thirty–six patients were included in the study and provided informed consent. MRI scans were performed with T2W-MRI and DCE-MRI on a 3T multi-transmit system. Two observers (with 12 and 25 years of experience) independently interpreted T2W-MRI prior to DCE-MRI data (maps of pharmacokinetic parameters) to localize bladder tumors. The pathological examination of cystectomy bladder specimens was used as a reference gold standard. The McNemar test was performed to evaluate the differences in sensitivity, specificity, and accuracy. Kappa scores were calculated to assess interobserver agreement. Results The sensitivity, specificity, and accuracy of the localization with T2W-MRI alone were 81% (29/36), 63% (5/8) and 77% (34/44) for observer 1, and 72% (26/36), 63% (5/8), and 70% (31/44) for observer 2. With additional DCE-MRI available, these values were 92% (33/36), 75% (6/8), and 89% (39/44) for observer 1, and 92% (33/36), 63% (5/8), and 86% (38/44) for observer 2. DCE-MRI significantly (P < 0.01) improved the sensitivity and accuracy for observer 2. For the twenty-three patients treated with chemotherapy, DCE-MRI also significantly (P < 0.02) improved the sensitivity and accuracy of bladder cancer localization with T2W-MRI alone for observer 2. Kappa scores were 0.63 for T2W-MRI alone, and 0.78 for additional DCE-MRI. Out of seven sub-centimeter malignant tumors, four (57%) were identified on T2W images and six (86%) on DCE maps. Out of eleven malignant tumors within the bladder wall thickening, six (55%) were found on T2W images and ten (91%) on DCE maps. Conclusions Compared to conventional T2W-MRI alone, the addition of DCE-MRI improved interobserver agreement as

  4. SU-E-J-193: Feasibility of MRI-Only Based IMRT Planning for Pancreatic Cancer

    SciTech Connect

    Prior, P; Botros, M; Chen, X; Paulson, E; Erickson, B; Li, X

    2014-06-01

    Purpose: With the increasing use of MRI simulation and the advent of MRI-guided delivery, it is desirable to use MRI only for treatment planning. In this study, we assess the dosimetric difference between MRI- and CTbased IMRT planning for pancreatic cancer. Methods: Planning CTs and MRIs acquired for a representative pancreatic cancer patient were used. MRI-based planning utilized forced relative electron density (rED) assignment of organ specific values from IRCU report 46, where rED = 1.029 for PTV and a rED = 1.036 for non-specified tissue (NST). Six IMRT plans were generated with clinical dose-volume (DV) constraints using a research Monaco planning system employing Monte Carlo dose calculation with optional perpendicular magnetic field (MF) of 1.5T. The following five plans were generated and compared with the planning CT: 1.) CT plan with MF and dose recalculation without optimization; 2.) MRI (T2) plan with target and OARs redrawn based on MRI, forced rED, no MF, and recalculation without optimization; 3.) Similar as in 2 but with MF; 4.) MRI plan with MF but without optimization; and 5.) Similar as in 4 but with optimization. Results: Generally, noticeable differences in PTV point doses and DV parameters (DVPs) between the CT-and MRI-based plans with and without the MF were observed. These differences between the optimized plans were generally small, mostly within 2%. Larger differences were observed in point doses and mean doses for certain OARs between the CT and MRI plan, mostly due to differences between image acquisition times. Conclusion: MRI only based IMRT planning for pancreatic cancer is feasible. The differences observed between the optimized CT and MRI plans with or without the MF were practically negligible if excluding the differences between MRI and CT defined structures.

  5. Myocardial strain estimated from standard cine MRI closely represents strain estimated from dedicated strain-encoded MRI.

    PubMed

    Allan, Andrew; Gao, Hao; McComb, Christie; Berry, Colin

    2011-01-01

    A method of non-rigid image registration was developed and evaluated for the purpose of quantifying myocardial displacement and strain from cine MRI using DENSE MRI as the reference standard. The objective of this paper was to study the potential use of cine MRI with image registration, as a means of measuring strain. The local displacement of the left ventricle was modelled by free-form deformations using b-splines. Cardiac MRI images were obtained from four healthy volunteers at 1.5T and analysed by the implementation of image registration algorithms in cine data and with DENSE view in DENSE data. The results indicated there was less than 3% difference between the strain values obtained from cine and DENSE scans averaging across the regions of the left ventricle in healthy subjects (n=4). There lies great potential in the implementation of cine MRI as a means of strain estimation. As such the measurement of strain from standard cine MRI poses an appealing and potentially clinically useful new option for assessing patients with myocardial dysfunction.

  6. Across Languages, Space, and Time: A Review of the Role of Cross-Language Similarity in L2 (Morpho)Syntactic Processing as Revealed by fMRI and ERP Methods

    ERIC Educational Resources Information Center

    Tolentino, Leida C.; Tokowicz, Natasha

    2011-01-01

    This review examines whether similarity between the first language (L1) and second language (L2) influences the (morpho)syntactic processing of the L2, using both neural location and temporal processing information. Results from functional magnetic resonance imaging (fMRI) and event-related potential (ERP) studies show that nonnative speakers can…

  7. The power of using functional fMRI on small rodents to study brain pharmacology and disease

    PubMed Central

    Jonckers, Elisabeth; Shah, Disha; Hamaide, Julie; Verhoye, Marleen; Van der Linden, Annemie

    2015-01-01

    Functional magnetic resonance imaging (fMRI) is an excellent tool to study the effect of pharmacological modulations on brain function in a non-invasive and longitudinal manner. We introduce several blood oxygenation level dependent (BOLD) fMRI techniques, including resting state (rsfMRI), stimulus-evoked (st-fMRI), and pharmacological MRI (phMRI). Respectively, these techniques permit the assessment of functional connectivity during rest as well as brain activation triggered by sensory stimulation and/or a pharmacological challenge. The first part of this review describes the physiological basis of BOLD fMRI and the hemodynamic response on which the MRI contrast is based. Specific emphasis goes to possible effects of anesthesia and the animal’s physiological conditions on neural activity and the hemodynamic response. The second part of this review describes applications of the aforementioned techniques in pharmacologically induced, as well as in traumatic and transgenic disease models and illustrates how multiple fMRI methods can be applied successfully to evaluate different aspects of a specific disorder. For example, fMRI techniques can be used to pinpoint the neural substrate of a disease beyond previously defined hypothesis-driven regions-of-interest. In addition, fMRI techniques allow one to dissect how specific modifications (e.g., treatment, lesion etc.) modulate the functioning of specific brain areas (st-fMRI, phMRI) and how functional connectivity (rsfMRI) between several brain regions is affected, both in acute and extended time frames. Furthermore, fMRI techniques can be used to assess/explore the efficacy of novel treatments in depth, both in fundamental research as well as in preclinical settings. In conclusion, by describing several exemplary studies, we aim to highlight the advantages of functional MRI in exploring the acute and long-term effects of pharmacological substances and/or pathology on brain functioning along with several methodological

  8. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  9. PCA-based groupwise image registration for quantitative MRI.

    PubMed

    Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

    2016-04-01

    Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as

  10. TH-A-BRF-11: Image Intensity Non-Uniformities Between MRI Simulation and Diagnostic MRI

    SciTech Connect

    Paulson, E

    2014-06-15

    Purpose: MRI simulation for MRI-based radiotherapy demands that patients be setup in treatment position, which frequently involves use of alternative radiofrequency (RF) coil configurations to accommodate immobilized patients. However, alternative RF coil geometries may exacerbate image intensity non-uniformities (IINU) beyond those observed in diagnostic MRI, which may challenge image segmentation and registration accuracy as well as confound studies assessing radiotherapy response when MR simulation images are used as baselines for evaluation. The goal of this work was to determine whether differences in IINU exist between MR simulation and diagnostic MR images. Methods: ACR-MRI phantom images were acquired at 3T using a spin-echo sequence (TE/TR:20/500ms, rBW:62.5kHz, TH/skip:5/5mm). MR simulation images were obtained by wrapping two flexible phased-array RF coils around the phantom. Diagnostic MR images were obtained by placing the phantom into a commercial phased-array head coil. Pre-scan normalization was enabled in both cases. Images were transferred offline and corrected for IINU using the MNI N3 algorithm. Coefficients of variation (CV=σ/μ) were calculated for each slice. Wilcoxon matched-pairs and Mann-Whitney tests compared CV values between original and N3 images and between MR simulation and diagnostic MR images. Results: Significant differences in CV were detected between original and N3 images in both MRI simulation and diagnostic MRI groups (p=0.010, p=0.010). In addition, significant differences in CV were detected between original MR simulation and original and N3 diagnostic MR images (p=0.0256, p=0.0016). However, no significant differences in CV were detected between N3 MR simulation images and original or N3 diagnostic MR images, demonstrating the importance of correcting MR simulation images beyond pre-scan normalization prior to use in radiotherapy. Conclusions: Alternative RF coil configurations used in MRI simulation can Result in

  11. SU-E-J-192: Verification of 4D-MRI Internal Target Volume Using Cine MRI

    SciTech Connect

    Lafata, K; Czito, B; Palta, M; Bashir, M; Yin, F; Cai, J

    2014-06-01

    Purpose: To investigate the accuracy of 4D-MRI in determining the Internal Target Volume (ITV) used in radiation oncology treatment planning of liver cancers. Cine MRI is used as the standard baseline in establishing the feasibility and accuracy of 4D-MRI tumor motion within the liver. Methods: IRB approval was obtained for this retrospective study. Analysis was performed on MR images from four patients receiving external beam radiation therapy for liver cancer at our institution. Eligible patients received both Cine and 4D-MRI scans before treatment. Cine images were acquired sagittally in real time at a slice bisecting the tumor, while 4D images were acquired volumetrically. Cine MR DICOM headers were manipulated such that each respiratory frame was assigned a unique slice location. This approach permitted the treatment planning system (Eclipse, Varian Medical Systems) to recognize a complete respiratory cycle as a “volume”, where the gross tumor was contoured temporally. Software was developed to calculate the union of all frame contours in the structure set, resulting in the corresponding plane of the ITV projecting through the middle of the tumor, defined as the Internal Target Area (ITA). This was repeated for 4D-MRI, at the corresponding slice location, allowing a direct comparison of ITAs obtained from each modality. Results: Four patients have been analyzed. ITAs contoured from 4D-MRI correlate with contours from Cine MRI. The mean error of 4D values relative to Cine values is 7.67 +/− 2.55 %. No single ITA contoured from 4D-MRI demonstrated more than 10.5 % error compared to its Cine MRI counterpart. Conclusion: Motion management is a significant aspect of treatment planning within dynamic environments such as the liver, where diaphragmatic and cardiac activity influence plan accuracy. This small pilot study suggests that 4D-MRI based ITA measurements agree with Cine MRI based measurements, an important step towards clinical implementation. NIH 1R21

  12. [Study on cine view of relative enhancement ratio map in O2-enhanced MRI].

    PubMed

    Fujii, Keita; Watanabe, Yasushi; Hanaoka, Shouhei; Motoyoshi, Kouichi; Goto, Masami; Amemiya, Shiori; Ino, Kenji; Akahane, Masaaki; Yano, Keiichi; Ohtomo, Kuni

    2014-11-01

    Magnetic resonance imaging (MRI) enables the evaluation of organ structure and function. Oxygen-enhanced MRI (O2-enhanced MRI) is a method for evaluating the pulmonary ventilation function using oxygen as a contrast agent. We created the Cine View of Relative Enhancement Ratio Map (Cine RER map) in O2-enhanced MRI to easily observe the contrast effect for clinical use. Relative enhancement ratio (RER) was determined as the pixel values of the Cine RER map. Moreover, six healthy volunteers underwent O2-enhanced MRI to determine the appropriate scale width of the Cine RER map. We calculated each RER and set 0 to 1.27 as the scale width of the Cine RER map based on the results. The Cine RER map made it possible to observe the contrast effect over time and thus is a convenient tool for evaluating the pulmonary ventilation function in O2-enhanced MRI.

  13. Acute vertigo in an anesthesia provider during exposure to a 3T MRI scanner.

    PubMed

    Gorlin, Andrew; Hoxworth, Joseph M; Pavlicek, William; Thunberg, Christopher A; Seamans, David

    2015-01-01

    Vertigo induced by exposure to the magnetic field of a magnetic resonance imaging (MRI) scanner is a well-known phenomenon within the radiology community but is not widely appreciated by other clinical specialists. Here, we describe a case of an anesthetist experiencing acute vertigo while providing sedation to a patient undergoing a 3 Tesla MRI scan. After discussing previous reports, and the evidence surrounding MRI-induced vertigo, we review potential etiologies that include the effects of both static and time-varying magnetic fields on the vestibular apparatus. We conclude our review by discussing the occupational standards that exist for MRI exposure and methods to minimize the risks of MRI-induced vertigo for clinicians working in the MRI environment. PMID:25792858

  14. Acute vertigo in an anesthesia provider during exposure to a 3T MRI scanner

    PubMed Central

    Gorlin, Andrew; Hoxworth, Joseph M; Pavlicek, William; Thunberg, Christopher A; Seamans, David

    2015-01-01

    Vertigo induced by exposure to the magnetic field of a magnetic resonance imaging (MRI) scanner is a well-known phenomenon within the radiology community but is not widely appreciated by other clinical specialists. Here, we describe a case of an anesthetist experiencing acute vertigo while providing sedation to a patient undergoing a 3 Tesla MRI scan. After discussing previous reports, and the evidence surrounding MRI-induced vertigo, we review potential etiologies that include the effects of both static and time-varying magnetic fields on the vestibular apparatus. We conclude our review by discussing the occupational standards that exist for MRI exposure and methods to minimize the risks of MRI-induced vertigo for clinicians working in the MRI environment. PMID:25792858

  15. RF HEATING OF MRI-ASSISTED CATHETER STEERING COILS FOR INTERVENTIONAL MRI

    PubMed Central

    Settecase, Fabio; Hetts, Steven W.; Martin, Alastair J.; Roberts, Timothy P. L.; Bernhardt, Anthony F.; Evans, Lee; Malba, Vincent; Saeed, Maythem; Arenson, Ronald L.; Kucharzyk, Walter; Wilson, Mark W.

    2010-01-01

    RATIONALE AND OBJECTIVES To assess magnetic resonance imaging (MRI) radiofrequency (RF) related heating of conductive wire coils used in magnetically steerable endovascular catheters. MATERIALS AND METHODS A 3-axis microcoil was fabricated onto a 1.8 Fr catheter tip. In vitro testing was performed in a 1.5 T MRI system using an agarose gel filled vessel phantom, a transmit/receive body RF coil and a steady state free precession (SSFP) pulse sequence, and a fluoroptic thermometry system. Temperature was measured without simulated blood flow at varying distances from magnet isocenter and varying flip angles. Additional experiments were performed with laser-lithographed single-axis microcoil-tipped microcatheters in air and in a saline bath with varied grounding of the microcoil wires. Preliminary in vivo evaluation of RF heating was performed in pigs at 1.5 T with coil-tipped catheters in various positions in the common carotid arteries with SSFP pulse sequence on and off, and under physiologic flow and zero flow conditions. RESULTS In tissue-mimicking agarose gel, RF heating resulted in a maximal temperature increase of 0.35°C after 15 minutes of imaging, 15 cm from magnet isocenter. For a single axis microcoil, maximal temperature increases were 0.73-1.91°C in air and 0.45-0.55°C in saline. In vivo, delayed contrast enhanced MRI revealed no evidence of vascular injury and histopathological sections from the common carotid arteries confirmed the lack of vascular damage. CONCLUSIONS Microcatheter tip microcoils for endovascular catheter steering in MRI experience minimal RF heating under the conditions tested. These data provide the basis for further in vivo testing of this promising technology for endovascular interventional MRI. PMID:21075019

  16. Outcome of MRI-guided vacuum-assisted breast biopsy – initial experience at Institute of Oncology Ljubljana, Slovenia

    PubMed Central

    Zebic-Sinkovec, Marta; Hertl, Kristijana; Kadivec, Maksimiljan; Cavlek, Mihael; Podobnik, Gasper; Snoj, Marko

    2012-01-01

    Background Like all breast imaging modalities MRI has limited specificity and the positive predictive value for lesions detected by MRI alone ranges between 15 and 50%. MRI guided procedures (needle biopsy, presurgical localisation) are mandatory for suspicious findings visible only at MRI, with potential influence on therapeutic decision. The aim of this retrospective study was to evaluate our initial clinical experience with MRI-guided vacuum-assisted breast biopsy as an alternative to surgical excision and to investigate the outcome of MRI-guided breast biopsy as a function of the MRI features of the lesions. Patients and methods. In 14 women (median age 51 years) with 14 MRI-detected lesions, MRI-guided vacuum-assisted breast biopsy was performed. We evaluated the MRI findings that led to biopsy and we investigated the core and postoperative histology results and follow-up data. Results The biopsy was technically successful in 14 (93%) of 15 women. Of 14 biopsies in 14 women, core histology revealed 6 malignant (6/14, 43%), 6 benign (6/14, 43%) and 2 high-risk (2/14, 14%) lesions. Among the 6 cancer 3 were invasive and 3 were ductal carcinoma in situ (DCIS). The probability of malignancy in our experience was higher for non-mass lesion type and for washout and plateau kinetics. Conclusions Our initial experience confirms that MRI-guided vacuum-assisted biopsy is fast, safe and accurate alternative to surgical biopsy for breast lesions detected at MRI only. PMID:23077445

  17. Delineating potential epileptogenic areas utilizing resting functional magnetic resonance imaging (fMRI) in epilepsy patients.

    PubMed

    Pizarro, Ricardo; Nair, Veena; Meier, Timothy; Holdsworth, Ryan; Tunnell, Evelyn; Rutecki, Paul; Sillay, Karl; Meyerand, Mary E; Prabhakaran, Vivek

    2016-08-01

    Seizure localization includes neuroimaging like electroencephalogram, and magnetic resonance imaging (MRI) with limited ability to characterize the epileptogenic network. Temporal clustering analysis (TCA) characterizes epileptogenic network congruent with interictal epileptiform discharges by clustering together voxels with transient signals. We generated epileptogenic areas for 12 of 13 epilepsy patients with TCA, congruent with different areas of seizure onset. Resting functional MRI (fMRI) scans are noninvasive, and can be acquired quickly, in patients with different levels of severity and function. Analyzing resting fMRI data using TCA is quick and can complement clinical methods to characterize the epileptogenic network. PMID:27362339

  18. MRI Stealth” robot for prostate interventions

    PubMed Central

    STOIANOVICI, DAN; SONG, DANNY; PETRISOR, DORU; URSU, DANIEL; MAZILU, DUMITRU; MUTENER, MICHAEL; SCHAR, MICHAEL; PATRICIU, ALEXANDRU

    2011-01-01

    The paper reports an important achievement in MRI instrumentation, a pneumatic, fully actuated robot located within the scanner alongside the patient and operating under remote control based on the images. Previous MRI robots commonly used piezoelectric actuation limiting their compatibility. Pneumatics is an ideal choice for MRI compatibility because it is decoupled from electromagnetism, but pneumatic actuators were hardly controllable. This achievement was possible due to a recent technology breakthrough, the invention of a new type of pneumatic motor, PneuStep (1), designed for the robot reported here with uncompromised MRI compatibility, high-precision, and medical safety. MrBot is one of the “MRI stealth” robots today (the second is described in this issue by Zangos et al.). Both of these systems are also multi-imager compatible, being able to operate with the imager of choice or cross-imaging modalities. For MRI compatibility the robot is exclusively constructed of nonmagnetic and dielectric materials such as plastics, ceramics, crystals, rubbers and is electricity free. Light-based encoding is used for feedback, so that all electric components are distally located outside the imager’s room. MRI robots are modern, digital medical instruments in line with advanced imaging equipment and methods. These allow for accessing patients within closed bore scanners and performing interventions under direct (in scanner) imaging feedback. MRI robots could allow e.g. to biopsy small lesions imaged with cutting edge cancer imaging methods, or precisely deploy localized therapy at cancer foci. Our robot is the first to show the feasibility of fully automated in-scanner interventions. It is customized for the prostate and operates transperineally for needle interventions. It can accommodate various needle drivers for different percutaneous procedures such as biopsy, thermal ablations, or brachytherapy. The first needle driver is customized for fully automated low

  19. QUESPOWR MRI: QUantification of Exchange as a function of Saturation Power On the Water Resonance.

    PubMed

    Randtke, Edward A; Pagel, Mark D; Cárdenas-Rodríguez, Julio

    2016-09-01

    QUantification of Exchange as a function of Saturation Power On the Water Resonance (QUESPOWR) MRI is a new method that can estimate chemical exchange rates. This method acquires a series of OPARACHEE MRI acquisitions with a range of RF powers for the WALTZ16(∗) pulse train, which are applied on the water resonance. A QUESPOWR plot can be generated from the power dependence of the % water signal, which is similar to a QUESP plot that is generated from CEST MRI acquisition methods with RF saturation applied off-resonance from water. A QUESPOWR plot can be quantitatively analyzed using linear fitting methods to provide estimates of average chemical exchange rates. Analyses of the shapes of QUESPOWR plots can also be used to estimate relative differences in average chemical exchange rates and concentrations of biomolecules. The performance of QUESPOWR MRI was assessed via simulations, an in vitro study with iopamidol, and an in vivo study with a mouse model of mammary carcinoma. The results showed that QUESPOWR MRI is especially sensitive to chemical exchange between water and biomolecules that have intermediate to fast chemical exchange rates and chemical shifts that are close to water, which are notoriously difficult to assess with other CEST MRI methods. In addition, in vivo QUESPOWR MRI detected acidic tumor tissues relative to normal tissues that are pH-neutral, and therefore may be a new paradigm for tumor detection with MRI. PMID:27404128

  20. QUESPOWR MRI: QUantification of Exchange as a function of Saturation Power On the Water Resonance

    NASA Astrophysics Data System (ADS)

    Randtke, Edward A.; Pagel, Mark D.; Cárdenas-Rodríguez, Julio

    2016-09-01

    QUantification of Exchange as a function of Saturation Power On the Water Resonance (QUESPOWR) MRI is a new method that can estimate chemical exchange rates. This method acquires a series of OPARACHEE MRI acquisitions with a range of RF powers for the WALTZ16∗ pulse train, which are applied on the water resonance. A QUESPOWR plot can be generated from the power dependence of the % water signal, which is similar to a QUESP plot that is generated from CEST MRI acquisition methods with RF saturation applied off-resonance from water. A QUESPOWR plot can be quantitatively analyzed using linear fitting methods to provide estimates of average chemical exchange rates. Analyses of the shapes of QUESPOWR plots can also be used to estimate relative differences in average chemical exchange rates and concentrations of biomolecules. The performance of QUESPOWR MRI was assessed via simulations, an in vitro study with iopamidol, and an in vivo study with a mouse model of mammary carcinoma. The results showed that QUESPOWR MRI is especially sensitive to chemical exchange between water and biomolecules that have intermediate to fast chemical exchange rates and chemical shifts that are close to water, which are notoriously difficult to assess with other CEST MRI methods. In addition, in vivo QUESPOWR MRI detected acidic tumor tissues relative to normal tissues that are pH-neutral, and therefore may be a new paradigm for tumor detection with MRI.

  1. Evaluation of Referenceless Thermometry in MRI-Guided Focused Ultrasound Surgery of Uterine Fibroids

    NASA Astrophysics Data System (ADS)

    McDannold, Nathan; Tempany, Clare; Jolesz, Ferenc; Hynynen, Kullervo

    2006-05-01

    Purpose: A recently described method to produce MRI-based temperature images from individual phase maps (referenceless thermometry) was tested in images acquired during MRI-guided focused ultrasound surgery of uterine fibroids. Methods: Temperature measurements, noise in unheated areas, and thermal dose contours from 100 sonications as measured by the referenceless method were compared to images constructed with the standard phase-difference technique. Results: The agreement between temperature measurements was good, with 92% having a difference from the phase difference method less than or equal to 3°C. Conclusions: The referenceless method appears to be adequate for temperature monitoring of MRI-guided focused ultrasound in fibroids.

  2. Multivariate pattern analysis of fMRI: The early beginnings

    PubMed Central

    Haxby, James. V.

    2012-01-01

    In 2001, we published a paper on the representation of faces and objects in ventral temporal cortex that introduced a new method for fMRI analysis, which subsequently came to be called multivariate pattern analysis (MVPA). MVPA now refers to a diverse set of methods that analyze neural responses as patterns of activity that reflect the varying brain states that a cortical field or system can produce. This paper recounts the circumstances and events that led to the original study and later developments and innovations that have greatly expanded this approach to fMRI data analysis, leading to its widespread application. PMID:22425670

  3. Manipulation and tracking of superparamagnetic nanoparticles using MRI.

    PubMed

    Darton, Nicholas J; Sederman, Andrew J; Ionescu, Adrian; Ducati, Caterina; Darton, Richard C; Gladden, Lynn F; Slater, Nigel K H

    2008-10-01

    The use of magnetic fields in magnetic resonance imaging (MRI) for the tracking and delivery of chemotherapeutics bound to superparamagnetic nanoparticles offers a promising method for the non-invasive treatment of inoperable tumours. Here we demonstrate that superparamagnetic magnetite nanoparticles fabricated by an easily scalable method can be driven and tracked in real time at high velocities in vitro using MRI hardware. Force balance calculations are consistent with the magnetic properties of individual 10 nm diameter particles that move collectively as micron sized agglomerates with hydrodynamic diameter similar to that inferred from zero-magnetic-field dynamic light scattering measurements.

  4. Prospective multiaxial motion correction for fMRI.

    PubMed

    Ward, H A; Riederer, S J; Grimm, R C; Ehman, R L; Felmlee, J P; Jack, C R

    2000-03-01

    Corruption of the image time series due to interimage head motion limits the clinical utility of functional MRI. This paper presents a method for real-time prospective correction of rotation and translation in all six degrees of rigid body motion. By incorporating an orbital navigator (ONAV) echo for each of the sagittal, axial, and coronal planes into the fMRI pulse sequence, rotation and translation can be measured and the spatial orientation of the image acquisition sequence that follows can be corrected prospectively in as little as 160 msec. Testing of the method using a computerized motion phantom capable of performing complex multiaxial motion showed subdegree rotational and submillimeter translational accuracy over a range of +/-8 degrees and +/-8 mm of motion. In vivo images demonstrate correction of simultaneous through-plane and in-plane motion and improved detection of fMRI activation in the presence of head motion.

  5. Resting-state fMRI confounds and cleanup.

    PubMed

    Murphy, Kevin; Birn, Rasmus M; Bandettini, Peter A

    2013-10-15

    The goal of resting-state functional magnetic resonance imaging (fMRI) is to investigate the brain's functional connections by using the temporal similarity between blood oxygenation level dependent (BOLD) signals in different regions of the brain "at rest" as an indicator of synchronous neural activity. Since this measure relies on the temporal correlation of fMRI signal changes between different parts of the brain, any non-neural activity-related process that affects the signals will influence the measure of functional connectivity, yielding spurious results. To understand the sources of these resting-state fMRI confounds, this article describes the origins of the BOLD signal in terms of MR physics and cerebral physiology. Potential confounds arising from motion, cardiac and respiratory cycles, arterial CO₂ concentration, blood pressure/cerebral autoregulation, and vasomotion are discussed. Two classes of techniques to remove confounds from resting-state BOLD time series are reviewed: 1) those utilising external recordings of physiology and 2) data-based cleanup methods that only use the resting-state fMRI data itself. Further methods that remove noise from functional connectivity measures at a group level are also discussed. For successful interpretation of resting-state fMRI comparisons and results, noise cleanup is an often over-looked but essential step in the analysis pipeline.

  6. Automated Localization of Multiple Pelvic Bone Structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2016-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are at present identified manually on MRI to locate reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures automatically. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this paper, we present a model that combines support vector machines and nonlinear regression capturing global and local information to automatically identify the bounding boxes of bone structures on MRI. The model identifies the location of the pelvic bone structures by establishing the association between their relative locations and using local information such as texture features. Results show that the proposed method is able to locate the bone structures of interest accurately (dice similarity index >0.75) in 87-91% of the images. This research aims to enable accurate, consistent, and fully automated localization of bone structures on MRI to facilitate and improve the diagnosis of health conditions such as female POP.

  7. Neuronal or Hemodynamic? Grappling with the Functional MRI Signal

    PubMed Central

    2014-01-01

    Abstract Magnetic resonance imaging (MRI) and functional MRI (fMRI) continue to advance because creative physicists, engineers, neuroscientists, clinicians, and physiologists find new ways for extracting more information from the signal. Innovations in pulse sequence design, paradigm design, and processing methods have advanced the field and firmly established fMRI as a cornerstone for understanding the human brain. In this article, the field of fMRI is described through consideration of the central problem of separating hemodynamic from neuronal information. Discussed here are examples of how pulse sequences, activation paradigms, and processing methods are integrated such that novel, high-quality information can be obtained. Examples include the extraction of information such as activation onset latency, metabolic rate, neuronal adaptation, vascular patency, vessel diameter, vigilance, and subvoxel activation. Experimental measures include time series latency, hemodynamic shape, MR phase, multivoxel patterns, ratios of activation-related R2* to R2, metabolic rate changes, fluctuation correlations and frequencies, changes in fluctuation correlations and frequencies over time, resting correlation states, echo time dependence, and more. PMID:25093397

  8. Realignment strategies for awake-monkey fMRI data.

    PubMed

    Stoewer, Steffen; Goense, Jozien; Keliris, Georgios A; Bartels, Andreas; Logothetis, Nikos K; Duncan, John; Sigala, Natasha

    2011-12-01

    Functional magnetic resonance imaging (fMRI) experiments with awake nonhuman primates (NHPs) have recently seen a surge of applications. However, the standard fMRI analysis tools designed for human experiments are not optimal for NHP data collected at high fields. One major difference is the experimental setup. Although real head movement is impossible for NHPs, MRI image series often contain visible motion artifacts. Animal body movement results in image position changes and geometric distortions. Since conventional realignment methods are not appropriate to address such differences, algorithms tailored specifically for animal scanning become essential. We have implemented a series of high-field NHP specific methods in a software toolbox, fMRI Sandbox (http://kyb.tuebingen.mpg.de/~stoewer/), which allows us to use different realignment strategies. Here we demonstrate the effect of different realignment strategies on the analysis of awake-monkey fMRI data acquired at high field (7 T). We show that the advantage of using a nonstandard realignment algorithm depends on the amount of distortion in the dataset. While the benefits for less distorted datasets are minor, the improvement of statistical maps for heavily distorted datasets is significant.

  9. Human brain functional MRI and DTI visualization with virtual reality.

    PubMed

    Chen, Bin; Moreland, John; Zhang, Jingyu

    2011-12-01

    Magnetic resonance diffusion tensor imaging (DTI) and functional MRI (fMRI) are two active research areas in neuroimaging. DTI is sensitive to the anisotropic diffusion of water exerted by its macromolecular environment and has been shown useful in characterizing structures of ordered tissues such as the brain white matter, myocardium, and cartilage. The diffusion tensor provides two new types of information of water diffusion: the magnitude and the spatial orientation of water diffusivity inside the tissue. This information has been used for white matter fiber tracking to review physical neuronal pathways inside the brain. Functional MRI measures brain activations using the hemodynamic response. The statistically derived activation map corresponds to human brain functional activities caused by neuronal activities. The combination of these two methods provides a new way to understand human brain from the anatomical neuronal fiber connectivity to functional activities between different brain regions. In this study, virtual reality (VR) based MR DTI and fMRI visualization with high resolution anatomical image segmentation and registration, ROI definition and neuronal white matter fiber tractography visualization and fMRI activation map integration is proposed. Rationale and methods for producing and distributing stereoscopic videos are also discussed. PMID:23256049

  10. Outcome Classification of Preschool Children with Autism Spectrum Disorders Using Mri Brain Measures.

    ERIC Educational Resources Information Center

    Akshoomoff, Natacha; Lord, Catherine; Lincoln, Alan J.; Courchesne, Rachel Y.; Carper, Ruth A.; Townsend, Jeanne; Courchesne, Eric

    2004-01-01

    Objective: To test the hypothesis that a combination of magnetic resonance imaging (MRI) brain measures obtained during early childhood distinguish children with autism spectrum disorders (ASD) from typically developing children and is associated with functional outcome. Method: Quantitative MRI technology was used to measure gray and white matter…

  11. Ethical and Practical Considerations in the Management of Incidental Findings in Pediatric MRI Studies

    ERIC Educational Resources Information Center

    Kumra, Sanjiv; Ashtari, Manzar; Anderson, Britt; Cervellione, Kelly L.; Kan, Li

    2006-01-01

    Objective: The authors examined the ethical and practical management issues resulting from the detection of incidental abnormal findings on magnetic resonance imaging (MRI) research studies in healthy pediatric volunteers. Method: A retrospective examination of the findings from 60 clinical reports of research MRI scans from a cohort of healthy…

  12. Correlation between MRI and Arthroscopy in Diagnosis of Shoulder Pathology

    PubMed Central

    Bhonsle, Sachin; Mehta, Sonu

    2016-01-01

    Introduction Shoulder pain can cause significant pain, discomfort and reduce the ability to perform activities of daily living, thus making it the third most common cause of musculoskeletal consultation. The current gold standard diagnostic investigation is arthroscopy. MRI is a proved sensitive and accurate non-invasive tool in investigating shoulder pathology, but false and misleading results are equally reported. Aim The aim of the study is to compare the efficacy of MRI in diagnosing shoulder pathologies in comparison to arthroscopy, considering arthroscopy as the gold standard. Materials and Methods Thirty nine consecutive patients, between 18-80 years of age, presenting with chronic shoulder pain or instability of more than 6 weeks, or with clinical signs of impingement or tear were included in the study. MRI of the shoulder joint was done followed by shoulder arthroscopy. The data collected was analysed for the significant correlation between MRI of shoulder and arthroscopic findings by kappa statistics. Results Out of 39 patients, Rotator cuff (RC) tear was the most common pathology. MRI showed excellent sensitivity in the diagnosis of rotator cuff tears (0.91) and osteochondral defects (OCD), very good sensitivity for Bankart’s lesion (0.8) and had poor sensitivity to detect SLAP tear (0.15). MRI was specific for all shoulder pathologies. MRI detected RC tears with kappa score of 0.73, Bankart’s tear and OCD’s with kappa score of 0.83 and 1.0 respectively and SLAP lesion with kappa score of 0.14. The accuracy of MRI was highest in diagnosing OCD’s (1.0), followed by RC tear (0.9), Bankart’s tear (0.9) and accuracy was least in diagnosing SLAP lesion (0.7). False negative results were more than false positives. Conclusion The present study supports that MRI is effective in diagnosing rotator cuff tears, Bankart’s tear and ostechondral defects but was not found to be helpful in diagnosing SLAP lesions. MRI and arthroscopy have complimentary roles

  13. Brain Morphometry using MRI in Schizophrenia Patients

    NASA Astrophysics Data System (ADS)

    Abanshina, I.; Pirogov, Yu.; Kupriyanov, D.; Orlova, V.

    2010-01-01

    Schizophrenia has been the focus of intense neuroimaging research. Although its fundamental pathobiology remains elusive, neuroimaging studies provide evidence of abnormalities of cerebral structure and function in patients with schizophrenia. We used morphometry as a quantitative method for estimation of volume of brain structures. Seventy eight right-handed subjects aged 18-45 years were exposed to MRI-examination. Patients were divided into 3 groups: patients with schizophrenia, their relatives and healthy controls. The volumes of interested structures (caudate nucleus, putamen, ventricles, frontal and temporal lobe) were measured using T2-weighted MR-images. Correlations between structural differences and functional deficit were evaluated.

  14. MRI artefacts after Bonebridge implantation.

    PubMed

    Steinmetz, C; Mader, I; Arndt, S; Aschendorff, A; Laszig, R; Hassepass, F

    2014-07-01

    The new transcutaneous bone conduction implant (BCI) Bonebridge (BB, MED-EL) allows the skin to remain intact and therefore overcomes some issues related to percutaneous systems, such as skin reaction around the external screw and cosmetic complaints. According to manufacturer, BB is MRI conditional up to 1,5 Tesla (T). The artefact of the neurocranium after BB implantation is extensive as shown in the present report. This has to be taken into account when patients suffering conductive, mixed or single-sided hearing loss with candidacy for a BCI are counselled. In patients with comorbid intracranial tumour or other diseases of the brain that require imaging control scans with MRI percutaneous, BCI should be the implant of choice considering the very small artefact of the percutaneous screw in MRI.

  15. Quantitative assessment of synovitis in Legg-Calvé-Perthes disease using gadolinium-enhanced MRI.

    PubMed

    Neal, David C; O'Brien, Jack C; Burgess, Jamie; Jo, Chanhee; Kim, Harry K W

    2015-03-01

    A quantitative method to assess hip synovitis in Legg-Calvé-Perthes disease (LCPD) is not currently available. To develop this method, the areas of synovial enhancement on gadolinium-enhanced MRI (Gd-MRI) were measured by two independent observers. The volume of synovial enhancement was significantly increased in the initial and the fragmentation stages of LCPD (Waldenström stages I and II), with a persistence of synovitis into the reossification stage (stage III). The Gd-MRI method had high interobserver and intraobserver agreements and may serve as a useful method to monitor the effect of various treatments on hip synovitis in LCPD. PMID:25305048

  16. Characterizing and differentiating task-based and resting state fMRI signals via two-stage sparse representations.

    PubMed

    Zhang, Shu; Li, Xiang; Lv, Jinglei; Jiang, Xi; Guo, Lei; Liu, Tianming

    2016-03-01

    A relatively underexplored question in fMRI is whether there are intrinsic differences in terms of signal composition patterns that can effectively characterize and differentiate task-based or resting state fMRI (tfMRI or rsfMRI) signals. In this paper, we propose a novel two-stage sparse representation framework to examine the fundamental difference between tfMRI and rsfMRI signals. Specifically, in the first stage, the whole-brain tfMRI or rsfMRI signals of each subject were composed into a big data matrix, which was then factorized into a subject-specific dictionary matrix and a weight coefficient matrix for sparse representation. In the second stage, all of the dictionary matrices from both tfMRI/rsfMRI data across multiple subjects were composed into another big data-matrix, which was further sparsely represented by a cross-subjects common dictionary and a weight matrix. This framework has been applied on the recently publicly released Human Connectome Project (HCP) fMRI data and experimental results revealed that there are distinctive and descriptive atoms in the cross-subjects common dictionary that can effectively characterize and differentiate tfMRI and rsfMRI signals, achieving 100% classification accuracy. Moreover, our methods and results can be meaningfully interpreted, e.g., the well-known default mode network (DMN) activities can be recovered from the very noisy and heterogeneous aggregated big-data of tfMRI and rsfMRI signals across all subjects in HCP Q1 release. PMID:25732072

  17. Patient Outcomes in Canceled MRI-Guided Breast Biopsies

    PubMed Central

    Niell, Bethany L.; Lee, Janie M.; Johansen, Christopher; Halpern, Elkan F.; Rafferty, Elizabeth A.

    2013-01-01

    OBJECTIVE. The reported frequency of aborted MRI-guided breast biopsies ranges from 8% to 17%, usually secondary to nonvisualization at attempted biopsy. Our study examines the frequency of MRI-guided breast biopsies aborted because of lesion nonvisualization and the subsequent risk of malignancy. MATERIALS AND METHODS. We identified 350 patients and 445 lesions scheduled for MRI-guided biopsy between January 1, 2007, and December 31, 2009. Medical records and imaging studies were reviewed to ascertain patient demographics, lesion and imaging characteristics, and subsequent pathology results. Chi-square statistics were calculated for patient level analyses. RESULTS. MRI-guided biopsies were aborted in 13% (56/445) of lesions and 15% (53/350; 95% CI, 11.6–19.3%) of patients because of nonvisualization of the biopsy target at the time of attempted biopsy. Of these 53 patients, 50 patients had follow-up data available. Malignancy was subsequently diagnosed in five of those 50 patients (10%; 95% CI, 3.3–21.8%) patients, three with invasive ductal carcinomas and two with ductal carcinoma in situ. The mean time to malignant diagnosis from the date of aborted biopsy was 2.6 months (range, 1.1–6.9 months). CONCLUSION. Informed consent for MRI-guided breast biopsies should include discussion of biopsy cancellation because of nonvisualization of the target lesion. The low yet significant risk of malignancy in patients subsequent to an aborted MRI-guided breast biopsy warrants short-term follow-up MRI after a canceled biopsy. PMID:24370148

  18. Incorporating MRI structural information into bioluminescence tomography: system, heterogeneous reconstruction and in vivo quantification

    PubMed Central

    Zhang, Jun; Chen, Duofang; Liang, Jimin; Xue, Huadan; Lei, Jing; Wang, Qin; Chen, Dongmei; Meng, Ming; Jin, Zhengyu; Tian, Jie

    2014-01-01

    Combining two or more imaging modalities to provide complementary information has become commonplace in clinical practice and in preclinical and basic biomedical research. By incorporating the structural information provided by computed tomography (CT) or magnetic resonance imaging (MRI), the ill poseness nature of bioluminescence tomography (BLT) can be reduced significantly, thus improve the accuracies of reconstruction and in vivo quantification. In this paper, we present a small animal imaging system combining multi-view and multi-spectral BLT with MRI. The independent MRI-compatible optical device is placed at the end of the clinical MRI scanner. The small animal is transferred between the light tight chamber of the optical device and the animal coil of MRI via a guide rail during the experiment. After the optical imaging and MRI scanning procedures are finished, the optical images are mapped onto the MRI surface by interactive registration between boundary of optical images and silhouette of MRI. Then, incorporating the MRI structural information, a heterogeneous reconstruction algorithm based on finite element method (FEM) with L 1 normalization is used to reconstruct the position, power and region of the light source. In order to validate the feasibility of the system, we conducted experiments of nude mice model implanted with artificial light source and quantitative analysis of tumor inoculation model with MDA-231-GFP-luc. Preliminary results suggest the feasibility and effectiveness of the prototype system. PMID:24940545

  19. 3–5 BI-RADs Microcalcifications: Correlation between MRI and Histological Findings

    PubMed Central

    Fiaschetti, Valeria; Pistolese, Chiara Adriana; Perretta, Tommaso; Cossu, Elsa; Arganini, Chiara; Salimbeni, Claudia; Scarano, Angela Lia; Arduini, Silvia; Simonetti, Giovanni

    2011-01-01

    Purpose. To evaluate the correlation between MRI and histopathological findings in patients with mammographically detected 3–5 BI-RAD (Breast Imaging Reporting And Data Systems) microcalcifications and to allow a better surgical planning. Materials and Method. 62 female Patients (age 50 ± 12) with screening detected 3–5 BI-RAD microcalcifications underwent dynamic 3 T contrast-enhanced breast MRI. After 30-day (range 24–36 days) period, 55 Patients underwent biopsy using stereotactic vacuum-assisted biopsy (VAB), 5 Patients underwent stereotactic mammographically guided biopsy, and 2 Patients underwent MRI-guided VAB. Results. Microhistology examination demonstrated 36 malignant lesions and 26 benign lesions. The analysis of MRI findings identified 8 cases of MRI BI-RADS 5, 23 cases of MRI BI-RADS 4, 11 cases of MRI BI-RADS 3, 4 cases type A and 7 cases type B, and 20 cases of MRI BI-RADS 1-2. MRI sensitivity, specificity, positive predictive value, and negative predictive value were 88.8%, 76.9%, 84.2%, and 83.3%, respectively. PMID:22084735

  20. Widespread inflammation in CLIPPERS syndrome indicated by autopsy and ultra-high-field 7T MRI

    PubMed Central

    Blaabjerg, Morten; Ruprecht, Klemens; Sinnecker, Tim; Kondziella, Daniel; Niendorf, Thoralf; Kerrn-Jespersen, Bjørg Morell; Lindelof, Mette; Lassmann, Hans; Kristensen, Bjarne Winther; Paul, Friedemann

    2016-01-01

    Objective: To examine if there is widespread inflammation in the brain of patients with chronic lymphocytic inflammation with pontine perivascular enhancement responsive to steroids (CLIPPERS) syndrome by using histology and ultra-high-field MRI at 7.0T. Methods: We performed a detailed neuropathologic examination in 4 cases, including 1 autopsy case, and studied 2 additional patients by MRI at 7.0T to examine (1) extension of inflammation to areas appearing normal on 3.0T MRI, (2) potential advantages of 7.0T MRI compared to 3.0T MRI in reflecting widespread inflammation, perivascular pathology, and axonal damage, and (3) the possibility of lymphoma. Results: In the autopsy case, perivascular inflammation dominated by CD4+ T cells was not only detected in the brainstem and cerebellum but also in brain areas with normal appearance on 3.0T MRI, including supratentorial regions and cranial nerve roots. There was no evidence of lymphoma in any of the 4 patients. The 7.0T MRI in clinical remission also revealed supratentorial lesions and perivascular pathology in vivo with contrast-enhancing lesions centered around a small venous vessel. Ultra-high-field MRI at 7.0T disclosed prominent T1 hypointensities in the brainstem, which were not seen on 3.0T MRI. This corresponded to neuropathologic detection of axonal injury in the autopsy case. Conclusion: Our findings suggest more widespread perivascular inflammation and postinflammatory axonal injury in patients with CLIPPERS. PMID:27144217

  1. The Raven MRI teaching file

    SciTech Connect

    Lufkin, R.B.; Bradley, W.G. Jr.; Brant-Zawadzki, M.

    1990-01-01

    This book presents individually bound guides for each section of the body, the 1,000 concise and clearly illustrated case files cover neoplastic, non-neoplastic, degenerative, inflammatory, congenital, and acquired disease of the brain, head and neck, spine, musculoskeletal system, cardiovascular system, chest, abdomen, and male and female pelvis. It focuses on specific body regions; one is devoted to pediatric MRI; and one reviews the principles of MRI and identifies frequently encountered artifacts. It contains 100 completed case studies, with high-resolution MR images.

  2. Blind compressive sensing dynamic MRI

    PubMed Central

    Lingala, Sajan Goud; Jacob, Mathews

    2013-01-01

    . Our phase transition experiments demonstrate that the BCS scheme provides much better recovery rates than classical Fourier-based CS schemes, while being only marginally worse than the dictionary aware setting. Since the overhead in additionally estimating the dictionary is low, this method can be very useful in dynamic MRI applications, where the signal is not sparse in known dictionaries. We demonstrate the utility of the BCS scheme in accelerating contrast enhanced dynamic data. We observe superior reconstruction performance with the BCS scheme in comparison to existing low rank and compressed sensing schemes. PMID:23542951

  3. Quantitative MRI techniques of cartilage composition

    PubMed Central

    Matzat, Stephen J.; van Tiel, Jasper; Gold, Garry E.

    2013-01-01

    Due to aging populations and increasing rates of obesity in the developed world, the prevalence of osteoarthritis (OA) is continually increasing. Decreasing the societal and patient burden of this disease motivates research in prevention, early detection of OA, and novel treatment strategies against OA. One key facet of this effort is the need to track the degradation of tissues within joints, especially cartilage. Currently, conventional imaging techniques provide accurate means to detect morphological deterioration of cartilage in the later stages of OA, but these methods are not sensitive to the subtle biochemical changes during early disease stages. Novel quantitative techniques with magnetic resonance imaging (MRI) provide direct and indirect assessments of cartilage composition, and thus allow for earlier detection and tracking of OA. This review describes the most prominent quantitative MRI techniques to date—dGEMRIC, T2 mapping, T1rho mapping, and sodium imaging. Other, less-validated methods for quantifying cartilage composition are also described—Ultrashort echo time (UTE), gagCEST, and diffusion-weighted imaging (DWI). For each technique, this article discusses the proposed biochemical correlates, as well its advantages and limitations for clinical and research use. The article concludes with a detailed discussion of how the field of quantitative MRI has progressed to provide information regarding two specific patient populations through clinical research—patients with anterior cruciate ligament rupture and patients with impingement in the hip. While quantitative imaging techniques continue to rapidly evolve, specific challenges for each technique as well as challenges to clinical applications remain. PMID:23833729

  4. Vascular autorescaling of fMRI (VasA fMRI) improves sensitivity of population studies: A pilot study

    PubMed Central

    Kazan, Samira M.; Mohammadi, Siawoosh; Callaghan, Martina F.; Flandin, Guillaume; Huber, Laurentius; Leech, Robert; Kennerley, Aneurin; Windischberger, Christian; Weiskopf, Nikolaus

    2016-01-01

    The blood oxygenation level-dependent (BOLD) signal is widely used for functional magnetic resonance imaging (fMRI) of brain function in health and disease. The statistical power of fMRI group studies is significantly hampered by high inter-subject variance due to differences in baseline vascular physiology. Several methods have been proposed to account for physiological vascularization differences between subjects and hence improve the sensitivity in group studies. However, these methods require the acquisition of additional reference scans (such as a full resting-state fMRI session or ASL-based calibrated BOLD). We present a vascular autorescaling (VasA) method, which does not require any additional reference scans. VasA is based on the observation that slow oscillations (< 0.1 Hz) in arterial blood CO2 levels occur naturally due to changes in respiration patterns. These oscillations yield fMRI signal changes whose amplitudes reflect the blood oxygenation levels and underlying local vascularization and vascular responsivity. VasA estimates proxies of the amplitude of these CO2-driven oscillations directly from the residuals of task-related fMRI data without the need for reference scans. The estimates are used to scale the amplitude of task-related fMRI responses, to account for vascular differences. The VasA maps compared well to cerebrovascular reactivity (CVR) maps and cerebral blood volume maps based on vascular space occupancy (VASO) measurements in four volunteers, speaking to the physiological vascular basis of VasA. VasA was validated in a wide variety of tasks in 138 volunteers. VasA increased t-scores by up to 30% in specific brain areas such as the visual cortex. The number of activated voxels was increased by up to 200% in brain areas such as the orbital frontal cortex while still controlling the nominal false-positive rate. VasA fMRI outperformed previously proposed rescaling approaches based on resting-state fMRI data and can be readily applied to

  5. Complete fourier direct magnetic resonance imaging (CFD-MRI) for diffusion MRI

    PubMed Central

    Özcan, Alpay

    2013-01-01

    The foundation for an accurate and unifying Fourier-based theory of diffusion weighted magnetic resonance imaging (DW–MRI) is constructed by carefully re-examining the first principles of DW–MRI signal formation and deriving its mathematical model from scratch. The derivations are specifically obtained for DW–MRI signal by including all of its elements (e.g., imaging gradients) using complex values. Particle methods are utilized in contrast to conventional partial differential equations approach. The signal is shown to be the Fourier transform of the joint distribution of number of the magnetic moments (at a given location at the initial time) and magnetic moment displacement integrals. In effect, the k-space is augmented by three more dimensions, corresponding to the frequency variables dual to displacement integral vectors. The joint distribution function is recovered by applying the Fourier transform to the complete high-dimensional data set. In the process, to obtain a physically meaningful real valued distribution function, phase corrections are applied for the re-establishment of Hermitian symmetry in the signal. Consequently, the method is fully unconstrained and directly presents the distribution of displacement integrals without any assumptions such as symmetry or Markovian property. The joint distribution function is visualized with isosurfaces, which describe the displacement integrals, overlaid on the distribution map of the number of magnetic moments with low mobility. The model provides an accurate description of the molecular motion measurements via DW–MRI. The improvement of the characterization of tissue microstructure leads to a better localization, detection and assessment of biological properties such as white matter integrity. The results are demonstrated on the experimental data obtained from an ex vivo baboon brain. PMID:23596401

  6. [Magnetic resonance imaging in the diagnosis of gastric cancer: X-ray versus MRI anatomic findings].

    PubMed

    Portnoĭ, L M; Denisova, L B; Stashuk, G A; Nefedova, V O

    2000-01-01

    The paper assesses the present-day role of MRI in the diagnosis of gastric cancer. The authors consider the major prerequisites for the main aim of their study to be: 1) a dramatic incidence of diffuse (endophytic) gastric carcinoma, which requires significant correction of today's approaches to its diagnosis and 2) a rather biased and, in the authors' opinion, present-day mainly negative attitude towards MRI of the stomach as a diagnostic method for its tumor lesions. By applying the X-ray-MRI anatomic principle to the comparative study of MRI findings in 50 patients with predominantly gastric intramural carcinoma and in 25 patients without gastric tumors (controls), the authors present their methods for gastric MRI, the MRI semiotics of gastric cancer by concurrently touching upon a variety of problems that characterize the potentialities of MRI of the stomach in the diagnosis of its tumor lesions, including their differential diagnosis. As a result, the authors highly appreciate gastric MRI and consider this method to be included into the diagnostic algorithm of radiation techniques used in the diagnosis of gastric cancer, which should occupy its definite diagnostic place.

  7. TH-A-BRF-08: Deformable Registration of MRI and CT Images for MRI-Guided Radiation Therapy

    SciTech Connect

    Zhong, H; Wen, N; Gordon, J; Movsas, B; Chetty, I

    2014-06-15

    Purpose: To evaluate the quality of a commercially available MRI-CT image registration algorithm and then develop a method to improve the performance of this algorithm for MRI-guided prostate radiotherapy. Methods: Prostate contours were delineated on ten pairs of MRI and CT images using Eclipse. Each pair of MRI and CT images was registered with an intensity-based B-spline algorithm implemented in Velocity. A rectangular prism that contains the prostate volume was partitioned into a tetrahedral mesh which was aligned to the CT image. A finite element method (FEM) was developed on the mesh with the boundary constraints assigned from the Velocity generated displacement vector field (DVF). The resultant FEM displacements were used to adjust the Velocity DVF within the prism. Point correspondences between the CT and MR images identified within the prism could be used as additional boundary constraints to enforce the model deformation. The FEM deformation field is smooth in the interior of the prism, and equal to the Velocity displacements at the boundary of the prism. To evaluate the Velocity and FEM registration results, three criteria were used: prostate volume conservation and center consistence under contour mapping, and unbalanced energy of their deformation maps. Results: With the DVFs generated by the Velocity and FEM simulations, the prostate contours were warped from MRI to CT images. With the Velocity DVFs, the prostate volumes changed 10.2% on average, in contrast to 1.8% induced by the FEM DVFs. The average of the center deviations was 0.36 and 0.27 cm, and the unbalance energy was 2.65 and 0.38 mJ/cc3 for the Velocity and FEM registrations, respectively. Conclusion: The adaptive FEM method developed can be used to reduce the error of the MIbased registration algorithm implemented in Velocity in the prostate region, and consequently may help improve the quality of MRI-guided radiation therapy.

  8. Paramagnetic lanthanide chelates for multicontrast MRI.

    PubMed

    Cakić, Nevenka; Savić, Tanja; Stricker-Shaver, Janice; Truffault, Vincent; Platas-Iglesias, Carlos; Mirkes, Christian; Pohmann, Rolf; Scheffler, Klaus; Angelovski, Goran

    2016-07-28

    The preparation of a paramagnetic chelator that serves as a platform for multicontrast MRI, and can be utilized either as a T1-weighted, paraCEST or (19)F MRI contrast agent is reported. Its europium(iii) complex exhibits an extremely slow water exchange rate which is optimal for the use in CEST MRI. The potential of this platform was demonstrated through a series of MRI studies on tube phantoms and animals. PMID:27291157

  9. Building an EEG-fMRI Multi-Modal Brain Graph: A Concurrent EEG-fMRI Study

    PubMed Central

    Yu, Qingbao; Wu, Lei; Bridwell, David A.; Erhardt, Erik B.; Du, Yuhui; He, Hao; Chen, Jiayu; Liu, Peng; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D.

    2016-01-01

    The topological architecture of brain connectivity has been well-characterized by graph theory based analysis. However, previous studies have primarily built brain graphs based on a single modality of brain imaging data. Here we develop a framework to construct multi-modal brain graphs using concurrent EEG-fMRI data which are simultaneously collected during eyes open (EO) and eyes closed (EC) resting states. FMRI data are decomposed into independent components with associated time courses by group independent component analysis (ICA). EEG time series are segmented, and then spectral power time courses are computed and averaged within 5 frequency bands (delta; theta; alpha; beta; low gamma). EEG-fMRI brain graphs, with EEG electrodes and fMRI brain components serving as nodes, are built by computing correlations within and between fMRI ICA time courses and EEG spectral power time courses. Dynamic EEG-fMRI graphs are built using a sliding window method, versus static ones treating the entire time course as stationary. In global level, static graph measures and properties of dynamic graph measures are different across frequency bands and are mainly showing higher values in eyes closed than eyes open. Nodal level graph measures of a few brain components are also showing higher values during eyes closed in specific frequency bands. Overall, these findings incorporate fMRI spatial localization and EEG frequency information which could not be obtained by examining only one modality. This work provides a new approach to examine EEG-fMRI associations within a graph theoretic framework with potential application to many topics. PMID:27733821

  10. Anatomical evaluation of CT-MRI combined femoral model

    PubMed Central

    Lee, Yeon S; Seon, Jong K; Shin, Vladimir I; Kim, Gyu-Ha; Jeon, Moongu

    2008-01-01

    Background Both CT and MRI are complementary to each other in that CT can produce a distinct contour of bones, and MRI can show the shape of both ligaments and bones. It will be ideal to build a CT-MRI combined model to take advantage of complementary information of each modality. This study evaluated the accuracy of the combined femoral model in terms of anatomical inspection. Methods Six normal porcine femora (180 ± 10 days, 3 lefts and 3 rights) with ball markers were scanned by CT and MRI. The 3D/3D registration was performed by two methods, i.e. the landmark-based 3 points-to-3 points and the surface matching using the iterative closest point (ICP) algorithm. The matching accuracy of the combined model was evaluated with statistical global deviation and locally measure anatomical contour-based deviation. Statistical analysis to assess any significant difference between accuracies of those two methods was performed using univariate repeated measures ANOVA with the Turkey post hoc test. Results This study revealed that the local 2D contour-based measurement of matching deviation was 0.5 ± 0.3 mm in the femoral condyle, and in the middle femoral shaft. The global 3D contour matching deviation of the landmark-based matching was 1.1 ± 0.3 mm, but local 2D contour deviation through anatomical inspection was much larger as much as 3.0 ± 1.8 mm. Conclusion Even with human-factor derived errors accumulated from segmentation of MRI images, and limited image quality, the matching accuracy of CT-&-MRI combined 3D models was 0.5 ± 0.3 mm in terms of local anatomical inspection. PMID:18234068

  11. [RSF model optimization and its application to brain tumor segmentation in MRI].

    PubMed

    Cheng, Zhaoning; Song, Zhijian

    2013-04-01

    Magnetic resonance imaging (MRI) is usually obscure and non-uniform in gray, and the tumors inside are poorly circumscribed, hence the automatic tumor segmentation in MRI is very difficult. Region-scalable fitting (RSF) energy model is a new segmentation approach for some uneven grayscale images. However, the level set formulation (LSF) of RSF model is not suitable for the environment with different grey level distribution inside and outside the intial contour, and the complex intensity environment of MRI always makes it hard to get ideal segmentation results. Therefore, we improved the model by a new LSF and combined it with the mean shift method, which can be helpful for tumor segmentation and has better convergence and target direction. The proposed method has been utilized in a series of studies for real MRI images, and the results showed that it could realize fast, accurate and robust segmentations for brain tumors in MRI, which has great clinical significance. PMID:23858745

  12. [Magnetic resonance imaging in the diagnosis of renal neoplasms : MRI - histopathological comparison].

    PubMed

    Dombrovskií, V I

    2000-01-01

    The study evaluates the diagnostic of the MRI in the discovery and characterizing renal neoplasms. The principle of the comparative study of MRI, other diagnostic modalities and histopathological data was applied by the author, using a large pool statistically significant clinical material (419 cases). Renal cell carcinoma--the most wide-spread renal parenchyma's tumor, was selected as a morphological model (302 cases). As a result of this investigation, the MRI semiotics of renal cell carcinoma was more precisely defined and detailed and this method's high level of sensitivity (98.4%) was detected, concerning the detection of such a type of pathology. The MRI data reliably reflect (r > 0.8; P < 0.05) the true morphological structure of the tumor's growth, the secondary tumor's tissue alterations and its interaction with surrounding anatomical formations. Thus, MRI is appreciated as a method of choice for oncological urology.

  13. Cervical Spine MRI in Abused Infants.

    ERIC Educational Resources Information Center

    Feldman, Kenneth W.; And Others

    1997-01-01

    This study attempted to use cervical spine magnetic resonance imaging (MRI) to detect cord injury in 12 dead children with head injury from child abuse. Eighty percent of children autopsied had small cervical spine hemorrhages; MRI did not identify them and did not identify cord injury in any child studied, indicating that MRI scans are probably…

  14. Multiparametric MRI and targeted prostate biopsy: Improvements in cancer detection, localization, and risk assessment

    PubMed Central

    Bjurlin, Marc A.; Mendhiratta, Neil; Wysock, James S.

    2016-01-01

    Introduction Multiparametric-MRI (mp-MRI) is an evolving noninvasive imaging modality that increases the accurate localization of prostate cancer at the time of MRI targeted biopsy, thereby enhancing clinical risk assessment, and improving the ability to appropriately counsel patients regarding therapy. Material and methods We used MEDLINE/PubMed to conduct a comprehensive search of the English medical literature. Articles were reviewed, data was extracted, analyzed, and summarized. In this review, we discuss the mp-MRI prostate exam, its role in targeted prostate biopsy, along with clinical applications and outcomes of MRI targeted biopsies. Results Mp-MRI, consisting of T2-weighted imaging, diffusion-weighted imaging, dynamic contrast-enhanced imaging, and possibly MR spectroscopy, has demonstrated improved specificity in prostate cancer detection as compared to conventional T2-weighted images alone. An MRI suspicion score has been developed and is depicted using an institutional Likert or, more recently, a standardized reporting scale (PI-RADS). Techniques of MRI-targeted biopsy include in-gantry MRI guided biopsy, TRUS-guided visual estimation biopsy, and software co-registered MRI-US guided biopsy (MRI-US fusion). Among men with no previous biopsy, MRI-US fusion biopsy demonstrates up to a 20% increase in detection of clinically significant cancers compared to systematic biopsy while avoiding a significant portion of low risk disease. These data suggest a potential role in reducing over-detection and, ultimately, over-treatment. Among men with previous negative biopsy, 72–87% of cancers detected by MRI targeted biopsy are clinically significant. Among men with known low risk cancer, repeat biopsy by MR-targeting improves risk stratification in selecting men appropriate for active surveillance secondarily reducing the need for repetitive biopsy during surveillance. Conclusions Use of mp-MRI for targeting prostate biopsies has the potential to reduce the

  15. Automatic EEG-assisted retrospective motion correction for fMRI (aE-REMCOR).

    PubMed

    Wong, Chung-Ki; Zotev, Vadim; Misaki, Masaya; Phillips, Raquel; Luo, Qingfei; Bodurka, Jerzy

    2016-04-01

    Head motions during functional magnetic resonance imaging (fMRI) impair fMRI data quality and introduce systematic artifacts that can affect interpretation of fMRI results. Electroencephalography (EEG) recordings performed simultaneously with fMRI provide high-temporal-resolution information about ongoing brain activity as well as head movements. Recently, an EEG-assisted retrospective motion correction (E-REMCOR) method was introduced. E-REMCOR utilizes EEG motion artifacts to correct the effects of head movements in simultaneously acquired fMRI data on a slice-by-slice basis. While E-REMCOR is an efficient motion correction approach, it involves an independent component analysis (ICA) of the EEG data and identification of motion-related ICs. Here we report an automated implementation of E-REMCOR, referred to as aE-REMCOR, which we developed to facilitate the application of E-REMCOR in large-scale EEG-fMRI studies. The aE-REMCOR algorithm, implemented in MATLAB, enables an automated preprocessing of the EEG data, an ICA decomposition, and, importantly, an automatic identification of motion-related ICs. aE-REMCOR has been used to perform retrospective motion correction for 305 fMRI datasets from 16 subjects, who participated in EEG-fMRI experiments conducted on a 3T MRI scanner. Performance of aE-REMCOR has been evaluated based on improvement in temporal signal-to-noise ratio (TSNR) of the fMRI data, as well as correction efficiency defined in terms of spike reduction in fMRI motion parameters. The results show that aE-REMCOR is capable of substantially reducing head motion artifacts in fMRI data. In particular, when there are significant rapid head movements during the scan, a large TSNR improvement and high correction efficiency can be achieved. Depending on a subject's motion, an average TSNR improvement over the brain upon the application of aE-REMCOR can be as high as 27%, with top ten percent of the TSNR improvement values exceeding 55%. The average

  16. The application of MRI and MRS in psychiatry and performance evaluation of magnetic field homogeneity in MRI

    NASA Astrophysics Data System (ADS)

    Chen, Hua Hsuan

    Magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) is a safe non-invasive tool to study the physiological mechanisms of the human brain. MRS has the capability to provide the information regarding neurochemicals in brains of patients with neuropsychiatric disorders. Therefore, to produce measurable and interpretable information in MRI and MRS, a quality control (QC) program is required. Magnetic field homogeneity (MFH) is an important factor for QC when the volume sizes and neurochemical levels are quantified. Poor main (B0) MFH leads to artifacts, signal losses and broadened line widths. The American College of Radiology's (ACR) MRI QC manual mandates annual checks of MFH, suggesting tests using spectral line widths (FWHM) and phase-difference (Deltaϕ) maps. A new method, dubbed the bandwidth-difference (DeltaBW) method, is proposed along with a prototype phantom for determining MFH. The DeltaBW method is compared with standard methods and has also been tested in different model MRI systems from various manufacturers. Direct comparisons of the data obtained using the DeltaBW method demonstrated good agreement with data obtained using the linewidth method and the frequency map data provided by one MRI system manufacturer. As a result, the DeltaBW method produces measurements of MFH at various Diameter Sphere Volume (DSV) values that can be obtained from a single set of phantom images. The conclusion of the study is that the accuracy of DeltaBW B0 homogeneity measurements of MFH is comparable to the other methods tested while the ease of measurement in practical clinical setting is considerably improved.

  17. MRI Biosensors: A Short Primer

    PubMed Central

    Louie, Angelique

    2013-01-01

    Interest in Magnetic Resonance Imaging (MRI) contrast agents for molecular imaging of biological function experienced a surge of excitement approximately 20 years ago with the development of the first activatable contrast agents that could act as biosensors and turn “on” in response to a specific biological activity. This brief tutorial, based on a short course lecture from the 2011 ISMRM meeting, provides an overview of underlying principles governing the design of biosensing contrast agents. We describe mechanisms by which a magnetic resonance imaging (MRI) contrast agent can be made into a sensor for both T1 and T2 types contrast agents. Examples of biological activities that can interact with a contrast agent are discussed using specific examples from the recent literature to illustrate the primary mechanisms of action that have been utilized to achieve activation. MRI sensors for pH, ion binding, enzyme cleavage, and oxidation-reduction are presented. This article is not meant to be an exhaustive review, but an illustrative primer to explain how activation can be achieved for an MRI contrast agent. Chemical exchange saturation transfer (CEST) is not covered as these agents were covered in a separate lecture. PMID:23996662

  18. MRI of Little Leaguer's shoulder.

    PubMed

    Hatem, Stephen F; Recht, Michael P; Profitt, Brad

    2006-02-01

    The MRI appearance of 'Little Leaguer's shoulder' has not been previously reported in the radiology literature. Purported etiologies include proximal humeral epiphyseolysis, osteochondrosis of the proximal humeral epiphysis, stress fracture of the proximal humeral epiphyseal plate, and rotational stress fracture of the proximal humeral epiphyseal plate. We describe magnetic resonance imaging findings in four patients and review the literature.

  19. MRI findings in cobalamin deficiency.

    PubMed

    Krishna, Kavita K; Arafat, Abou-Sharbin Maher; Ichaporia, Nasli Rustom; Jain, M M

    2003-01-01

    A 55 year old male presented 2 years after a jejuno-iliectomy with weakness of all limbs, paraesthesiae, and difficulty in walking. Clinical examination revealed loss of posterior column sensations. Investigations were suggestive of a deficiency of vitamin B12 and folate. MRI showed a band of hyperintensity on T2 image, in the dorsal portion of the spinal cord.

  20. Manganese-Enhanced MRI: Biological Applications in Neuroscience

    PubMed Central

    Malheiros, Jackeline Moraes; Paiva, Fernando Fernandes; Longo, Beatriz Monteiro; Hamani, Clement; Covolan, Luciene

    2015-01-01

    Magnetic resonance imaging (MRI) is an excellent non-invasive tool to investigate biological systems. The administration of the paramagnetic divalent ion manganese (Mn2+) enhances MRI contrast in vivo. Due to similarities between Mn2+ and calcium (Ca2+), the premise of manganese-enhanced MRI (MEMRI) is that the former may enter neurons and other excitable cells through voltage-gated Ca2+ channels. As such, MEMRI has been used to trace neuronal pathways, define morphological boundaries, and study connectivity in morphological and functional imaging studies. In this article, we provide a brief overview of MEMRI and discuss recently published data to illustrate the usefulness of this method, particularly in animal models. PMID:26217304

  1. Manganese-Enhanced MRI: Biological Applications in Neuroscience.

    PubMed

    Malheiros, Jackeline Moraes; Paiva, Fernando Fernandes; Longo, Beatriz Monteiro; Hamani, Clement; Covolan, Luciene

    2015-01-01

    Magnetic resonance imaging (MRI) is an excellent non-invasive tool to investigate biological systems. The administration of the paramagnetic divalent ion manganese (Mn(2+)) enhances MRI contrast in vivo. Due to similarities between Mn(2+) and calcium (Ca(2+)), the premise of manganese-enhanced MRI (MEMRI) is that the former may enter neurons and other excitable cells through voltage-gated Ca(2+) channels. As such, MEMRI has been used to trace neuronal pathways, define morphological boundaries, and study connectivity in morphological and functional imaging studies. In this article, we provide a brief overview of MEMRI and discuss recently published data to illustrate the usefulness of this method, particularly in animal models.

  2. Improving MRI magnet thermal performance using variable density multilayer insulation

    NASA Astrophysics Data System (ADS)

    Zia, Jalal; Rutherford, William; Einziger, William

    2012-06-01

    Careful techniques for multilayer insulation (MLI) wrapping of MRI magnet cryostats have been shown to be critical in establishing a net Zero Helium Boil Off. Traditional MLI together with a cryocooler have been used in such 'Zero Boil Off' cryostats for many years. This paper discusses how the evolution in design of MRI magnet cryostats is challenging traditional MLI. By looking at the fundamental design equations for MLI, new insight can be gained into improving the design using variable density insulation. A new, proprietary method for creating variable density in MLI was devised and the resulting blankets were applied to MRI magnets. Results show a 10% improvement in insulation performance and a 42% improvement in material cost of the MLI. This new Variable Density MLI also holds promise for application to other liquid helium cryostats.

  3. New insights into lung diseases using hyperpolarized gas MRI.

    PubMed

    Flors, L; Altes, T A; Mugler, J P; de Lange, E E; Miller, G W; Mata, J F; Ruset, I C; Hersman, F W

    2015-01-01

    Hyperpolarized (HP) gases are a new class of contrast agents that permit to obtain high temporal and spatial resolution magnetic resonance images (MRI) of the lung airspaces. HP gas MRI has become important research tool not only for morphological and functional evaluation of normal pulmonary physiology but also for regional quantification of pathologic changes occurring in several lung diseases. The purpose of this work is to provide an introduction to MRI using HP noble gases, describing both the basic principles of the technique and the new information about lung disease provided by clinical studies with this method. The applications of the technique in normal subjects, smoking related lung disease, asthma, and cystic fibrosis are reviewed.

  4. Why does the small-Pm approximation suppress MRI?

    NASA Astrophysics Data System (ADS)

    Herron, Isom; Ji, Hantao; Goodman, Jeremy

    2003-11-01

    Axisymmetric stability of viscous resistive magnetized Couette flow is re-examined, with emphasis on flows that would be hydrodynamically stable according Rayleigh's criterion: opposing gradients of angular velocity and specific angular momentum. In this regime, magnetorotational instabilities (MRI) may occur. The governing system in cylindrical coordinates is of tenth order. It is proved, by methods based on those of Synge and Chandrasekhar, that by dropping one term from the system, MRI is suppressed, in fact no instability at all occurs, with insulating boundary conditions. This term is usually neglected because it has a small factor P_m, magnetic Reynolds number; nevertheless, it is crucially important. This approach is also suggestive that the principle of exchange of stabilities will hold for MRI in this regime.

  5. Multiple-Mouse MRI with Multiple Arrays of Receive Coils

    PubMed Central

    Ramirez, Marc S.; Esparza-Coss, Emilio; Bankson, James A.

    2010-01-01

    Compared to traditional single-animal imaging methods, multiple-mouse MRI has been shown to dramatically improve imaging throughput and reduce the potentially prohibitive cost for instrument access. To date, up to a single radiofrequency coil has been dedicated to each animal being simultaneously scanned, thus limiting the sensitivity, flexibility, and ultimate throughput. The purpose of this study was to investigate the feasibility of multiple-mouse MRI with a phased-array coil dedicated to each animal. A dual-mouse imaging system, consisting of a pair of two-element phased-array coils, was developed and used to achieve acceleration factors greater than the number of animals scanned at once. By simultaneously scanning two mice with a retrospectively gated cardiac cine MRI sequence, a three-fold acceleration was achieved with SNR in the heart that is equivalent to that achieved with an unaccelerated scan using a commercial mouse birdcage coil. PMID:20146352

  6. Imaging of the aortic valve with MRI and CT angiography.

    PubMed

    Harvey, J J; Hoey, E T D; Ganeshan, A

    2013-12-01

    The aortic valve may be affected by a wide range of congenital and acquired diseases. Echocardiography is the main non-invasive imaging technique for assessing patho-anatomical alterations of the aortic valve and adjacent structures and in many cases is sufficient to establish a diagnosis and/or guide treatment decisions. Recent technological advances in magnetic resonance imaging (MRI) and multidetector computed tomography (MDCT) have enabled these techniques to play a complimentary role in certain clinical scenarios and as such can be useful problem-solving tools. Radiologists should be familiar with the indications, advantages, and limitations of MRI and MDCT in order to advise and direct an appropriate imaging strategy depending upon the clinical scenario. This article reviews the role of MRI and MDCT angiography for assessment of the aortic valve including relevant anatomy, scan acquisition protocols, and post-processing methods. An approach to interpretation and the key imaging features of commonly encountered aortic valvular diseases are discussed.

  7. Integrated Analysis of EEG and fMRI Using Sparsity of Spatial Maps.

    PubMed

    Samadi, S; Soltanian-Zadeh, H; Jutten, C

    2016-09-01

    Integration of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) is an open problem, which has motivated many researches. The most important challenge in EEG-fMRI integration is the unknown relationship between these two modalities. In this paper, we extract the same features (spatial map of neural activity) from both modality. Therefore, the proposed integration method does not need any assumption about the relationship of EEG and fMRI. We present a source localization method from scalp EEG signal using jointly fMRI analysis results as prior spatial information and source separation for providing temporal courses of sources of interest. The performance of the proposed method is evaluated quantitatively along with multiple sparse priors method and sparse Bayesian learning with the fMRI results as prior information. Localization bias and source distribution index are used to measure the performance of different localization approaches with or without a variety of fMRI-EEG mismatches on simulated realistic data. The method is also applied to experimental data of face perception of 16 subjects. Simulation results show that the proposed method is significantly stable against the noise with low localization bias. Although the existence of an extra region in the fMRI data enlarges localization bias, the proposed method outperforms the other methods. Conversely, a missed region in the fMRI data does not affect the localization bias of the common sources in the EEG-fMRI data. Results on experimental data are congruent with previous studies and produce clusters in the fusiform and occipital face areas (FFA and OFA, respectively). Moreover, it shows high stability in source localization against variations in different subjects. PMID:27460558

  8. Impact of the MLC on the MRI field distortion of a prototype MRI-linac

    SciTech Connect

    Kolling, Stefan; Keall, Paul; Oborn, Brad

    2013-12-15

    Purpose: To cope with intrafraction tumor motion, integrated MRI-linac systems for real-time image guidance are currently under development. The multileaf collimator (MLC) is a key component in every state-of-the-art radiotherapy treatment system, allowing for accurate field shaping and tumor tracking. This work quantifies the magnetic impact of a widely used MLC on the MRI field homogeneity for such a modality.Methods: The finite element method was employed to model a MRI-linac assembly comprised of a 1.0 T split-bore MRI magnet and the key ferromagnetic components of a Varian Millennium 120 MLC, namely, the leaves and motors. Full 3D magnetic field maps of the system were generated. From these field maps, the peak-to-peak distortion within the MRI imaging volume was evaluated over a 30 cm diameter sphere volume (DSV) around the isocenter and compared to a maximum preshim inhomogeneity of 300 μT. Five parametric studies were performed: (1) The source-to-isocenter distance (SID) was varied from 100 to 200 cm, to span the range of a compact system to that with lower magnetic coupling. (2) The MLC model was changed from leaves only to leaves with motors, to determine the contribution to the total distortion caused by MLC leaves and motors separately. (3) The system was configured in the inline or perpendicular orientation, i.e., the linac treatment beam was oriented parallel or perpendicular to the magnetic field direction. (4) The treatment field size was varied from 0 × 0 to 20×20 cm{sup 2}, to span the range of clinical treatment fields. (5) The coil currents were scaled linearly to produce magnetic field strengths B{sub 0} of 0.5, 1.0, and 1.5 T, to estimate how the MLC impact changes with B{sub 0}.Results: (1) The MLC-induced MRI field distortion fell continuously with increasing SID. (2) MLC leaves and motors were found to contribute to the distortion in approximately equal measure. (3) Due to faster falloff of the fringe field, the field

  9. Can Dynamic Contrast-Enhanced MRI (DCE-MRI) and Diffusion-Weighted MRI (DW-MRI) Evaluate Inflammation Disease

    PubMed Central

    Zhu, Jianguo; Zhang, Faming; Luan, Yun; Cao, Peng; Liu, Fei; He, Wenwen; Wang, Dehang

    2016-01-01

    Abstract The aim of the study was to investigate diagnosis efficacy of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI) in Crohn's disease (CD). To find out the correlations between functional MRI parameters including Ktrans, Kep, Ve, Vp, and apparent diffusion coefficient (ADC) with a serologic biomarker. The relationships between pharmacokinetic parameters and ADC were also studied. Thirty-two patients with CD (22 men, 10 women; mean age: 30.5 years) and 18 healthy volunteers without any inflammatory disease (10 men, 8 women; mean age, 34.11 years) were enrolled into this approved prospective study. Pearson analysis was used to evaluate the correlation between Ktrans, Kep, Ve, Vp, and C-reactive protein (CRP), ADC, and CRP respectively. The diagnostic efficacy of the functional MRI parameters in terms of sensitivity and specificity were analyzed by receiver operating characteristic (ROC) curve analyses. Optimal cut-off values of each functional MRI parameters for differentiation of inflammatory from normal bowel were determined according to the Youden criterion. Mean value of Ktrans in the CD group was significantly higher than that of normal control group. Similar results were observed for Kep and Ve. On the contrary, the ADC value was lower in the CD group than that in the control group. Ktrans and Ve were shown to be correlated with CRP (r = 0.725, P < 0.001; r = 0.533, P = 0.002), meanwhile ADC showed negative correlation with CRP (r = −0.630, P < 0.001). There were negative correlations between the pharmacokinetic parameters and ADC, such as Ktrans to ADC (r = −0.856, P < 0.001), and Ve to ADC (r = −0.451, P = 0.01). The area under the curve (AUC) was 0.994 for Ktrans (P < 0.001), 0.905 for ADC (P < 0.001), 0.806 for Ve (P < 0.001), and 0.764 for Kep (P = 0.002). The cut-off point of the Ktrans was found to be 0.931 min–1. This value provided the best trade-off between

  10. Bayesian Models for fMRI Data Analysis

    PubMed Central

    Zhang, Linlin; Guindani, Michele; Vannucci, Marina

    2015-01-01

    Functional magnetic resonance imaging (fMRI), a noninvasive neuroimaging method that provides an indirect measure of neuronal activity by detecting blood flow changes, has experienced an explosive growth in the past years. Statistical methods play a crucial role in understanding and analyzing fMRI data. Bayesian approaches, in particular, have shown great promise in applications. A remarkable feature of fully Bayesian approaches is that they allow a flexible modeling of spatial and temporal correlations in the data. This paper provides a review of the most relevant models developed in recent years. We divide methods according to the objective of the analysis. We start from spatio-temporal models for fMRI data that detect task-related activation patterns. We then address the very important problem of estimating brain connectivity. We also touch upon methods that focus on making predictions of an individual's brain activity or a clinical or behavioral response. We conclude with a discussion of recent integrative models that aim at combining fMRI data with other imaging modalities, such as EEG/MEG and DTI data, measured on the same subjects. We also briefly discuss the emerging field of imaging genetics. PMID:25750690

  11. Safety and Technique of Ferumoxytol Administration for MRI

    PubMed Central

    Vasanawala, Shreyas S.; Nguyen, Kim-Lien; Hope, Michael D.; Bridges, Mellena D.; Hope, Thomas A.; Reeder, Scott B.; Bashir, Mustafa R.

    2016-01-01

    Ferumoxytol is an ultrasmall superparamagnetic iron oxide agent marketed for the treatment of anemia. There has been increasing interest in its properties as an MRI contrast agent as well as greater awareness of its adverse event profile. This mini-review summarizes the current state of knowledge of the risks of ferumoxytol and methods of administration. PMID:26890830

  12. Speech Perception in MRI Scanner Noise by Persons with Aphasia

    ERIC Educational Resources Information Center

    Healy, Eric W.; Moser, Dana C.; Morrow-Odom, K. Leigh; Hall, Deborah A.; Fridriksson, Julius

    2007-01-01

    Purpose: To examine reductions in performance on auditory tasks by aphasic and neurologically intact individuals as a result of concomitant magnetic resonance imaging (MRI) scanner noise. Method: Four tasks together forming a continuum of linguistic complexity were developed. They included complex-tone pitch discrimination, same-different…

  13. The effect of Gibbs ringing artifacts on measures derived from diffusion MRI.

    PubMed

    Perrone, Daniele; Aelterman, Jan; Pižurica, Aleksandra; Jeurissen, Ben; Philips, Wilfried; Leemans, Alexander

    2015-10-15

    Diffusion-weighted (DW) magnetic resonance imaging (MRI) is a unique method to investigate microstructural tissue properties noninvasively and is one of the most popular methods for studying the brain white matter in vivo. To obtain reliable statistical inferences with diffusion MRI, however, there are still many challenges, such as acquiring high-quality DW-MRI data (e.g., high SNR and high resolution), careful data preprocessing (e.g., correcting for subject motion and eddy current induced geometric distortions), choosing the appropriate diffusion approach (e.g., diffusion tensor imaging (DTI), diffusion kurtosis imaging (DKI), or diffusion spectrum MRI), and applying a robust analysis strategy (e.g., tractography based or voxel based analysis). Notwithstanding the numerous efforts to optimize many steps in this complex and lengthy diffusion analysis pipeline, to date, a well-known artifact in MRI--i.e., Gibbs ringing (GR)--has largely gone unnoticed or deemed insignificant as a potential confound in quantitative DW-MRI analysis. Considering the recent explosion of diffusion MRI applications in biomedical and clinical applications, a systematic and comprehensive investigation is necessary to understand the influence of GR on the estimation of diffusion measures. In this work, we demonstrate with simulations and experimental DW-MRI data that diffusion estimates are significantly affected by GR artifacts and we show that an off-the-shelf GR correction procedure based on total variation already can alleviate this issue substantially.

  14. Cortical feature analysis and machine learning improves detection of “MRI-negative” focal cortical dysplasia

    PubMed Central

    Ahmed, Bilal; Brodley, Carla E.; Blackmon, Karen E.; Kuzniecky, Ruben; Barash, Gilad; Carlson, Chad; Quinn, Brian T.; Doyle, Werner; French, Jacqueline; Devinsky, Orrin; Thesen, Thomas

    2015-01-01

    Focal cortical dysplasia (FCD) is the most common cause of pediatric epilepsy and the third most common lesion in adults with treatment-resistant epilepsy. Advances in MRI have revolutionized the diagnosis of FCD, resulting in higher success rates for resective epilepsy surgery. However, many histologically confirmed FCD patients have normal pre-surgical MRI studies (‘MRI-negative’), making pre-surgical diagnosis difficult. The purpose of this study is to test whether a novel MRI post-processing method successfully detects histopathologically-verified FCD in a sample of patients without visually appreciable lesions. We applied an automated quantitative morphometry approach which computed five surface-based MRI features and combined them in a machine learning model to classify lesional and non-lesional vertices. Accuracy was defined by classifying contiguous vertices as “lesional” when they fell within the surgical resection region. Our multivariate method correctly detected the lesion in 6 of 7 MRI-positive patients, which is comparable with the detection rates that have been reported in univariate vertex-based morphometry studies. More significantly, in patients that were MRI-negative, machine learning correctly identified 14 out of 24 FCD lesions (58%). This was achieved after separating abnormal thickness and thinness into distinct classifiers, as well as separating sulcal and gyral regions. Results demonstrate that MRI-negative images contain sufficient information to aid in the in-vivo detection of visually elusive FCD lesions. PMID:26037845

  15. Towards MRI-guided linear accelerator control: gating on an MRI accelerator.

    PubMed

    Crijns, S P M; Kok, J G M; Lagendijk, J J W; Raaymakers, B W

    2011-08-01

    To boost the possibilities of image guidance in radiotherapy by providing images with superior soft-tissue contrast during treatment, we pursue diagnostic quality MRI functionality integrated with a linear accelerator. Large respiration-induced semi-periodic target excursions hamper treatment of cancer of the abdominal organs. Methods to compensate in real time for such motion are gating and tracking. These strategies are most effective in cases where anatomic motion can be visualized directly, which supports the use of an integrated MRI accelerator. We establish here an infrastructure needed to realize gated radiation delivery based on MR feedback and demonstrate its potential as a first step towards more advanced image guidance techniques. The position of a phantom subjected to one-dimensional periodic translation is tracked with the MR scanner. Real-time communication with the MR scanner and control of the radiation beam are established. Based on the time-resolved position of the phantom, gated radiation delivery to the phantom is realized. Dose distributions for dynamic delivery conditions with varying gating windows are recorded on gafchromic film. The similarity between dynamically and statically obtained dose profiles gradually increases as the gating window is decreased. With gating windows of 5 mm, we obtain sharp dose profiles. We validate our gating implementation by comparing measured dose profiles to theoretical profiles calculated using the knowledge of the imposed motion pattern. Excellent correspondence is observed. At the same time, we show that real-time on-line reconstruction of the accumulated dose can be performed using time-resolved target position information. This facilitates plan adaptation not only on a fraction-to-fraction scale but also during one fraction, which is especially valuable in highly accelerated treatment strategies. With the currently established framework and upcoming improvements to our prototype-integrated MRI accelerator

  16. In Vivo Proton Beam Range Verification Using Spine MRI Changes

    SciTech Connect

    Gensheimer, Michael F.; Yock, Torunn I.; Liebsch, Norbert J.; Sharp, Gregory C.; Paganetti, Harald; Madan, Neel; Grant, P. Ellen; Bortfeld, Thomas

    2010-09-01

    Purpose: In proton therapy, uncertainty in the location of the distal dose edge can lead to cautious treatment plans that reduce the dosimetric advantage of protons. After radiation exposure, vertebral bone marrow undergoes fatty replacement that is visible on magnetic resonance imaging (MRI). This presents an exciting opportunity to observe radiation dose distribution in vivo. We used quantitative spine MRI changes to precisely detect the distal dose edge in proton radiation patients. Methods and Materials: We registered follow-up T1-weighted MRI images to planning computed tomography scans from 10 patients who received proton spine irradiation. A radiation dose-MRI signal intensity curve was created using the lateral beam penumbra in the sacrum. This curve was then used to measure range errors in the lumbar spine. Results: In the lateral penumbra, there was an increase in signal intensity with higher dose throughout the full range of 0-37.5 Gy (RBE). In the distal fall-off region, the beam sometimes appeared to penetrate farther than planned. The mean overshoot in 10 patients was 1.9 mm (95% confidence interval, 0.8-3.1 mm), on the order of the uncertainties inherent to our range verification method. Conclusions: We have demonstrated in vivo proton range verification using posttreatment spine MRI changes. Our analysis suggests the presence of a systematic overshoot of a few millimeters in some proton spine treatments, but the range error does not exceed the uncertainty incorporated into the treatment planning margin. It may be possible to extend our technique to MRI sequences that show early bone marrow changes, enabling adaptive treatment modification.

  17. Advances in Clinical PET/MRI Instrumentation.

    PubMed

    Herzog, Hans; Lerche, Christoph

    2016-04-01

    In 2010, the first whole-body PET/MRI scanners installed for clinical use were the sequential Philips PET/MRI with PMT-based, TOF-capable technology and the integrated simultaneous Siemens PET/MRI. Avalanche photodiodes as non-magneto-sensitive readout electronics allowed PET integrated within the MRI. The experiences with these scanners showed that improvements of software aspects, such as attenuation correction, were necessary and that efficient protocols combining optimally PET and MRI must be still developed. In 2014, General Electric issued an integrated PET/MRI with SiPM-based PET detectors, allowing TOF-PET. Looking at the MRI components of current PET/MR imaging systems, primary improvements come from sequences and new coils.

  18. FPGA-based RF interference reduction techniques for simultaneous PET-MRI.

    PubMed

    Gebhardt, P; Wehner, J; Weissler, B; Botnar, R; Marsden, P K; Schulz, V

    2016-05-01

    The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) as a multi-modal imaging technique is considered very promising and powerful with regard to in vivo disease progression examination, therapy response monitoring and drug development. However, PET-MRI system design enabling simultaneous operation with unaffected intrinsic performance of both modalities is challenging. As one of the major issues, both the PET detectors and the MRI radio-frequency (RF) subsystem are exposed to electromagnetic (EM) interference, which may lead to PET and MRI signal-to-noise ratio (SNR) deteriorations. Early digitization of electronic PET signals within the MRI bore helps to preserve PET SNR, but occurs at the expense of increased amount of PET electronics inside the MRI and associated RF field emissions. This raises the likelihood of PET-related MRI interference by coupling into the MRI RF coil unwanted spurious signals considered as RF noise, as it degrades MRI SNR and results in MR image artefacts. RF shielding of PET detectors is a commonly used technique to reduce PET-related RF interferences, but can introduce eddy-current-related MRI disturbances and hinder the highest system integration. In this paper, we present RF interference reduction methods which rely on EM field coupling-decoupling principles of RF receive coils rather than suppressing emitted fields. By modifying clock frequencies and changing clock phase relations of digital circuits, the resulting RF field emission is optimised with regard to a lower field coupling into the MRI RF coil, thereby increasing the RF silence of PET detectors. Our methods are demonstrated by performing FPGA-based clock frequency and phase shifting of digital silicon photo-multipliers (dSiPMs) used in the PET modules of our MR-compatible Hyperion II (D) PET insert. We present simulations and magnetic-field map scans visualising the impact of altered clock phase pattern on the spatial RF field

  19. FPGA-based RF interference reduction techniques for simultaneous PET-MRI.

    PubMed

    Gebhardt, P; Wehner, J; Weissler, B; Botnar, R; Marsden, P K; Schulz, V

    2016-05-01

    The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) as a multi-modal imaging technique is considered very promising and powerful with regard to in vivo disease progression examination, therapy response monitoring and drug development. However, PET-MRI system design enabling simultaneous operation with unaffected intrinsic performance of both modalities is challenging. As one of the major issues, both the PET detectors and the MRI radio-frequency (RF) subsystem are exposed to electromagnetic (EM) interference, which may lead to PET and MRI signal-to-noise ratio (SNR) deteriorations. Early digitization of electronic PET signals within the MRI bore helps to preserve PET SNR, but occurs at the expense of increased amount of PET electronics inside the MRI and associated RF field emissions. This raises the likelihood of PET-related MRI interference by coupling into the MRI RF coil unwanted spurious signals considered as RF noise, as it degrades MRI SNR and results in MR image artefacts. RF shielding of PET detectors is a commonly used technique to reduce PET-related RF interferences, but can introduce eddy-current-related MRI disturbances and hinder the highest system integration. In this paper, we present RF interference reduction methods which rely on EM field coupling-decoupling principles of RF receive coils rather than suppressing emitted fields. By modifying clock frequencies and changing clock phase relations of digital circuits, the resulting RF field emission is optimised with regard to a lower field coupling into the MRI RF coil, thereby increasing the RF silence of PET detectors. Our methods are demonstrated by performing FPGA-based clock frequency and phase shifting of digital silicon photo-multipliers (dSiPMs) used in the PET modules of our MR-compatible Hyperion II (D) PET insert. We present simulations and magnetic-field map scans visualising the impact of altered clock phase pattern on the spatial RF field

  20. FPGA-based RF interference reduction techniques for simultaneous PET-MRI

    NASA Astrophysics Data System (ADS)

    Gebhardt, P.; Wehner, J.; Weissler, B.; Botnar, R.; Marsden, P. K.; Schulz, V.

    2016-05-01

    The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) as a multi-modal imaging technique is considered very promising and powerful with regard to in vivo disease progression examination, therapy response monitoring and drug development. However, PET-MRI system design enabling simultaneous operation with unaffected intrinsic performance of both modalities is challenging. As one of the major issues, both the PET detectors and the MRI radio-frequency (RF) subsystem are exposed to electromagnetic (EM) interference, which may lead to PET and MRI signal-to-noise ratio (SNR) deteriorations. Early digitization of electronic PET signals within the MRI bore helps to preserve PET SNR, but occurs at the expense of increased amount of PET electronics inside the MRI and associated RF field emissions. This raises the likelihood of PET-related MRI interference by coupling into the MRI RF coil unwanted spurious signals considered as RF noise, as it degrades MRI SNR and results in MR image artefacts. RF shielding of PET detectors is a commonly used technique to reduce PET-related RF interferences, but can introduce eddy-current-related MRI disturbances and hinder the highest system integration. In this paper, we present RF interference reduction methods which rely on EM field coupling-decoupling principles of RF receive coils rather than suppressing emitted fields. By modifying clock frequencies and changing clock phase relations of digital circuits, the resulting RF field emission is optimised with regard to a lower field coupling into the MRI RF coil, thereby increasing the RF silence of PET detectors. Our methods are demonstrated by performing FPGA-based clock frequency and phase shifting of digital silicon photo-multipliers (dSiPMs) used in the PET modules of our MR-compatible Hyperion II D PET insert. We present simulations and magnetic-field map scans visualising the impact of altered clock phase pattern on the spatial RF field distribution

  1. FPGA-based RF interference reduction techniques for simultaneous PET–MRI

    NASA Astrophysics Data System (ADS)

    Gebhardt, P.; Wehner, J.; Weissler, B.; Botnar, R.; Marsden, P. K.; Schulz, V.

    2016-05-01

    The combination of positron emission tomography (PET) and magnetic resonance imaging (MRI) as a multi-modal imaging technique is considered very promising and powerful with regard to in vivo disease progression examination, therapy response monitoring and drug development. However, PET–MRI system design enabling simultaneous operation with unaffected intrinsic performance of both modalities is challenging. As one of the major issues, both the PET detectors and the MRI radio-frequency (RF) subsystem are exposed to electromagnetic (EM) interference, which may lead to PET and MRI signal-to-noise ratio (SNR) deteriorations. Early digitization of electronic PET signals within the MRI bore helps to preserve PET SNR, but occurs at the expense of increased amount of PET electronics inside the MRI and associated RF field emissions. This raises the likelihood of PET-related MRI interference by coupling into the MRI RF coil unwanted spurious signals considered as RF noise, as it degrades MRI SNR and results in MR image artefacts. RF shielding of PET detectors is a commonly used technique to reduce PET-related RF interferences, but can introduce eddy-current-related MRI disturbances and hinder the highest system integration. In this paper, we present RF interference reduction methods which rely on EM field coupling–decoupling principles of RF receive coils rather than suppressing emitted fields. By modifying clock frequencies and changing clock phase relations of digital circuits, the resulting RF field emission is optimised with regard to a lower field coupling into the MRI RF coil, thereby increasing the RF silence of PET detectors. Our methods are demonstrated by performing FPGA-based clock frequency and phase shifting of digital silicon photo-multipliers (dSiPMs) used in the PET modules of our MR-compatible Hyperion II D PET insert. We present simulations and magnetic-field map scans visualising the impact of altered clock phase pattern on the spatial RF field

  2. Bayesian estimation of the hemodynamic response function in functional MRI

    NASA Astrophysics Data System (ADS)

    Marrelec, G.; Benali, H.; Ciuciu, P.; Poline, J.-B.

    2002-05-01

    Functional MRI (fMRI) is a recent, non-invasive technique allowing for the evolution of brain processes to be dynamically followed in various cognitive or behavioral tasks. In BOLD fMRI, what is actually measured is only indirectly related to neuronal activity through a process that is still under investigation. A convenient way to analyze BOLD fMRI data consists of considering the whole brain as a system characterized by a transfer response function, called the Hemodynamic Response Function (HRF). Precise and robust estimation of the HRF has not been achieved yet: parametric methods tend to be robust but require too strong constraints on the shape of the HRF, whereas non-parametric models are not reliable since the problem is badly conditioned. We therefore propose a full Bayesian, non-parametric method that makes use of basic but relevant a priori knowledge about the underlying physiological process to make robust inference about the HRF. We show that this model is very robust to decreasing signal-to-noise ratio and to the actual noise sampling distribution. We finally apply the method to real data, revealing a wide variety of HRF shapes.

  3. Bayesian segmentation of brainstem structures in MRI.

    PubMed

    Iglesias, Juan Eugenio; Van Leemput, Koen; Bhatt, Priyanka; Casillas, Christen; Dutt, Shubir; Schuff, Norbert; Truran-Sacrey, Diana; Boxer, Adam; Fischl, Bruce

    2015-06-01

    In this paper we present a method to segment four brainstem structures (midbrain, pons, medulla oblongata and superior cerebellar peduncle) from 3D brain MRI scans. The segmentation method relies on a probabilistic atlas of the brainstem and its neighboring brain structures. To build the atlas, we combined a dataset of 39 scans with already existing manual delineations of the whole brainstem and a dataset of 10 scans in which the brainstem structures were manually labeled with a protocol that was specifically designed for this study. The resulting atlas can be used in a Bayesian framework to segment the brainstem structures in novel scans. Thanks to the generative nature of the scheme, the segmentation method is robust to changes in MRI contrast or acquisition hardware. Using cross validation, we show that the algorithm can segment the structures in previously unseen T1 and FLAIR scans with great accuracy (mean error under 1mm) and robustness (no failures in 383 scans including 168 AD cases). We also indirectly evaluate the algorithm with a experiment in which we study the atrophy of the brainstem in aging. The results show that, when used simultaneously, the volumes of the midbrain, pons and medulla are significantly more predictive of age than the volume of the entire brainstem, estimated as their sum. The results also demonstrate that the method can detect atrophy patterns in the brainstem structures that have been previously described in the literature. Finally, we demonstrate that the proposed algorithm is able to detect differential effects of AD on the brainstem structures. The method will be implemented as part of the popular neuroimaging package FreeSurfer.

  4. Interpolation of vector fields from human cardiac DT-MRI.

    PubMed

    Yang, F; Zhu, Y M; Rapacchi, S; Luo, J H; Robini, M; Croisille, P

    2011-03-01

    There has recently been increased interest in developing tensor data processing methods for the new medical imaging modality referred to as diffusion tensor magnetic resonance imaging (DT-MRI). This paper proposes a method for interpolating the primary vector fields from human cardiac DT-MRI, with the particularity of achieving interpolation and denoising simultaneously. The method consists of localizing the noise-corrupted vectors using the local statistical properties of vector fields, removing the noise-corrupted vectors and reconstructing them by using the thin plate spline (TPS) model, and finally applying global TPS interpolation to increase the resolution in the spatial domain. Experiments on 17 human hearts show that the proposed method allows us to obtain higher resolution while reducing noise, preserving details and improving direction coherence (DC) of vector fields as well as fiber tracking. Moreover, the proposed method perfectly reconstructs azimuth and elevation angle maps. PMID:21317482

  5. MRI Volume Fusion Based on 3D Shearlet Decompositions

    PubMed Central

    Duan, Chang; Wang, Shuai; Wang, Xue Gang; Huang, Qi Hong

    2014-01-01

    Nowadays many MRI scans can give 3D volume data with different contrasts, but the observers may want to view various contrasts in the same 3D volume. The conventional 2D medical fusion methods can only fuse the 3D volume data layer by layer, which may lead to the loss of interframe correlative information. In this paper, a novel 3D medical volume fusion method based on 3D band limited shearlet transform (3D BLST) is proposed. And this method is evaluated upon MRI T2* and quantitative susceptibility mapping data of 4 human brains. Both the perspective impression and the quality indices indicate that the proposed method has a better performance than conventional 2D wavelet, DT CWT, and 3D wavelet, DT CWT based fusion methods. PMID:24817880

  6. MRI thermometry: Fast mapping of RF-induced heating along conductive wires.

    PubMed

    Ehses, Philipp; Fidler, Florian; Nordbeck, Peter; Pracht, Eberhard D; Warmuth, Marcus; Jakob, Peter M; Bauer, Wolfgang R

    2008-08-01

    Conductive implants are in most cases a strict contraindication for MRI examinations, as RF pulses applied during the MRI measurement can lead to severe heating of the surrounding tissue. Understanding and mapping of these heating effects is therefore crucial for determining the circumstances under which patient examinations are safe. The use of fluoroptic probes is the standard procedure for monitoring these heating effects. However, the observed temperature increase is highly dependent on the positioning of such a probe, as it can only determine the temperature locally. Temperature mapping with MRI after RF heating can be used, but cooling effects during imaging lead to a significant underestimation of the heating effect. In this work, an MRI thermometry method was combined with an MRI heating sequence, allowing for temperature mapping during RF heating. This technique may provide new opportunities for implant safety investigations.

  7. MRI-guided biopsies and minimally invasive therapy for prostate cancer

    PubMed Central

    Ghai, Sangeet; Trachtenberg, John

    2015-01-01

    Recent advances in multiparametric magnetic resonance imaging (mp-MRI) have led to a paradigm shift in the diagnosis and management of prostate cancer (PCa). Its sensitivity in detecting clinically significant cancer and the ability to localize the tumor within the prostate gland has opened up discussion on targeted diagnosis and therapy in PCa. Use of mp-MRI in conjunction with prostate-specific antigen followed by targeted biopsy allows for a better diagnostic pathway than transrectal ultrasound (TRUS) biopsy and improves the diagnosis of PCa. Improved detection of PCa by mp-MRI has also opened up opportunities for focal therapy within the organ while reducing the incidence of side-effects associated with the radical treatment methods for PCa. This review discusses the evidence and techniques for in-bore MRI-guided prostate biopsy and provides an update on the status of MRI-guided targeted focal therapy in PCa. PMID:26166964

  8. fMRI Brain-Computer Interface: A Tool for Neuroscientific Research and Treatment

    PubMed Central

    Sitaram, Ranganatha; Caria, Andrea; Veit, Ralf; Gaber, Tilman; Rota, Giuseppina; Kuebler, Andrea; Birbaumer, Niels

    2007-01-01

    Brain-computer interfaces based on functional magnetic resonance imaging (fMRI-BCI) allow volitional control of anatomically specific regions of the brain. Technological advancement in higher field MRI scanners, fast data acquisition sequences, preprocessing algorithms, and robust statistical analysis are anticipated to make fMRI-BCI more widely available and applicable. This noninvasive technique could potentially complement the traditional neuroscientific experimental methods by varying the activity of the neural substrates of a region of interest as an independent variable to study its effects on behavior. If the neurobiological basis of a disorder (e.g., chronic pain, motor diseases, psychopathy, social phobia, depression) is known in terms of abnormal activity in certain regions of the brain, fMRI-BCI can be targeted to modify activity in those regions with high specificity for treatment. In this paper, we review recent results of the application of fMRI-BCI to neuroscientific research and psychophysiological treatment. PMID:18274615

  9. Ultrasound vs. MRI in the assessment of rotator cuff structure prior to shoulder arthroplasty

    PubMed Central

    Fischer, Christian Alexander; Weber, Marc-André; Neubecker, Clément; Bruckner, Thomas; Tanner, Michael; Zeifang, Felix

    2015-01-01

    Background/Aims We compared the accuracy of US to 3 T Tesla MRI for the detection of rotator cuff and long biceps tendon pathologies before joint replacement. Methods 45 patients were prospectively included. Results For the supraspinatus tendon, the accuracy of US when using MRI as reference was 91.1%. For the infraspinatus tendon, the accuracy with MRI as reference was 84.4%. The subscapularis tendon was consistently assessed by US and MRI in 35/45 patients (accuracy 77.8%). For the long biceps tendon the accuracy was 86.7%. Conclusion US detection of rotator cuff and biceps tendon integrity is comparable to MRI and should be preferred in revision cases. PMID:25829757

  10. Prostate contouring in MRI guided biopsy

    PubMed Central

    Vikal, Siddharth; Haker, Steven; Tempany, Clare; Fichtinger, Gabor

    2010-01-01

    With MRI possibly becoming a modality of choice for detection and staging of prostate cancer, fast and accurate outlining of the prostate is required in the volume of clinical interest. We present a semi-automatic algorithm that uses a priori knowledge of prostate shape to arrive at the final prostate contour. The contour of one slice is then used as initial estimate in the neighboring slices. Thus we propagate the contour in 3D through steps of refinement in each slice. The algorithm makes only minimum assumptions about the prostate shape. A statistical shape model of prostate contour in polar transform space is employed to narrow search space. Further, shape guidance is implicitly imposed by allowing only plausible edge orientations using template matching. The algorithm does not require region-homogeneity, discriminative edge force, or any particular edge profile. Likewise, it makes no assumption on the imaging coils and pulse sequences used and it is robust to the patient's pose (supine, prone, etc.). The contour method was validated using expert segmentation on clinical MRI data. We recorded a mean absolute distance of 2.0 ± 0.6 mm and dice similarity coefficient of 0.93 ± 0.3 in midsection. The algorithm takes about 1 second per slice. PMID:21132083

  11. Prostate contouring in MRI guided biopsy.

    PubMed

    Vikal, Siddharth; Haker, Steven; Tempany, Clare; Fichtinger, Gabor

    2009-03-27

    With MRI possibly becoming a modality of choice for detection and staging of prostate cancer, fast and accurate outlining of the prostate is required in the volume of clinical interest. We present a semi-automatic algorithm that uses a priori knowledge of prostate shape to arrive at the final prostate contour. The contour of one slice is then used as initial estimate in the neighboring slices. Thus we propagate the contour in 3D through steps of refinement in each slice. The algorithm makes only minimum assumptions about the prostate shape. A statistical shape model of prostate contour in polar transform space is employed to narrow search space. Further, shape guidance is implicitly imposed by allowing only plausible edge orientations using template matching. The algorithm does not require region-homogeneity, discriminative edge force, or any particular edge profile. Likewise, it makes no assumption on the imaging coils and pulse sequences used and it is robust to the patient's pose (supine, prone, etc.). The contour method was validated using expert segmentation on clinical MRI data. We recorded a mean absolute distance of 2.0 ± 0.6 mm and dice similarity coefficient of 0.93 ± 0.3 in midsection. The algorithm takes about 1 second per slice. PMID:21132083

  12. MRI guidance for focused ultrasound surgery

    NASA Astrophysics Data System (ADS)

    McDannold, Nathan; Hynynen, Kullervo

    2005-09-01

    Magnetic resonance imaging (MRI) based monitoring has been shown in recent years to enhance the effectiveness of minimally or noninvasive thermal therapy techniques, such as focused ultrasound surgery. MR imaging's unique soft tissue contrast and ability to image in three dimensions and in any orientation make it extremely useful for treatment planning and for imaging the tissue response to the therapy. The temperature sensitivity of several intrinsic parameters enables MRI to visualize and quantify the progress an ongoing thermal treatment. The most useful temperature-sensitive parameter appears to be the proton resonant frequency, which allows for precise and accurate temperature measurements in water-based tissues. By acquiring a time series of quantitative temperature images, it is possible to monitor the accumulated thermal dose delivered to the target tissue and accurately predict the areas that are thermally ablated, while at the same time ensuring nearby critical structures are not heated. The method is currently used in an FDA approved focused ultrasound device for the treatment of uterine fibroids. Our research and clinical experience with these techniques will be reviewed.

  13. MRI and ultrasonography in Morton's neuroma: Diagnostic accuracy and correlation

    PubMed Central

    Torres-Claramunt, R; Ginés, A; Pidemunt, G; Puig, Ll; de Zabala, S

    2012-01-01

    Background: The diagnosis of Morton's neuroma is based primarily on clinical findings. Ultrasonography (US) and magnetic resonance image (MRI) studies are considered complementary diagnostic techniques. The aim of this study was to establish the correlation and sensitivity of both techniques used to diagnose Morton's neuroma. Materials and Methods: Thirty seven patients (43 intermetatarsal spaces) with Morton's neuroma operated were retrospectively reviewed. In all cases MRI or ultrasound was performed to complement clinical diagnosis of Morton's neuroma. In all cases, a histopathological examination confirmed the diagnosis. Estimates of sensitivity were made and correlation (kappa statistics) was assessed for both techniques. Results: Twenty seven women and 10 men participated with a mean age of 60 years. Double lesions presented in six patients. The second intermetatarsal space was affected in 10 patients and the third in 33 patients. An MRI was performed in 41 cases and a US in 23 cases. In 21 patients, both an MRI and a US were performed. With regard to the 41 MRIs performed, 34 were positive for Morton's neuroma and 7 were negative. MRI sensitivity was 82.9% [95% confidence interval (CI): 0.679–0.929]. Thirteen out of 23 US performed were positive and 10 US were negative. US sensitivity was 56.5% (95% CI: 0.345–0.768). Relative to the 21 patients on whom both techniques were carried out, the agreement between both techniques was poor (kappa statistics 0.31). Conclusion: Although ancillary studies may be required to confirm the clinical diagnosis in some cases, they are probably not necessary for the diagnosis of Morton's neuroma. MRI had a higher sensitivity than US and should be considered the technique of choice in those cases. However, a negative result does not exclude the diagnosis (false negative 17%). PMID:22719120

  14. 3D MRI volume sizing of knee meniscus cartilage.

    PubMed

    Stone, K R; Stoller, D W; Irving, S G; Elmquist, C; Gildengorin, G

    1994-12-01

    Meniscal replacement by allograft and meniscal regeneration through collagen meniscal scaffolds have been recently reported. To evaluate the effectiveness of a replaced or regrown meniscal cartilage, a method for measuring the size and function of the regenerated tissue in vivo is required. To solve this problem, we developed and evaluated a magnetic resonance imaging (MRI) technique to measure the volume of meniscal tissues. Twenty-one intact fresh cadaver knees were evaluated and scanned with MRI for meniscal volume sizing. The sizing sequence was repeated six times for each of 21 lateral and 12 medial menisci. The menisci were then excised and measured by water volume displacement. Each volume displacement measurement was repeated six times. The MRI technique employed to measure the volume of the menisci was shown to correspond to that of the standard measure of volume and was just as precise. However, the MRI technique consistently underestimated the actual volume. The average of the coefficient of variation for lateral volumes was 0.04 and 0.05 for the water and the MRI measurements, respectively. For medial measurements it was 0.04 and 0.06. The correlation for the lateral menisci was r = 0.45 (p = 0.04) and for the medial menisci it was r = 0.57 (p = 0.05). We conclude that 3D MRI is precise and repeatable but not accurate when used to measure meniscal volume in vivo and therefore may only be useful for evaluating changes in meniscal allografts and meniscal regeneration templates over time.

  15. Focal Ablation of Prostate Cancer: Four Roles for MRI Guidance

    PubMed Central

    Sommer, Graham; Bouley, Donna; Gill, Harcharan; Daniel, Bruce; Pauly, Kim Butts; Diederich, Christopher

    2014-01-01

    Introduction There is currently a great deal of interest in the possible use of focal therapies for prostate cancer, since such treatments offer the prospect for control or cure of the primary disease with minimal side effects. Many forms of thermal therapy have been proposed for focal ablation of prostate cancer, including laser, high intensity ultrasound and cryotherapy. This review will demonstrate the important roles that MRI guidance can offer to such focal ablation, focusing on the use of high intensity ultrasonic applicators as an example of one promising technique. Materials and Methods Transurethral and interstitial high intensity ultrasonic applicators, designed specifically for ablation of prostate tissue were tested extensively in vivo in a canine model. The roles of MRI in positioning the devices, monitoring prostate ablation, and depicting ablated tissue were assessed using appropriate MRI sequences. Results MRI guidance provides a very effective tool for the positioning of ablative devices in the prostate, and thermal monitoring successfully predicted ablation of prostate tissue when a threshold of 52°C was achieved. Contrast enhanced MRI accurately depicted the distribution of ablated prostate tissue, which is resorbed at 30 days. Conclusions Guidance of thermal therapies for focal ablation of prostate cancer will likely prove critically dependent on MRI functioning in four separate roles. Our studies indicate that in 3 roles: device positioning; thermal monitoring of prostate ablation; and depiction of ablated prostate tissue, MR techniques are highly accurate and likely to be of great benefit in focal prostate cancer ablation. A fourth critical role, identification of cancer within the gland for targeting of thermal therapy, is more problematic at present, but will likely become practical with further technological advances. PMID:23587506

  16. Adaptive cyclic physiologic noise modeling and correction in functional MRI.

    PubMed

    Beall, Erik B

    2010-03-30

    Physiologic noise in BOLD-weighted MRI data is known to be a significant source of the variance, reducing the statistical power and specificity in fMRI and functional connectivity analyses. We show a dramatic improvement on current noise correction methods in both fMRI and fcMRI data that avoids overfitting. The traditional noise model is a Fourier series expansion superimposed on the periodicity of parallel measured breathing and cardiac cycles. Correction using this model results in removal of variance matching the periodicity of the physiologic cycles. Using this framework allows easy modeling of noise. However, using a large number of regressors comes at the cost of removing variance unrelated to physiologic noise, such as variance due to the signal of functional interest (overfitting the data). It is our hypothesis that there are a small variety of fits that describe all of the significantly coupled physiologic noise. If this is true, we can replace a large number of regressors used in the model with a smaller number of the fitted regressors and thereby account for the noise sources with a smaller reduction in variance of interest. We describe these extensions and demonstrate that we can preserve variance in the data unrelated to physiologic noise while removing physiologic noise equivalently, resulting in data with a higher effective SNR than with current corrections techniques. Our results demonstrate a significant improvement in the sensitivity of fMRI (up to a 17% increase in activation volume for fMRI compared with higher order traditional noise correction) and functional connectivity analyses.

  17. Role of MRI in multiple sclerosis I: inflammation and lesions.

    PubMed

    Zivadinov, Robert; Bakshi, Rohit

    2004-01-01

    Conventional magnetic resonance imaging (MRI) can improve accuracy in the diagnosis of multiple sclerosis (MS). Metrics derived from conventional MRI are now routinely used to detect therapeutic effects and extend clinical observations. Hyperintense lesions on T2-weighted MRI scans are related primarily to increased water content and thus cannot distinguish between inflammation, edema, demyelination, Wallerian degeneration, and axonal loss. In addition, T2-weighted and post-contrast images are not sufficiently sensitive to detect occult disease affecting normal appearing gray and white matter. They do not show a reliable correlation with clinical measures of disability and do not provide a complete assessment of therapeutic outcomes. In the past few years a host of advanced MRI techniques and analysis methods have been introduced for the assessment of MS. These MRI techniques appear to have better reliability as surrogate markers for monitoring the pathologic processes that most likely are related to disease activity and clinical progression. They are able to reveal a range of tissue changes that include edema, inflammation, demyelination, axonal loss, and neurodegeneration. Therefore, in a disease with a high degree of longitudinal variability of clinical signs and symptoms within and between patients, and with no current adequate biological markers of disease progression, non-conventional MRI techniques provide a powerful tool to non-invasively study pathological substrates of overt lesions and normal appearing brain tissue. In particular, the use of these techniques is promising in elucidating mechanisms underlying the accumulation of tissue damage, repair and functional reorganization of neural pathways in patients with MS.

  18. K-Bayes reconstruction for perfusion MRI. I: concepts and application.

    PubMed

    Kornak, John; Young, Karl; Schuff, Norbert; Du, Antao; Maudsley, Andrew A; Weiner, Michael W

    2010-06-01

    Despite the continued spread of magnetic resonance imaging (MRI) methods in scientific studies and clinical diagnosis, MRI applications are mostly restricted to high-resolution modalities, such as structural MRI. While perfusion MRI gives complementary information on blood flow in the brain, its reduced resolution limits its power for detecting specific disease effects on perfusion patterns. This reduced resolution is compounded by artifacts such as partial volume effects, Gibbs ringing, and aliasing, which are caused by necessarily limited k-space sampling and the subsequent use of discrete Fourier transform (DFT) reconstruction. In this study, a Bayesian modeling procedure (K-Bayes) is developed for the reconstruction of perfusion MRI. The K-Bayes approach (described in detail in Part II: Modeling and Technical Development) combines a process model for the MRI signal in k-space with a Markov random field prior distribution that incorporates high-resolution segmented structural MRI information. A simulation study was performed to determine qualitative and quantitative improvements in K-Bayes reconstructed images compared with those obtained via DFT. The improvements were validated using in vivo perfusion MRI data of the human brain. The K-Bayes reconstructed images were demonstrated to provide reduced bias, increased precision, greater effect sizes, and higher resolution than those obtained using DFT.

  19. [Technical novelties, latest diagnostic options in the MRI and CT diagnostics of colorectal cancer].

    PubMed

    Jederán, Éva; Gõdény, Mária

    2015-09-01

    Diagnostic and therapeutic options of colorectal cancer (CRC) have changed over the past decade. Imaging plays a major role, thus the use of scanning methods is recommended by guidelines. Accurate staging, evaluation of treatment efficacy and identification of residual and recurrent tumors are required for the modern management of colorectal cancer. If adequate technical background is provided, magnetic resonance imaging (MRI) gives the information upon which therapeutic options may be determined. High-resolution MRI scans can be interpreted as maps providing functional and molecular information. Diffusion-weighted MRI (DW-MRI) has shown promising results regarding the determination of tumor volume and evaluation of treatment efficacy. Perfusion dynamic contrast-enhanced MRI (P-DCE-MRI) is the subject of research in the early assessment of treatment efficacy. Magnetic resonance spectroscopic imaging (MRSI) is a procedure utilizing biochemical analysis. Its application in CRC is under investigation. Clinical effectiveness of PET-MRI (hardware-based combination of MRI and positron emission tomography) is also being studied. Diagnostic value of computed tomographic colonography (CTC) has been proven in the detection of CRC as well as of polyps. PMID:26339907

  20. Highly accelerated real-time cardiac cine MRI using k-t SPARSE-SENSE.

    PubMed

    Feng, Li; Srichai, Monvadi B; Lim, Ruth P; Harrison, Alexis; King, Wilson; Adluru, Ganesh; Dibella, Edward V R; Sodickson, Daniel K; Otazo, Ricardo; Kim, Daniel

    2013-07-01

    For patients with impaired breath-hold capacity and/or arrhythmias, real-time cine MRI may be more clinically useful than breath-hold cine MRI. However, commercially available real-time cine MRI methods using parallel imaging typically yield relatively poor spatio-temporal resolution due to their low image acquisition speed. We sought to achieve relatively high spatial resolution (∼2.5 × 2.5 mm(2)) and temporal resolution (∼40 ms), to produce high-quality real-time cine MR images that could be applied clinically for wall motion assessment and measurement of left ventricular function. In this work, we present an eightfold accelerated real-time cardiac cine MRI pulse sequence using a combination of compressed sensing and parallel imaging (k-t SPARSE-SENSE). Compared with reference, breath-hold cine MRI, our eightfold accelerated real-time cine MRI produced significantly worse qualitative grades (1-5 scale), but its image quality and temporal fidelity scores were above 3.0 (adequate) and artifacts and noise scores were below 3.0 (moderate), suggesting that acceptable diagnostic image quality can be achieved. Additionally, both eightfold accelerated real-time cine and breath-hold cine MRI yielded comparable left ventricular function measurements, with coefficient of variation <10% for left ventricular volumes. Our proposed eightfold accelerated real-time cine MRI with k-t SPARSE-SENSE is a promising modality for rapid imaging of myocardial function.

  1. fMRI at High Spatial Resolution: Implications for BOLD-Models.

    PubMed

    Goense, Jozien; Bohraus, Yvette; Logothetis, Nikos K

    2016-01-01

    As high-resolution functional magnetic resonance imaging (fMRI) and fMRI of cortical layers become more widely used, the question how well high-resolution fMRI signals reflect the underlying neural processing, and how to interpret laminar fMRI data becomes more and more relevant. High-resolution fMRI has shown laminar differences in cerebral blood flow (CBF), volume (CBV), and neurovascular coupling. Features and processes that were previously lumped into a single voxel become spatially distinct at high resolution. These features can be vascular compartments such as veins, arteries, and capillaries, or cortical layers and columns, which can have differences in metabolism. Mesoscopic models of the blood oxygenation level dependent (BOLD) response therefore need to be expanded, for instance, to incorporate laminar differences in the coupling between neural activity, metabolism and the hemodynamic response. Here we discuss biological and methodological factors that affect the modeling and interpretation of high-resolution fMRI data. We also illustrate with examples from neuropharmacology and the negative BOLD response how combining BOLD with CBF- and CBV-based fMRI methods can provide additional information about neurovascular coupling, and can aid modeling and interpretation of high-resolution fMRI.

  2. fMRI at High Spatial Resolution: Implications for BOLD-Models

    PubMed Central

    Goense, Jozien; Bohraus, Yvette; Logothetis, Nikos K.

    2016-01-01

    As high-resolution functional magnetic resonance imaging (fMRI) and fMRI of cortical layers become more widely used, the question how well high-resolution fMRI signals reflect the underlying neural processing, and how to interpret laminar fMRI data becomes more and more relevant. High-resolution fMRI has shown laminar differences in cerebral blood flow (CBF), volume (CBV), and neurovascular coupling. Features and processes that were previously lumped into a single voxel become spatially distinct at high resolution. These features can be vascular compartments such as veins, arteries, and capillaries, or cortical layers and columns, which can have differences in metabolism. Mesoscopic models of the blood oxygenation level dependent (BOLD) response therefore need to be expanded, for instance, to incorporate laminar differences in the coupling between neural activity, metabolism and the hemodynamic response. Here we discuss biological and methodological factors that affect the modeling and interpretation of high-resolution fMRI data. We also illustrate with examples from neuropharmacology and the negative BOLD response how combining BOLD with CBF- and CBV-based fMRI methods can provide additional information about neurovascular coupling, and can aid modeling and interpretation of high-resolution fMRI. PMID:27445782

  3. A multichannel, real-time MRI RF power monitor for independent SAR determination

    SciTech Connect

    El-Sharkawy, AbdEl-Monem M.; Qian Di; Bottomley, Paul A.; Edelstein, William A.

    2012-05-15

    Purpose: Accurate measurements of the RF power delivered during clinical MRI are essential for safety and regulatory compliance, avoiding inappropriate restrictions on clinical MRI sequences, and for testing the MRI safety of peripheral and interventional devices at known RF exposure levels. The goal is to make independent RF power measurements to test the accuracy of scanner-reported specific absorption rate (SAR) over the extraordinary range of operating conditions routinely encountered in MRI. Methods: A six channel, high dynamic range, real-time power profiling system was designed and built for monitoring power delivery during MRI up to 440 MHz. The system was calibrated and used in two 3 T scanners to measure power applied to human subjects during MRI scans. The results were compared with the scanner-reported SAR. Results: The new power measurement system has highly linear performance over a 90 dB dynamic range and a wide range of MRI duty cycles. It has about 0.1 dB insertion loss that does not interfere with scanner operation. The measurements of whole-body SAR in volunteers showed that scanner-reported SAR was significantly overestimated by up to about 2.2 fold. Conclusions: The new power monitor system can accurately and independently measure RF power deposition over the wide range of conditions routinely encountered during MRI. Scanner-reported SAR values are not appropriate for setting exposure limits during device or pulse sequence testing.

  4. [Technical novelties, latest diagnostic options in the MRI and CT diagnostics of colorectal cancer].

    PubMed

    Jederán, Éva; Gõdény, Mária

    2015-09-01

    Diagnostic and therapeutic options of colorectal cancer (CRC) have changed over the past decade. Imaging plays a major role, thus the use of scanning methods is recommended by guidelines. Accurate staging, evaluation of treatment efficacy and identification of residual and recurrent tumors are required for the modern management of colorectal cancer. If adequate technical background is provided, magnetic resonance imaging (MRI) gives the information upon which therapeutic options may be determined. High-resolution MRI scans can be interpreted as maps providing functional and molecular information. Diffusion-weighted MRI (DW-MRI) has shown promising results regarding the determination of tumor volume and evaluation of treatment efficacy. Perfusion dynamic contrast-enhanced MRI (P-DCE-MRI) is the subject of research in the early assessment of treatment efficacy. Magnetic resonance spectroscopic imaging (MRSI) is a procedure utilizing biochemical analysis. Its application in CRC is under investigation. Clinical effectiveness of PET-MRI (hardware-based combination of MRI and positron emission tomography) is also being studied. Diagnostic value of computed tomographic colonography (CTC) has been proven in the detection of CRC as well as of polyps.

  5. A multichannel, real-time MRI RF power monitor for independent SAR determination

    PubMed Central

    El-Sharkawy, AbdEl-Monem M.; Qian, Di; Bottomley, Paul A.; Edelstein, William A.

    2012-01-01

    Purpose: Accurate measurements of the RF power delivered during clinical MRI are essential for safety and regulatory compliance, avoiding inappropriate restrictions on clinical MRI sequences, and for testing the MRI safety of peripheral and interventional devices at known RF exposure levels. The goal is to make independent RF power measurements to test the accuracy of scanner-reported specific absorption rate (SAR) over the extraordinary range of operating conditions routinely encountered in MRI. Methods: A six channel, high dynamic range, real-time power profiling system was designed and built for monitoring power delivery during MRI up to 440 MHz. The system was calibrated and used in two 3 T scanners to measure power applied to human subjects during MRI scans. The results were compared with the scanner-reported SAR. Results: The new power measurement system has highly linear performance over a 90 dB dynamic range and a wide range of MRI duty cycles. It has about 0.1 dB insertion loss that does not interfere with scanner operation. The measurements of whole-body SAR in volunteers showed that scanner-reported SAR was significantly overestimated by up to about 2.2 fold. Conclusions: The new power monitor system can accurately and independently measure RF power deposition over the wide range of conditions routinely encountered during MRI. Scanner-reported SAR values are not appropriate for setting exposure limits during device or pulse sequence testing. PMID:22559603

  6. fMRI at High Spatial Resolution: Implications for BOLD-Models.

    PubMed

    Goense, Jozien; Bohraus, Yvette; Logothetis, Nikos K

    2016-01-01

    As high-resolution functional magnetic resonance imaging (fMRI) and fMRI of cortical layers become more widely used, the question how well high-resolution fMRI signals reflect the underlying neural processing, and how to interpret laminar fMRI data becomes more and more relevant. High-resolution fMRI has shown laminar differences in cerebral blood flow (CBF), volume (CBV), and neurovascular coupling. Features and processes that were previously lumped into a single voxel become spatially distinct at high resolution. These features can be vascular compartments such as veins, arteries, and capillaries, or cortical layers and columns, which can have differences in metabolism. Mesoscopic models of the blood oxygenation level dependent (BOLD) response therefore need to be expanded, for instance, to incorporate laminar differences in the coupling between neural activity, metabolism and the hemodynamic response. Here we discuss biological and methodological factors that affect the modeling and interpretation of high-resolution fMRI data. We also illustrate with examples from neuropharmacology and the negative BOLD response how combining BOLD with CBF- and CBV-based fMRI methods can provide additional information about neurovascular coupling, and can aid modeling and interpretation of high-resolution fMRI. PMID:27445782

  7. A multi-contrast MRI study of microstructural brain damage in patients with mild cognitive impairment

    PubMed Central

    Granziera, C.; Daducci, A.; Donati, A.; Bonnier, G.; Romascano, D.; Roche, A.; Bach Cuadra, M.; Schmitter, D.; Klöppel, S.; Meuli, R.; von Gunten, A.; Krueger, G.

    2015-01-01

    Objectives The aim of this study was to investigate pathological mechanisms underlying brain tissue alterations in mild cognitive impairment (MCI) using multi-contrast 3 T magnetic resonance imaging (MRI). Methods Forty-two MCI patients and 77 healthy controls (HC) underwent T1/T2* relaxometry as well as Magnetization Transfer (MT) MRI. Between-groups comparisons in MRI metrics were performed using permutation-based tests. Using MRI data, a generalized linear model (GLM) was computed to predict clinical performance and a support-vector machine (SVM) classification was used to classify MCI and HC subjects. Results Multi-parametric MRI data showed microstructural brain alterations in MCI patients vs HC that might be interpreted as: (i) a broad loss of myelin/cellular proteins and tissue microstructure in the hippocampus (p ≤ 0.01) and global white matter (p < 0.05); and (ii) iron accumulation in the pallidus nucleus (p ≤ 0.05). MRI metrics accurately predicted memory and executive performances in patients (p ≤ 0.005). SVM classification reached an accuracy of 75% to separate MCI and HC, and performed best using both volumes and T1/T2*/MT metrics. Conclusion Multi-contrast MRI appears to be a promising approach to infer pathophysiological mechanisms leading to brain tissue alterations in MCI. Likewise, parametric MRI data provide powerful correlates of cognitive deficits and improve automatic disease classification based on morphometric features. PMID:26236628

  8. Tailored RF Pulse Modulation for RF Refocussed Variable Flip Angle MRI

    NASA Astrophysics Data System (ADS)

    Shah, Ajit S.; Ortendahl, Douglas A.; Carlson, Joseph W.; Kramer, David M.; Crooks, Larry E.

    1989-05-01

    Advances in Magnetice Resonance Imaging (MRI) techniques have recently made MRI the imaging modality of choice for many applications of clinical imaging. MRI provides the diagnosing clinician a non-invasive method for obtaining soft tissue differentiation with sub-millimeter resolution. Clinical MRI techniques include 3-dimensional imaging, spectroscopic imaging, arterial angiography and cardiac imaging. One MRI technique which has recently gained popularity is a class of protocols known as variable/partial flip angle MRI. Partial flip angle MRI techniques are useful because of their ability to vary contrast between tissues and/or maintain a particular level of contrast with a reduction in acquisition time [1]. Variable flip angle techniques differ from conventional MRI protocols in that the initial RF excitation/rotation pulse is not constrained to a 90 degree rotation of the longitudinal magnetization. Instead, the initial excitation flip angle is calculated to provide improved contrast between two tissues and/or maximize the intensity of a particular tissue. For tissues with reduced TR/T1 ratios, variable flip angle techniques may also be used to increase the image signal to noise within a localized region.

  9. Direct MRI detection of the neuronal magnetic field: the effect of the dendrite branch.

    PubMed

    Huang, Ying-Ling; Xiong, Hong-Chuan; Yao, De-Zhong

    2010-09-21

    In recent years, neuronal current MRI (nc-MRI) was proposed as a new imaging method to directly map the magnetic field change caused by neuronal activity. Nc-MRI could offer improved spatial and temporal resolution compared to blood hemodynamics-based functional magnetic resonance imaging (fMRI). In this paper, with a finite current dipole as the model of dendrite or dendrite branch, we investigated the spatial distribution of the magnetic field generated by synchronously activated neurons to evaluate the possibility of nc-MRI. Our simulations imply that the existence of a dendrite branch may not only increase the strength of the neuronal magnetic field (NMF), but also raise the non-uniform and unsymmetry of the NMF; therefore, it can enhance the detectability of the neuronal current magnetic field by MRI directly. The results show that the signal phase shift is enlarged, but it is unstable and is still very small, <1 radian, while the magnitude signal may be strong enough for a typical MRI voxel to be detected. We suggest making further efforts to measure the magnitude signal which may induce a large effect in an nc-MRI experiment.

  10. MRI-based Preplanning Using CT and MRI Data Fusion in Patients With Cervical Cancer Treated With 3D-based Brachytherapy: Feasibility and Accuracy Study

    SciTech Connect

    Dolezel, Martin; Odrazka, Karel; Zizka, Jan; Vanasek, Jaroslav; Kohlova, Tereza; Kroulik, Tomas; Spitzer, Dusan; Ryska, Pavel; Tichy, Michal; Kostal, Milan; Jalcova, Lubica

    2012-09-01

    Purpose: Magnetic resonance imaging (MRI)-assisted radiation treatment planning enables enhanced target contouring. The purpose of this study is to analyze the feasibility and accuracy of computed tomography (CT) and MRI data fusion for MRI-based treatment planning in an institution where an MRI scanner is not available in the radiotherapy department. Methods and Materials: The registration inaccuracy of applicators and soft tissue was assessed in 42 applications with CT/MRI data fusion. The absolute positional difference of the center of the applicators was measured in four different planes from the top of the tandem to the cervix. Any inaccuracy of registration of soft tissue in relation to the position of applicators was determined and dose-volume parameters for MRI preplans and for CT/MRI fusion plans with or without target and organs at risk (OAR) adaptation were evaluated. Results: We performed 6,132 measurements in 42 CT/MRI image fusions. Median absolute difference of the center of tandem on CT and MRI was 1.1 mm. Median distance between the center of the right ovoid on CT and MRI was 1.7 and 1.9 mm in the laterolateral and anteroposterior direction, respectively. Corresponding values for the left ovoid were 1.6 and 1.8 mm. Rotation of applicators was 3.1 Degree-Sign . Median absolute difference in position of applicators in relation to soft tissue was 1.93, 1.50, 1.05, and 0.84 mm in the respective transverse planes, and 1.17, 1.28, 1.27, and 1.17 mm in selected angular directions. The dosimetric parameters for organs at risk on CT/MRI fusion plans without OAR adaptation were significantly impaired whereas the target coverage was not influenced. Planning without target adaptation led to overdosing of the target volume, especially high-risk clinical target volume - D{sub 90} 88.2 vs. 83.1 (p < 0.05). Conclusions: MRI-based preplanning with consecutive CT/MRI data fusion can be safe and feasible, with an acceptable inaccuracy of soft tissue registration.

  11. Magnetic Resonance Imaging (MRI) Markers for MRI-Guided High-Dose-Rate Brachytherapy: Novel Marker-Flange for Cervical Cancer and Marker Catheters for Prostate Cancer

    SciTech Connect

    Schindel, Joshua; Muruganandham, Manickam; Pigge, F. Christopher; Anderson, James; Kim, Yusung

    2013-06-01

    Purpose: To present a novel marker-flange, addressing source-reconstruction uncertainties due to the artifacts of a titanium intracavitary applicator used for magnetic resonance imaging (MRI)-guided high-dose-rate (HDR) brachytherapy (BT); and to evaluate 7 different MRI marker agents used for interstitial prostate BT and intracavitary gynecologic HDR BT when treatment plans are guided by MRI. Methods and Materials: Seven MRI marker agents were analyzed: saline solution, Conray-60, copper sulfate (CuSO{sub 4}) (1.5 g/L), liquid vitamin E, fish oil, 1% agarose gel (1 g agarose powder per 100 mL distilled water), and a cobalt–chloride complex contrast (C4) (CoCl{sub 2}/glycine = 4:1). A plastic, ring-shaped marker-flange was designed and tested on both titanium and plastic applicators. Three separate phantoms were designed to test the marker-flange, interstitial catheters for prostate BT, and intracavitary catheters for gynecologic HDR BT. T1- and T2-weighted MRI were analyzed for all markers in each phantom and quantified as percentages compared with a 3% agarose gel background. The geometric accuracy of the MR signal for the marker-flange was measured using an MRI-CT fusion. Results: The CuSO{sub 4} and C4 markers on T1-weighted MRI and saline on T2-weighted MRI showed the highest signals. The marker-flange showed hyper-signals of >500% with CuSO{sub 4} and C4 on T1-weighted MRI and of >400% with saline on T2-weighted MRI on titanium applicators. On T1-weighted MRI, the MRI signal inaccuracies of marker-flanges were measured <2 mm, regardless of marker agents, and that of CuSO{sub 4} was 0.42 ± 0.14 mm. Conclusion: The use of interstitial/intracavitary markers for MRI-guided prostate/gynecologic BT was observed to be feasible, providing accurate source pathway reconstruction. The novel marker-flange can produce extremely intense, accurate signals, demonstrating its feasibility for gynecologic HDR BT.

  12. Polycatechol Nanoparticle MRI Contrast Agents.

    PubMed

    Li, Yiwen; Huang, Yuran; Wang, Zhao; Carniato, Fabio; Xie, Yijun; Patterson, Joseph P; Thompson, Matthew P; Andolina, Christopher M; Ditri, Treffly B; Millstone, Jill E; Figueroa, Joshua S; Rinehart, Jeffrey D; Scadeng, Miriam; Botta, Mauro; Gianneschi, Nathan C

    2016-02-01

    Amphiphilic triblock copolymers containing Fe(III) -catecholate complexes formulated as spherical- or cylindrical-shaped micellar nanoparticles (SMN and CMN, respectively) are described as new T1-weighted agents with high relaxivity, low cytotoxicity, and long-term stability in biological fluids. Relaxivities of both SMN and CMN exceed those of established gadolinium chelates across a wide range of magnetic field strengths. Interestingly, shape-dependent behavior is observed in terms of the particles' interactions with HeLa cells, with CMN exhibiting enhanced uptake and contrast via magnetic resonance imaging (MRI) compared with SMN. These results suggest that control over soft nanoparticle shape will provide an avenue for optimization of particle-based contrast agents as biodiagnostics. The polycatechol nanoparticles are proposed as suitable for preclinical investigations into their viability as gadolinium-free, safe, and effective imaging agents for MRI contrast enhancement. PMID:26681255

  13. Retroperitoneal bronchogenic cyst: MRI findings.

    PubMed

    Castro, R; Oliveira, M I; Fernandes, T; Madureira, A J

    2013-01-01

    The authors describe a case of a retroperitoneal bronchogenic cyst in a 36-year-old female. She presented with abdominal pain, nausea, and vomiting. An MRI scan revealed an 8 cm cystic lesion in the left upper retroperitoneum, with intermediate signal on T2-weighted images, high signal on T1 weighted images, and lack of internal enhancement after gadolinium. After laparoscopic excision, the histology findings were compatible with a bronchogenic cyst, which is extremely uncommon in the retroperitoneum.

  14. Sources of Variation Influencing Concordance between Functional MRI and Direct Cortical Stimulation in Brain Tumor Surgery

    PubMed Central

    Morrison, Melanie A.; Tam, Fred; Garavaglia, Marco M.; Hare, Gregory M. T.; Cusimano, Michael D.; Schweizer, Tom A.; Das, Sunit; Graham, Simon J.

    2016-01-01

    Object: Preoperative functional magnetic resonance imaging (fMRI) remains a promising method to aid in the surgical management of patients diagnosed with brain tumors. For patients that are candidates for awake craniotomies, surgical decisions can potentially be improved by fMRI but this depends on the level of concordance between preoperative brain maps and the maps provided by the gold standard intraoperative method, direct cortical stimulation (DCS). There have been numerous studies of the concordance between fMRI and DCS using sensitivity and specificity measures, however the results are variable across studies and the key factors influencing variability are not well understood. Thus, the present work addresses the influence of technical factors on fMRI and DCS concordance. Methods: Motor and language mapping data were collected for a group of glioma patients (n = 14) who underwent both preoperative fMRI and intraoperative DCS in an awake craniotomy procedure for tumor removal. Normative fMRI data were also acquired in a healthy control group (n = 12). The fMRI and DCS mapping data were co-registered; true positive (TP), true negative (TN), false positive (FP), and false negative (FN) occurrences were tabulated over the exposed brain surface. Sensitivity and specificity were measured for the total group, and for the motor and language sub-groups. The influence of grid placement, fMRI statistical thresholding, and task standardization were assessed. Correlations between proportions of agreement and error were also carefully scrutinized to evaluate concordance in more detail. Results: Concordance was significantly better for motor vs. language mapping. There was an inverse relationship between TP and TN with increasing statistical threshold, and FP dominated the total error. Sensitivity and specificity were reduced when tasks were not standardized across fMRI and DCS. Conclusions: Although the agreement between fMRI and DCS is good, variability is introduced by

  15. MRI characteristics of midbrain tumours.

    PubMed

    Sun, B; Wang, C C; Wang, J

    1999-03-01

    We diagnosed 60 cases of midbrain tumours by MRI between 1993 to 1997. There were 39 males and 21 females, aged 2-64 years, mean 25.6 years. We found 38 patients with true intramedullary mid-brain tumours, 11 predominantly in the tectum, 20 in the tegmentum and 7 with a downward extension to the pons; there were 7 within the cerebral aqueduct. There were 22 patients with infiltrating midbrain tumours extending from adjacent structures, 11 cases each from the thalamus and pineal region. All patients received surgical treatment. Gross total resection was achieved in 42 cases, subtotal (> 75 %) resection in 18. Pathological diagnoses included 16 low-grade and 15 high-grade astrocytomas; 5 oligodendroastrocytomas; 2 ependymomas; 11 glioblastomas; and 11 pineal parenchymal or germ-cell tumours. Midbrain tumours are a heterogeneous group of neoplasms, with wide variation in clinical and MRI features, related to the site and type of tumour. MRI not only allows precise analysis of their growth pattern, but also can lead to a correct preoperative diagnosis in the majority of cases.

  16. Segmentation of knee MRI using structure enhanced local phase filtering

    NASA Astrophysics Data System (ADS)

    Lim, Mikhiel; Hacihaliloglu, Ilker

    2016-03-01

    The segmentation of bone surfaces from magnetic resonance imaging (MRI) data has applications in the quanti- tative measurement of knee osteoarthritis, surgery planning for patient specific total knee arthroplasty and its subsequent fabrication of artificial implants. However, due to the problems associated with MRI imaging such as low contrast between bone and surrounding tissues, noise, bias fields, and the partial volume effect, segmentation of bone surfaces continues to be a challenging operation. In this paper, a new framework is presented for the enhancement of knee MRI scans prior to segmentation in order to obtain high contrast bone images. During the first stage, a new contrast enhanced relative total variation (RTV) regularization method is used in order to remove textural noise from the bone structures and surrounding soft tissue interface. This salient bone edge information is further enhanced using a sparse gradient counting method based on L0 gradient minimization, which globally controls how many non-zero gradients are resulted in order to approximate prominent bone structures in a structure-sparsity-management manner. The last stage of the framework involves incorporation of local phase bone boundary information in order to provide an intensity invariant enhancement of contrast between the bone and surrounding soft tissue. The enhanced images are segmented using a fast random walker algorithm. Validation against expert segmentation was performed on 10 clinical knee MRI images, and achieved a mean dice similarity coefficient (DSC) of 0.975.

  17. Automatic MRI 2D brain segmentation using graph searching technique.

    PubMed

    Pedoia, Valentina; Binaghi, Elisabetta

    2013-09-01

    Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two-dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post-surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stability. PMID:23757180

  18. fMRI analysis software tools: an evaluation framework

    NASA Astrophysics Data System (ADS)

    Pedoia, Valentina; Colli, Vittoria; Strocchi, Sabina; Vite, Cristina; Binaghi, Elisabetta; Conte, Leopoldo

    2011-03-01

    Performance comparison of functional Magnetic Resonance Imaging (fMRI) software tools is a very difficult task. In this paper, a framework for comparison of fMRI analysis results obtained with different software packages is proposed. An objective evaluation is possible only after pre-processing steps that normalize input data in a standard domain. Segmentation and registration algorithms are implemented in order to classify voxels belonging to brain or not, and to find the non rigid transformation that best aligns the volume under inspection with a standard one. Through the definitions of intersection and union of fuzzy logic an index was defined which quantify information overlap between Statistical Parametrical Maps (SPMs). Direct comparison between fMRI results can only highlight differences. In order to assess the best result, an index that represents the goodness of the activation detection is required. The transformation of the activation map in a standard domain allows the use of a functional Atlas for labeling the active voxels. For each functional area the Activation Weighted Index (AWI) that identifies the mean activation level of whole area was defined. By means of this brief, but comprehensive description, it is easy to find a metric for the objective evaluation of a fMRI analysis tools. Trough the first evaluation method the situations where the SPMs are inconsistent were identified. The result of AWI analysis suggest which tool has higher sensitivity and specificity. The proposed method seems a valid evaluation tool when applied to an adequate number of patients.

  19. The circuitry of abulia: Insights from functional connectivity MRI

    PubMed Central

    Siegel, J.S.; Snyder, A.Z.; Metcalf, N.V.; Fucetola, R.P.; Hacker, C.D.; Shimony, J.S.; Shulman, G.L.; Corbetta, M.

    2014-01-01

    Background Functional imaging and lesion studies have associated willed behavior with the anterior cingulate cortex (ACC). Abulia is a syndrome characterized by apathy and deficiency of motivated behavior. Abulia is most frequently associated with ACC damage, but also occurs following damage to subcortical nuclei (striatum, globus pallidus, thalamic nuclei). We present resting state functional connectivity MRI (fcMRI) data from an individual who suffered a stroke leading to abulia. We hypothesized that, although structural imaging revealed no damage to the patient's ACC, fcMRI would uncover aberrant function in this region and in the relevant cortical networks. Methods Resting state correlations in the patient's gray matter were compared to those of age-matched controls. Using a novel method to identify abnormal patterns of functional connectivity in single subjects, we identified areas and networks with aberrant connectivity. Results Networks associated with memory (default mode network) and executive function (cingulo-opercular network) were abnormal. The patient's anterior cingulate was among the areas showing aberrant functional connectivity. In a rescan 3 years later, deficits remained stable and fcMRI findings were replicated. Conclusions These findings suggest that the aberrant functional connectivity mapping approach described may be useful for linking stroke symptoms to disrupted network connectivity. PMID:25379445

  20. Image segmentation and 3D visualization for MRI mammography

    NASA Astrophysics Data System (ADS)

    Li, Lihua; Chu, Yong; Salem, Angela F.; Clark, Robert A.

    2002-05-01

    MRI mammography has a number of advantages, including the tomographic, and therefore three-dimensional (3-D) nature, of the images. It allows the application of MRI mammography to breasts with dense tissue, post operative scarring, and silicon implants. However, due to the vast quantity of images and subtlety of difference in MR sequence, there is a need for reliable computer diagnosis to reduce the radiologist's workload. The purpose of this work was to develop automatic breast/tissue segmentation and visualization algorithms to aid physicians in detecting and observing abnormalities in breast. Two segmentation algorithms were developed: one for breast segmentation, the other for glandular tissue segmentation. In breast segmentation, the MRI image is first segmented using an adaptive growing clustering method. Two tracing algorithms were then developed to refine the breast air and chest wall boundaries of breast. The glandular tissue segmentation was performed using an adaptive thresholding method, in which the threshold value was spatially adaptive using a sliding window. The 3D visualization of the segmented 2D slices of MRI mammography was implemented under IDL environment. The breast and glandular tissue rendering, slicing and animation were displayed.

  1. Distribution of Hyperpolarized Xenon in the Brain Following Sensory Stimulation: Preliminary MRI Findings

    PubMed Central

    Mazzanti, Mary L.; Walvick, Ronn P.; Zhou, Xin; Sun, Yanping; Shah, Niral; Mansour, Joey; Gereige, Jessica; Albert, Mitchell S.

    2011-01-01

    In hyperpolarized xenon magnetic resonance imaging (HP 129Xe MRI), the inhaled spin-1/2 isotope of xenon gas is used to generate the MR signal. Because hyperpolarized xenon is an MR signal source with properties very different from those generated from wate