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Sample records for mri dgemric method

  1. The impact of the relaxivity definition on the quantitative measurement of glycosaminoglycans in cartilage by the MRI dGEMRIC method.

    PubMed

    Zheng, Shaokuan; Xia, Yang

    2010-01-01

    The relaxivities (R-values) of the gadolinium diethylene triamine pentaacetic acid (Gd(DTPA)2-) ions in a series of skim-milk solutions at 0-40% milk concentrations were measured using NMR spectroscopy. The R-value was found to be approximately linearly proportional to the concentration of the solid component in the milk solution. Using the R-value at 20% solid component (approximately the solid concentration in bovine nasal cartilage), the glycosaminoglycan concentration in bovine nasal cartilage can be quantified using the MRI delayed gadolinium-enhanced MRI of cartilage method without the customary scaling factor of 2. This finding is also supported by the measurements using 23Na NMR spectroscopy, 23Na inductively coupled plasma analysis, and biochemical assay. The choice of the R-value definition in the MRI delayed gadolinium-enhanced MRI of cartilage method is discussed, and the definition of Gd(DTPA)2- ions as "millimole per volume of tissue (or milk solution for substitution)" should be used.

  2. Delayed Gadolinium-Enhanced MRI of Cartilage (dGEMRIC) Shows No Change in Cartilage Structural Composition after Viscosupplementation in Patients with Early-Stage Knee Osteoarthritis

    PubMed Central

    van Tiel, Jasper; Reijman, Max; Bos, Pieter K.; Hermans, Job; van Buul, Gerben M.; Bron, Esther E.; Klein, Stefan; Verhaar, Jan A. N.; Krestin, Gabriel P.; Bierma-Zeinstra, Sita M. A.; Weinans, Harrie; Kotek, Gyula; Oei, Edwin H. G.

    2013-01-01

    Introduction Viscosupplementation with hyaluronic acid (HA) of osteoarthritic (OA) knee joints has a well-established positive effect on clinical symptoms. This effect, however, is only temporary and the working mechanism of HA injections is not clear. It was suggested that HA might have disease modifying properties because of its beneficial effect on cartilage sulphated glycosaminoglycan (sGAG) content. Delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) is a highly reproducible, non-invasive surrogate measure for sGAG content and hence composition of cartilage. The aim of this study was to assess whether improvement in cartilage structural composition is detected using dGEMRIC 14 weeks after 3 weekly injections with HA in patients with early-stage knee OA. Methods In 20 early-stage knee OA patients (KLG I-II), 3D dGEMRIC at 3T was acquired before and 14 weeks after 3 weekly injections with HA. To evaluate patient symptoms, the knee injury and osteoarthritis outcome score (KOOS) and a numeric rating scale (NRS) for pain were recorded. To evaluate cartilage composition, six cartilage regions in the knee were analyzed on dGEMRIC. Outcomes of dGEMRIC, KOOS and NRS before and after HA were compared using paired t-testing. Since we performed multiple t-tests, we applied a Bonferroni-Holm correction to determine statistical significance for these analyses. Results All KOOS subscales (‘pain’, ‘symptoms’, ‘daily activities’, ‘sports’ and ’quality of life’) and the NRS pain improved significantly 14 weeks after Viscosupplementation with HA. Outcomes of dGEMRIC did not change significantly after HA compared to baseline in any of the cartilage regions analyzed in the knee. Conclusions Our results confirm previous findings reported in the literature, showing persisting improvement in symptomatic outcome measures in early-stage knee OA patients 14 weeks after Viscosupplementation. Outcomes of dGEMRIC, however, did not change after Viscosupplementation

  3. [Cartilage quality in finger joints: delayed Gd(DTPA)²-enhanced MRI of the cartilage (dGEMRIC) at 3T].

    PubMed

    Miese, F R; Ostendorf, B; Wittsack, H-J; Reichelt, D C; Kröpil, P; Lanzman, R S; Mamisch, T C; Zilkens, C; Jellus, V; Quentin, M; Schneider, M; Scherer, A

    2010-10-01

    To evaluate the feasibility of molecular cartilage MRI in finger joints. Delayed Gd(DTPA)²-enhanced MRI of the cartilage (dGEMRIC) using a variable flip angle approach (VFA) was performed for the metacarpophalangeal (MCP) joints II and III in nine healthy volunteers and eighteen patients with rheumatoid arthritis (RA). The cartilage thickness was measured. Additionally, dGEMRIC was performed on proximal interphalangeal joints (PIP) in two patients with finger osteoarthritis (OA). the dGEMRIC index of the four evaluated cartilage areas was significantly decreased in RA patients compared to healthy subjects. The dGEMRIC index of MCP II phalangeal cartilage was 389.6 ± 85.5 msec vs. 558.7 ± 74.4 msec in healthy subjects. The metacarpal MCP II cartilage dGEMRIC index was 357.3 msec ± 97.1 msec vs. 490.0 ± 86.6 msec. The dGEMRIC indices of MCP III were: phalangeal 436.2 ± 113.6 msec in RA, 558.8 ± 115.5 msec in healthy subjects and metacarpal 398.0 ± 97.6 msec in RA and 529.6 ± 111.0 msec in healthy subjects. Age and cartilage thickness were not significantly different. In PIP joints of finger osteoarthritis patients, low dGEMRIC indices were noted, compared to the controls. The dGEMRIC of finger joints is feasible in patients with RA and finger OA. Morphologically normal cartilage shows significantly decreased dGEMRIC values in RA, pointing towards cartilage degeneration on a molecular level. Further studies are needed to establish the usefulness of this technique for early diagnosis, prognosis and therapy monitoring. © Georg Thieme Verlag KG Stuttgart · New York.

  4. Delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) of cadaveric shoulders: comparison of contrast dynamics in hyaline and fibrous cartilage after intraarticular gadolinium injection.

    PubMed

    Wiener, E; Hodler, J; Pfirrmann, C W A

    2009-01-01

    Delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) is a novel method to investigate cartilaginous and fibrocartilaginous structures. To investigate the contrast dynamics in hyaline and fibrous cartilage of the glenohumeral joint after intraarticular injection of gadopentetate dimeglumine. Transverse T(1) maps were acquired on a 1.5T scanner before and after intraarticular injection of 2.0 mmol/l gadopentetate dimeglumine in five cadaveric shoulders using a dual flip angle three-dimensional gradient echo (3D-GRE) sequence. The acquisition time for the T(1) maps was 5 min 5 s for the whole shoulder. Measurements were repeated every 15 min over 2.5 hours. Regions of interest (ROIs) covering the glenoid cartilage and the labrum were drawn to assess the temporal evolution of the relaxation parameters. T(1) of unenhanced hyaline cartilage of the glenoid was 568+/-34 ms. T(1) of unenhanced fibrous cartilage of the labrum was 552+/-38 ms. Significant differences (P=0.002 and 0.03) in the relaxation parameters were already measurable after 15 min. After 2 to 2.5 hours, hyaline and fibrous cartilage still demonstrated decreasing relaxation parameters, with a larger range of the T(1)(Gd) values in fibrous cartilage. T(1) and triangle Delta R(1) values of hyaline and fibrous cartilage after 2.5 hours were 351+/-16 ms and 1.1+/-0.09 s(-1), and 332+/-31 ms and 1.2+/-0.1 s(-1), respectively. A significant decrease in T(1)(Gd) was found 15 min after intraarticular contrast injection. Contrast accumulation was faster in hyaline than in fibrous cartilage. After 2.5 hours, contrast accumulation showed a higher rate of decrease in hyaline cartilage, but neither hyaline nor fibrous cartilage had reached equilibrium.

  5. 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.

  6. Cartilage health in high tibial osteotomy using dGEMRIC: Relationships with joint kinematics.

    PubMed

    d'Entremont, Agnes G; McCormack, Robert G; Agbanlog, Kenard; Horlick, Simon G D; Stone, Trevor B; Manzary, Mojieb M; Wilson, David R

    2015-06-01

    The aims of this study are to determine how opening-wedge high tibial osteotomy (HTO) affects cartilage health in the tibiofemoral (TF) joint and patella, and to explore relationships between TF and patellofemoral (PF) joint kinematics and cartilage health in HTO. 14 knees (13 subjects) with medial TF osteoarthritis (OA) were examined before HTO and 6 and 12 months after HTO using delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) to evaluate cartilage health at the TF joint and patella. They were also examined using a validated 3D MR knee kinematics measurement to obtain 11 rotations and translations at both TF and PF joints. No statistically significant differences in overall TF or patellar dGEMRIC score were found at 6 or 12 months after HTO. However three subjects had large decreases (mean 105 ms) in TF dGEMRIC at 6 months that recovered at 12 months. Kinematics for these subjects were compared to subjects who did not have decreases in TF dGEMRIC at 6 months (n=5). Differences were observed between groups with HTO in anterior and proximal tibial translation (mean differences 3.05 mm and 1.35 mm), and patellar flexion (mean difference 3.65°). These changes were consistent between 6 and 12 months, despite recovery of TF dGEMRIC values. We did not find significant differences in TF or patellar dGEMRIC before and after HTO with all subjects, however there were differences in kinematics between subjects who had a decrease in TF dGEMRIC at 6 months and those who did not. This suggests a link between joint kinematics and cartilage health in HTO. The effect of opening-wedge high tibial osteotomy on cartilage GAG concentration may be linked to specific changes in knee kinematics following surgery. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Planar dGEMRIC Maps May Aid Imaging Assessment of Cartilage Damage in Femoroacetabular Impingement.

    PubMed

    Bulat, Evgeny; Bixby, Sarah D; Siversson, Carl; Kalish, Leslie A; Warfield, Simon K; Kim, Young-Jo

    2016-02-01

    Three-dimensional (3-D) delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) helps quantify biochemical changes in articular cartilage that correlate with early-stage osteoarthritis. However, dGEMRIC analysis is performed slice by slice, limiting the potential of 3-D data to give an overall impression of cartilage biochemistry. We previously developed a computational algorithm to produce unfolded, or "planar," dGEMRIC maps of acetabular cartilage, but have neither assessed their application nor determined whether MRI-based grading of cartilage damage or dGEMRIC measurements predict intraoperative findings in hips with symptomatic femoroacetabular impingement (FAI). (1) Does imaging-based assessment of acetabular cartilage damage correlate with intraoperative findings in hips with symptomatic FAI? (2) Does the planar dGEMRIC map improve this correlation? (3) Does the planar map improve the correlation between the dGEMRIC index and MRI-based grading of cartilage damage in hips with symptomatic FAI? (4) Does the planar map improve imaging-based evaluation time for hips with symptomatic FAI? We retrospectively studied 47 hips of 45 patients with symptomatic FAI who underwent hip surgery between 2009 and 2013 and had a 1.5-T 3-D dGEMRIC scan within 6 months preoperatively. Our cohort included 25 males and 20 females with a mean ± SD age at surgery of 29 ± 11 years. Planar dGEMRIC maps were generated from isotropic, sagittal oblique TrueFISP and T1 sequences. A pediatric musculoskeletal radiologist with experience in hip MRI evaluated studies using radially reformatted sequences. For six acetabular subregions (anterior-peripheral [AP]; anterior-central [AC]; superior-peripheral [SP]; superior-central [SC]; posterior-peripheral [PP]; posterior-central [PC]), modified Outerbridge cartilage damage grades were recorded and region-of-interest T1 averages (the dGEMRIC index) were measured. Beck's intraoperative cartilage damage grades were compared with the Outerbridge

  8. Delayed Gadolinium-Enhanced MR Imaging of Cartilage (dGEMRIC) Following ACL Injury

    PubMed Central

    Fleming, Braden C.; Oksendahl, Heidi L.; Mehan, William A.; Portnoy, Roman; Fadale, Paul D.; Hulstyn, Michael J.; Bowers, Megan E.; Machan, Jason T.; Tung, Glenn A.

    2010-01-01

    Objective Early detection of glycosaminoglycan loss may provide insight into mechanisms of cartilage damage in the ACL-injured patient. We hypothesized that tibial and femoral dGEMRIC indices would be lower in the medial compartment of the ACL-injured knee than in the contralateral, uninjured knee, and that scan order (i.e. whether the injured or the uninjured knee was imaged first) would not affect the indices. Methods 15 subjects with unilateral ACL injuries recieved a double dose of gadolinium [Gd(DTPA)2−] intravenously. After 90 minutes, both knees were sequentially imaged. The injured knee was scanned first in the odd-numbered subjects and second in the even-numbered subjects. The dGEMRIC indices of the median slice of the medial compartment were determined using the MRIMapper software. Index comparisons were made between knee status (ACL-injured versus uninjured), scan order (ACL-injured first versus uninjured first), and cartilage location (tibia versus femur) using a mixed model. Results There was a significant difference in the mean dGEMRIC indices of the medial compartment between injured and uninjured knees (p<0.007). On average, there was a 13% decrease in the dGEMRIC index of the injured knee compared to the uninjured knee. There were no significant effects due to test order (p=0.800) or cartilage location (p=0.439). Conclusions The results demonstrate lower GAG concentrations in the medial compartment of the femoral and tibial articular cartilage of the ACL-injured knee when compared to the contralateral uninjured knee. The dGEMRIC indices were not sensitive to scan order; thus, sequential imaging of both knees is possible in this patient population. PMID:20188685

  9. Three-dimensional hip cartilage quality assessment of morphology and dGEMRIC by planar maps and automated segmentation

    PubMed Central

    Siversson, Carl; Akhondi-Asl, Alireza; Bixby, Sarah; Kim, Young-Jo; Warfield, Simon K.

    2015-01-01

    Objective The quantitative interpretation of hip cartilage MRI has been limited by the difficulty of identifying and delineating the cartilage in a 3D dataset, thereby reducing its routine usage. In this paper a solution is suggested by unfolding the cartilage to planar 2D maps on which both morphology and biochemical degeneration patterns can be investigated across the entire hip joint. Design Morphological TrueFISP and biochemical dGEMRIC hip images were acquired isotropically for 15 symptomatic subjects with mild or no radiographic osteoarthritis. A multi-template based label fusion technique was used to automatically segment the cartilage tissue, followed by a geometric projection algorithm to generate the planar maps. The segmentation performance was investigated through a leave-one-out study, for two different fusion methods and as a function of the number of utilized templates. Results For each of the generated planar maps, various patterns could be seen, indicating areas of healthy and degenerated cartilage. Dice coefficients for cartilage segmentation varied from 0.76 with four templates to 0.82 with 14 templates. Regional analysis suggests even higher segmentation performance in the superior half of the cartilage. Conclusions The proposed technique is the first of its kind to provide planar maps that enable straightforward quantitative assessment of hip cartilage morphology and dGEMRIC values. This technique may have important clinical applications for patient selection for hip preservation surgery, as well as for epidemiological studies of cartilage degeneration patterns. It is also shown that 10-15 templates are sufficient for accurate segmentation in this application. PMID:25278060

  10. No degeneration found in focal cartilage defects evaluated with dGEMRIC at 12-year follow-up.

    PubMed

    Engen, Cathrine Nørstad; Løken, Sverre; Årøen, Asbjørn; Ho, Charles; Engebretsen, Lars

    2017-02-01

    Background and purpose - The natural history of focal cartilage defects (FCDs) is still unresolved, as is the long-term cartilage quality after cartilage surgery. It has been suggested that delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) is a biomarker of early OA. We aimed to quantitatively evaluate the articular cartilage in knees with FCDs, 12 years after arthroscopic diagnosis. Patients and methods - We included 21 patients from a cohort of patients with knee pain who underwent arthroscopy in 1999. Patients with a full-thickness cartilage defect, stable knees, and at least 50% of both their menisci intact at baseline were eligible. 10 patients had cartilage repair performed at baseline (microfracture or autologous chondrocyte implantation), whereas 11 patients had either no additional surgery or simple debridement performed. Mean follow-up time was 12 (10-13) years. The morphology and biochemical features were evaluated with dGEMRIC and T2 mapping. Standing radiographs for Kellgren and Lawrence (K&L) classification of osteoarthritis (OA) were obtained. Knee function was assessed with VAS, Tegner, Lysholm, and KOOS. Results - The dGEMRIC showed varying results but, overall, no increased degeneration of the injured knees. Degenerative changes (K&L above 0) were, however, evident in 13 of the 21 knees. Interpretation - The natural history of untreated FCDs shows large dGEMRIC variations, as does the knee articular cartilage of surgically treated patients. In this study, radiographic OA changes did not correlate with cartilage quality, as assessed with dGEMRIC.

  11. No degeneration found in focal cartilage defects evaluated with dGEMRIC at 12-year follow-up

    PubMed Central

    Engen, Cathrine Nørstad; Løken, Sverre; Årøen, Asbjørn; Ho, Charles; Engebretsen, Lars

    2017-01-01

    Background and purpose — The natural history of focal cartilage defects (FCDs) is still unresolved, as is the long-term cartilage quality after cartilage surgery. It has been suggested that delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) is a biomarker of early OA. We aimed to quantitatively evaluate the articular cartilage in knees with FCDs, 12 years after arthroscopic diagnosis. Patients and methods — We included 21 patients from a cohort of patients with knee pain who underwent arthroscopy in 1999. Patients with a full-thickness cartilage defect, stable knees, and at least 50% of both their menisci intact at baseline were eligible. 10 patients had cartilage repair performed at baseline (microfracture or autologous chondrocyte implantation), whereas 11 patients had either no additional surgery or simple debridement performed. Mean follow-up time was 12 (10–13) years. The morphology and biochemical features were evaluated with dGEMRIC and T2 mapping. Standing radiographs for Kellgren and Lawrence (K&L) classification of osteoarthritis (OA) were obtained. Knee function was assessed with VAS, Tegner, Lysholm, and KOOS. Results — The dGEMRIC showed varying results but, overall, no increased degeneration of the injured knees. Degenerative changes (K&L above 0) were, however, evident in 13 of the 21 knees. Interpretation — The natural history of untreated FCDs shows large dGEMRIC variations, as does the knee articular cartilage of surgically treated patients. In this study, radiographic OA changes did not correlate with cartilage quality, as assessed with dGEMRIC. PMID:27882808

  12. T2* mapping and delayed gadolinium-enhanced magnetic resonance imaging in cartilage (dGEMRIC) of humeral articular cartilage--a histologically controlled study.

    PubMed

    Bittersohl, Bernd; Kircher, Jörn; Miese, Falk R; Dekkers, Christin; Habermeyer, Peter; Fröbel, Julia; Antoch, Gerald; Krauspe, Rüdiger; Zilkens, Christoph

    2015-10-01

    Cartilage biochemical imaging modalities that include the magnetic resonance imaging (MRI) techniques of T2* mapping (sensitive to water content and collagen fiber network) and delayed gadolinium-enhanced MRI of cartilage (dGEMRIC, sensitive to the glycosaminoglycan content) can be effective instruments for early diagnosis and reliable follow-up of cartilage damage. The purpose of this study was to provide T2* mapping and dGEMRIC values in various histologic grades of cartilage degeneration in humeral articular cartilage. A histologically controlled in vitro study was conducted that included human humeral head cartilage specimens with various histologic grades of cartilage degeneration. High-resolution, 3-dimensional (3D) T2* mapping and dGEMRIC were performed that enabled the correlation of MRI and histology data. Cartilage degeneration was graded according to the Mankin score, which evaluates surface morphology, cellularity, toluidine blue staining, and tidemark integrity. SPSS software was used for statistical analyses. Both MRI mapping values decreased significantly (P < .001) with increasing cartilage degeneration. Spearman rank analysis revealed a significant correlation (correlation coefficients ranging from -0.315 to 0.784; P < .001) between the various histologic parameters and the T2* and T1Gd mapping values. This study demonstrates the feasibility of 3D T2* and dGEMRIC to identify various histologic grades of cartilage damage of humeral articular cartilage. With regard to the advantages of these mapping techniques with high image resolution and the ability to accomplish a 3D biochemically sensitive imaging, we consider that these imaging techniques can make a positive contribution to the currently evolving science and practice of cartilage biochemical imaging. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  13. 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

  14. Fast iterative reconstruction method for PROPELLER MRI

    NASA Astrophysics Data System (ADS)

    Guo, Hongyu; Dai, Jianping; Shi, Jinquan

    2009-10-01

    Patient motion during scanning will introduce artifacts in the reconstructed image in MRI imaging. Periodically Rotated Overlapping Parallel Lines with Enhanced Reconstruction (PROPELLER) MRI is an effective technique to correct for motion artifacts. The iterative method that combine the preconditioned conjugate gradient (PCG) algorithm with nonuniform fast Fourier transformation (NUFFT) operations is applied to PROPELLER MRI in the paper. But the drawback of the method is long reconstruction time. In order to make it viable in clinical situation, parallel optimization of the iterative method on modern GPU using CUDA is proposed. The simulated data and in vivo data from PROPELLER MRI are respectively reconstructed in order to test the method. The experimental results show that image quality is improved compared with gridding method using the GPU based iterative method with compatible reconstruction time.

  15. Comparison of biochemical cartilage imaging techniques at 3 T MRI.

    PubMed

    Rehnitz, C; Kupfer, J; Streich, N A; Burkholder, I; Schmitt, B; Lauer, L; Kauczor, H-U; Weber, M-A

    2014-10-01

    To prospectively compare chemical-exchange saturation-transfer (CEST) with delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) and T2 mapping to assess the biochemical cartilage properties of the knee. Sixty-nine subjects were prospectively included (median age, 42 years; male/female = 32/37) in three cohorts: 10 healthy volunteers, 40 patients with clinically suspected cartilage lesions, and 19 patients about 1 year after microfracture therapy. T2 mapping, dGEMRIC, and CEST were performed at a 3 T MRI unit using a 15-channel knee coil. Parameter maps were evaluated using region-of-interest analysis of healthy cartilage, areas of chondromalacia and repair tissue. Differentiation of damaged from healthy cartilage was assessed using receiver-operating characteristic (ROC) analysis. Chondromalacia grade 2-3 had significantly higher CEST values (P = 0.001), lower dGEMRIC (T1-) values (P < 0.001) and higher T2 values (P < 0.001) when compared to the normal appearing cartilage. dGEMRIC and T2 mapping correlated moderately negative (Spearman coefficient r = -0.56, P = 0.0018) and T2 mapping and CEST moderately positive (r = 0.5, P = 0.007), while dGEMRIC and CEST did not significantly correlate (r = -0.311, P = 0.07). The repair tissue revealed lower dGEMRIC values (P < 0.001) and higher CEST values (P < 0.001) with a significant negative correlation (r = -0.589, P = 0.01), whereas T2 values were not different (P = 0.54). In healthy volunteers' cartilage, CEST and dGEMRIC showed moderate positive correlation (r = 0.56), however not reaching significance (P = 0.09). ROC-analysis demonstrated non-significant differences of T2 mapping vs CEST (P = 0.14), CEST vs dGEMRIC (P = 0.89), and T2 mapping vs dGEMRIC (P = 0.12). CEST is able to detect normal and damaged cartilage and is non-inferior in distinguishing both when compared to dGEMRIC and T2 mapping. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  16. In vivo biochemical 7.0 Tesla magnetic resonance: preliminary results of dGEMRIC, zonal T2, and T2* mapping of articular cartilage.

    PubMed

    Welsch, Goetz H; Mamisch, Tallal C; Hughes, Timothy; Zilkens, Christoph; Quirbach, Sebastian; Scheffler, Klaus; Kraff, Oliver; Schweitzer, Mark E; Szomolanyi, Pavol; Trattnig, Siegfried

    2008-09-01

    Ultra-high-field whole-body systems (7.0 T) have a high potential for future human in vivo magnetic resonance imaging (MRI). In musculoskeletal MRI, biochemical imaging of articular cartilage may benefit, in particular. Delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) and T2 mapping have shown potential at 3.0 T. Although dGEMRIC, allows the determination of the glycosaminoglycan content of articular cartilage, T2 mapping is a promising tool for the evaluation of water and collagen content. In addition, the evaluation of zonal variation, based on tissue anisotropy, provides an indicator of the nature of cartilage ie, hyaline or hyaline-like articular cartilage.Thus, the aim of our study was to show the feasibility of in vivo dGEMRIC, and T2 and T2* relaxation measurements, at 7.0 T MRI; and to evaluate the potential of T2 and T2* measurements in an initial patient study after matrix-associated autologous chondrocyte transplantation (MACT) in the knee. MRI was performed on a whole-body 7.0 T MR scanner using a dedicated circular polarization knee coil. The protocol consisted of an inversion recovery sequence for dGEMRIC, a multiecho spin-echo sequence for standard T2 mapping, a gradient-echo sequence for T2* mapping and a morphologic PD SPACE sequence. Twelve healthy volunteers (mean age, 26.7 +/- 3.4 years) and 4 patients (mean age, 38.0 +/- 14.0 years) were enrolled 29.5 +/- 15.1 months after MACT. For dGEMRIC, 5 healthy volunteers (mean age, 32.4 +/- 11.2 years) were included. T1 maps were calculated using a nonlinear, 2-parameter, least squares fit analysis. Using a region-of-interest analysis, mean cartilage relaxation rate was determined as T1 (0) for precontrast measurements and T1 (Gd) for postcontrast gadopentate dimeglumine [Gd-DTPA(2-)] measurements. T2 and T2* maps were obtained using a pixelwise, monoexponential, non-negative least squares fit analysis; region-of-interest analysis was carried out for deep and superficial cartilage aspects

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Emerging MRI methods in rheumatoid arthritis.

    PubMed

    Borrero, Camilo G; Mountz, James M; Mountz, John D

    2011-02-01

    New MRI techniques have been developed to assess not only the static anatomy of synovial hyperplasia, bone changes and cartilage degradation in patients with rheumatoid arthritis (RA), but also the activity of the physiological events that cause these changes. This enables an estimation of the rate of change in the synovium, bone and cartilage as a result of disease activity or in response to therapy. Typical MRI signs of RA in the pre-erosive phase include synovitis, bone marrow edema and subchondral cyst formation. Synovitis can be assessed by T2-weighted imaging, dynamic contrast-enhanced MRI or diffusion tensor imaging. Bone marrow edema can be detected on fluid-sensitive sequences such as short-tau inversion recovery or T2-weighted fast-spin echo sequences. Detection of small bone erosions in the early erosive phase using T1-weighted MRI has sensitivity comparable to CT. Numerous MRI techniques have been developed for quantitative assessment of potentially pathologic changes in cartilage composition that occur before frank morphologic changes. In this Review, we summarize the advances and new directions in the field of MRI, with an emphasis on their current state of development and application in RA.

  2. MRI Segmentation of the Human Brain: Challenges, Methods, and Applications

    PubMed Central

    Despotović, Ivana

    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. PMID:25945121

  3. 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.

  4. Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

    PubMed Central

    Jungmann, Pia M.; Baum, Thomas; Bauer, Jan S.; Karampinos, Dimitrios C.; Link, Thomas M.; Li, Xiaojuan; Trattnig, Siegfried; Rummeny, Ernst J.; Woertler, Klaus; Welsch, Goetz H.

    2014-01-01

    Background. New quantitative magnetic resonance imaging (MRI) techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), and diffusion weighted imaging (DWI) are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair. PMID:24877139

  5. Iterative Method for Predistortion of MRI Gradient Waveforms

    PubMed Central

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

    2014-01-01

    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

  6. Reducing temporal fluctuations in MRI with the multichannel method SENSE

    NASA Astrophysics Data System (ADS)

    Moeller, Steen; Van de Moortele, Pierre-Francois; Goerke, Ute; Uğurbil, Kâmil

    2006-03-01

    Multi-channel acquisition is employed in MRI to decrease total imaging time. In this paper, artifact free images are calculated by utilizing the difference in spatial encoding of the MR signal from neighboring channels. The encoding functions are estimated in the presence of noise and motion. For fMRI studies, the temporal stability of the signal is essential, since neuronal activity in the brain is detected by probing subtle BOLD (blood oxygen level dependent) signal changes. To ensure artifact free noise representation a new type of weight is used. By effectively selecting and eliminating low SNR pixels, increased temporal stability is achieved. Using the parallel imaging method SENSE the proposed method is tested with in-vivo data to ensure noise suppression and demonstrate correct assignment of fMRI activation.

  7. The Alzheimer's Disease Neuroimaging Initiative (ADNI): MRI Methods

    PubMed Central

    Jack, Clifford R.; Bernstein, Matt A.; Fox, Nick C.; Thompson, Paul; Alexander, Gene; Harvey, Danielle; Borowski, Bret; Britson, Paula J.; Whitwell, Jennifer L.; Ward, Chadwick; Dale, Anders M.; Felmlee, Joel P.; Gunter, Jeffrey L.; Hill, Derek L.G.; Killiany, Ron; Schuff, Norbert; Fox-Bosetti, Sabrina; Lin, Chen; Studholme, Colin; DeCarli, Charles S.; Krueger, Gunnar; Ward, Heidi A.; Metzger, Gregory J.; Scott, Katherine T.; Mallozzi, Richard; Blezek, Daniel; Levy, Joshua; Debbins, Josef P.; Fleisher, Adam S.; Albert, Marilyn; Green, Robert; Bartzokis, George; Glover, Gary; Mugler, John; Weiner, Michael W.

    2008-01-01

    The Alzheimer's Disease Neuroimaging Initiative (ADNI) is a longitudinal multisite observational study of healthy elders, mild cognitive impairment (MCI), and Alzheimer's disease. Magnetic resonance imaging (MRI), (18F)-fluorode-oxyglucose positron emission tomography (FDG PET), urine serum, and cerebrospinal fluid (CSF) biomarkers, as well as clinical/psychometric assessments are acquiredat multiple time points. All data will be cross-linked and made available to the general scientific community. The purpose of this report is to describe the MRI methods employed in ADNI. The ADNI MRI core established specifications thatguided protocol development. A major effort was devoted toevaluating 3D T1-weighted sequences for morphometric analyses. Several options for this sequence were optimized for the relevant manufacturer platforms and then compared in a reduced-scale clinical trial. The protocol selected for the ADNI study includes: back-to-back 3D magnetization prepared rapid gradient echo (MP-RAGE) scans; B1-calibration scans when applicable; and an axial proton density-T2 dual contrast (i.e., echo) fast spin echo/turbo spin echo (FSE/TSE) for pathology detection. ADNI MRI methods seek to maximize scientific utility while minimizing the burden placed on participants. The approach taken in ADNI to standardization across sites and platforms of the MRI protocol, postacquisition corrections, and phantom-based monitoring of all scanners could be used as a model for other multisite trials. PMID:18302232

  8. Validation of the hypercapnic calibrated fMRI method using DOT-fMRI fusion imaging

    PubMed Central

    Yücel, Meryem A.; Evans, Karleyton C.; Selb, Juliette; Huppert, Theodore J.; Boas, David A.; Gagnon, Louis

    2014-01-01

    Calibrated functional Magnetic Resonance Imaging (fMRI) is a widely used method to investigate brain function in terms of physiological quantities such as the cerebral metabolic rate of oxygen (CMRO2). The first and one of the most common methods of fMRI calibration is hypercapnic calibration. This is achieved via simultaneous measures of blood-oxygenation-level dependent (BOLD) and the arterial spin labeling (ASL) signals during a functional task that evokes regional changes in CMRO2. A subsequent acquisition is then required during which the subject inhales carbon dioxide for short periods of time. A calibration constant, typically labeled M, is then estimated from the hypercapnic data and is subsequently used together with the BOLD-ASL recordings to compute evoked changes in CMRO2 during the functional task. The computation of M assumes a constant CMRO2 during the CO2 inhalation, an assumption that has been questioned since the origin of calibrated fMRI. In this study we used Diffuse Optical Tomography (DOT) together with BOLD and ASL – an alternative calibration method that does not require any gas manipulation and therefore no constant CMRO2 assumption - to cross-validate the estimation of M obtained from a traditional hypercapnic calibration. We found a high correlation between the M values (R=0.87, p<0.01) estimated using these two approaches. The findings serve to validate the hypercapnic fMRI calibration technique and suggest that the inter-subject variability routinely obtained for M is reproducible with an alternative method and might therefore reflect inter-subject physiological variability. PMID:25196509

  9. Mathematical Methods for Diffusion MRI Processing

    PubMed Central

    Lenglet, C.; Campbell, J.S.W.; Descoteaux, M.; Haro, G.; Savadjiev, P.; Wassermann, D.; Anwander, A.; Deriche, R.; Pike, G.B.; Sapiro, G.; Siddiqi, K.; Thompson, P.

    2009-01-01

    In this article, we review recent mathematical models and computational methods for the processing of diffusion Magnetic Resonance Images, including state-of-the-art reconstruction of diffusion models, cerebral white matter connectivity analysis, and segmentation techniques. We focus on Diffusion Tensor Images (DTI) and Q-Ball Images (QBI). PMID:19063977

  10. Using the dGEMRIC technique to evaluate cartilage health in the presence of surgical hardware at 3T: comparison of inversion recovery and saturation recovery approaches.

    PubMed

    d'Entremont, Agnes G; Kolind, Shannon H; Mädler, Burkhard; Wilson, David R; MacKay, Alexander L

    2014-03-01

    To evaluate the effect of metal artifact reduction techniques on dGEMRIC T(1) calculation with surgical hardware present. We examined the effect of stainless-steel and titanium hardware on dGEMRIC T(1) maps. We tested two strategies to reduce metal artifact in dGEMRIC: (1) saturation recovery (SR) instead of inversion recovery (IR) and (2) applying the metal artifact reduction sequence (MARS), in a gadolinium-doped agarose gel phantom and in vivo with titanium hardware. T(1) maps were obtained using custom curve-fitting software and phantom ROIs were defined to compare conditions (metal, MARS, IR, SR). A large area of artifact appeared in phantom IR images with metal when T(I) ≤ 700 ms. IR maps with metal had additional artifact both in vivo and in the phantom (shifted null points, increased mean T(1) (+151 % IR ROI(artifact)) and decreased mean inversion efficiency (f; 0.45 ROI(artifact), versus 2 for perfect inversion)) compared to the SR maps (ROI(artifact): +13 % T(1) SR, 0.95 versus 1 for perfect excitation), however, SR produced noisier T(1) maps than IR (phantom SNR: 118 SR, 212 IR). MARS subtly reduced the extent of artifact in the phantom (IR and SR). dGEMRIC measurement in the presence of surgical hardware at 3T is possible with appropriately applied strategies. Measurements may work best in the presence of titanium and are severely limited with stainless steel. For regions near hardware where IR produces large artifacts making dGEMRIC analysis impossible, SR-MARS may allow dGEMRIC measurements. The position and size of the IR artifact is variable, and must be assessed for each implant/imaging set-up.

  11. Comparing classification methods for longitudinal fMRI studies.

    PubMed

    Schmah, Tanya; Yourganov, Grigori; Zemel, Richard S; Hinton, Geoffrey E; Small, Steven L; Strother, Stephen C

    2010-11-01

    We compare 10 methods of classifying fMRI volumes by applying them to data from a longitudinal study of stroke recovery: adaptive Fisher's linear and quadratic discriminant; gaussian naive Bayes; support vector machines with linear, quadratic, and radial basis function (RBF) kernels; logistic regression; two novel methods based on pairs of restricted Boltzmann machines (RBM); and K-nearest neighbors. All methods were tested on three binary classification tasks, and their out-of-sample classification accuracies are compared. The relative performance of the methods varies considerably across subjects and classification tasks. The best overall performers were adaptive quadratic discriminant, support vector machines with RBF kernels, and generatively trained pairs of RBMs.

  12. Evaluation of chondral repair using quantitative MRI.

    PubMed

    Nieminen, Miika T; Nissi, Mikko J; Mattila, Lauri; Kiviranta, Ilkka

    2012-12-01

    Various quantitative magnetic resonance imaging (qMRI) biomarkers, including but not limited to parametric MRI mapping, semiquantitative evaluation, and morphological assessment, have been successfully applied to assess cartilage repair in both animal and human studies. Through the interaction between interstitial water and constituent macromolecules the compositional and structural properties of cartilage can be evaluated. In this review a comprehensive view of a variety of quantitative techniques, particularly those involving parametric mapping, and their relationship to the properties of cartilage repair is presented. Some techniques, such as T2 relaxation time mapping and delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), are well established, while the full potential of more recently introduced techniques remain to be demonstrated. A combination of several MRI techniques is necessary for a comprehensive characterization of chondral repair. Copyright © 2012 Wiley Periodicals, Inc.

  13. MRI RF array decoupling method with magnetic wall distributed filters.

    PubMed

    Connell, Ian R O; Gilbert, Kyle M; Abou-Khousa, Mohamed A; Menon, Ravi S

    2015-04-01

    Multi-channel radio-frequency (RF) transmit coil arrays have been developed to mitigate many of the RF challenges associated with ultra-high field ( ≥ 7T) magnetic resonance imaging (MRI). These arrays can be used for parallel RF transmission to produce spatially tailored RF excitation over the field of view. However, the realization of such arrays remains a challenge due to significant reactive interaction between the array coils, i.e., mutual coupling. In this paper, a novel bandstop filter ("magnetic wall") is used in an MRI RF transmit array to decouple individual coils. The proposed decoupling method is inspired by periodic resonator designs commonly used in frequency selective surfaces and is used as a distributed RF filter to suppress the transmission of RF energy between coils in an array. The decoupling of the magnetic wall (MW) is analyzed in terms of equivalent circuits that include terms for both magnetic and electric coupling for an arbitrary number of MW resonant conductors. Both frequency-and time-domain full-wave simulations were performed to analyze a specific MW structure. The performance of the proposed method is experimentally validated for both first-order coupling and higher-order coupling with a three-coil 7T array setup. Analysis and measurements confirm that the rejection band of the MW can be tuned to provide high isolation in the presence of cross coupling between RF array coils.

  14. Patellar malalignment: a new method on knee MRI.

    PubMed

    Kurtul Yildiz, Hülya; Ekin, Elif Evrim

    2016-01-01

    The medial patellofemoral ligament (MPFLL)/lateral patellar retinaculum (LPR) ratio were assessed in knees as a means to detect patellar malalignment. We also aimed to evaluate the prevalence of the various types of trochlear dysplasia in patients with patellar malalignment. After approval of our institutional ethics committee, we conducted a retrospective study that included 450 consecutive patients to evaluate them for the presence of patellar malalignment. Parameters investigated were the trochlear type, sulcus angle, presence of a supratrochlear spur, MPFLL, LPR, patella alta, and patella baja by means of 1.5T magnetic resonance imaging (MRI). Overall, 133 patients were excluded because of the presence of major trauma, multiple ligament injuries, bipartite patella, and/or previous knee surgery. The Dejour classification was used to assess trochlear dysplasia. Two experienced radiologists (HKY, EEE) evaluated the images. Their concordance was assessed using the kappa (κ) test. The frequencies of patellar malalignment and trochlear dysplasia were 34.7 and 63.7 %, respectively. The frequency of trochlear dysplasia associated with patellar malalignment was 97.2 %. An MPFLL/LPR ratio of 1.033-1.041 had high sensitivity and specificity for malalignment. The researchers' concordance was good (κ = 0.89, SE = 0.034, P < 0.001). Trochlear dysplasia is frequently associated with patellar malalignment. An increased MPFLL/LPR ratio is useful for detecting patellar malalignment on knee MRI, which is a novel quantitative method based on ligament length.

  15. Anisotropic phantom to calibrate high-q diffusion MRI methods

    NASA Astrophysics Data System (ADS)

    Komlosh, M. E.; Benjamini, D.; Barnett, A. S.; Schram, V.; Horkay, F.; Avram, A. V.; Basser, P. J.

    2017-02-01

    A silicon oil-filled glass capillary array is proposed as an anisotropic diffusion MRI phantom. Together with a computational/theoretical pipeline these provide a gold standard for calibrating and validating high-q diffusion MRI experiments. The phantom was used to test high angular resolution diffusion imaging (HARDI) and double pulsed-field gradient (d-PFG) MRI acquisition schemes. MRI-based predictions of microcapillary diameter using both acquisition schemes were compared with results from optical microscopy. This phantom design can be used for quality control and quality assurance purposes and for testing and validating proposed microstructure imaging experiments and the processing pipelines used to analyze them.

  16. A method for simultaneous RF ablation and MRI.

    PubMed

    Zhang, Q; Chung, Y C; Lewin, J S; Duerk, J L

    1998-01-01

    Radiofrequency (RF) energy has many advantages in thermal tumor ablation protocols. With the recent development of open MRI systems, interventional MRI procedures, including thermal ablation, have become the focus of great research interest. However, the significant interference between RF generators and MR imagers has prevented simultaneous imaging and RF ablation and, until now, has limited the role of RF-based thermal therapy in interventional MRI. Here, a simple switching circuit designed with consideration of patient safety provides compatibility between open MRI systems and RF thermal lesion generators. The experimental results show that the switching circuit allows imaging during RF ablation and opens new opportunity for MR-guided thermal therapy.

  17. Integration of multimodal neuroimaging methods: a rationale for clinical applications of simultaneous EEG-fMRI.

    PubMed

    Vitali, Piera; Di Perri, Carol; Vaudano, Anna Elisabetta; Meletti, Stefano; Villani, Flavio

    2015-01-01

    Functional magnetic resonance imaging (fMRI), which has high spatial resolution, is increasingly used to evaluate cerebral functions in neurological and psychiatric diseases. The main limitation of fMRI is that it detects neural activity indirectly, through the associated slow hemodynamic variations. Because neurovascular coupling can be regionally altered by pathological conditions or drugs, fMRI responses may not truly reflect neural activity. Electroencephalography (EEG) recordings, which directly detect neural activity with optimal temporal resolution, can now be obtained during fMRI data acquisition. Therefore, there is a growing interest in combining the techniques to obtain simultaneous EEG-fMRI recordings. The EEG-fMRI approach has several promising clinical applications. The first is the detection of cortical areas involved in interictal and ictal epileptic activity. Second, combining evoked potentials with fMRI could be an accurate way to study eloquent cortical areas for the planning of neurosurgery or rehabilitation, circumventing the above-mentioned limitation of fMRI. Finally, the use of this approach to evaluate the functional connectivity of resting-state networks would extend the applications of EEG-fMRI to uncooperative or unconscious patients. Integration of multimodal neuroimaging methods: a rationale for clinical applications of simultaneous EEG-fMRI.

  18. Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI.

    PubMed

    Sauwen, N; Acou, M; Van Cauter, S; Sima, D M; Veraart, J; Maes, F; Himmelreich, U; Achten, E; Van Huffel, S

    2016-01-01

    Tumor segmentation is a particularly challenging task in high-grade gliomas (HGGs), as they are among the most heterogeneous tumors in oncology. An accurate delineation of the lesion and its main subcomponents contributes to optimal treatment planning, prognosis and follow-up. Conventional MRI (cMRI) is the imaging modality of choice for manual segmentation, and is also considered in the vast majority of automated segmentation studies. Advanced MRI modalities such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have already shown their added value in tumor tissue characterization, hence there have been recent suggestions of combining different MRI modalities into a multi-parametric MRI (MP-MRI) approach for brain tumor segmentation. In this paper, we compare the performance of several unsupervised classification methods for HGG segmentation based on MP-MRI data including cMRI, DWI, MRSI and PWI. Two independent MP-MRI datasets with a different acquisition protocol were available from different hospitals. We demonstrate that a hierarchical non-negative matrix factorization variant which was previously introduced for MP-MRI tumor segmentation gives the best performance in terms of mean Dice-scores for the pathologic tissue classes on both datasets.

  19. Head Motion and Correction Methods in Resting-state Functional MRI.

    PubMed

    Goto, Masami; Abe, Osamu; Miyati, Tosiaki; Yamasue, Hidenori; Gomi, Tsutomu; Takeda, Tohoru

    2016-01-01

    Resting-state functional magnetic resonance imaging (RS-fMRI) is used to investigate brain functional connectivity at rest. However, noise from human physiological motion is an unresolved problem associated with this technique. Following the unexpected previous result that group differences in head motion between control and patient groups caused group differences in the resting-state network with RS-fMRI, we reviewed the effects of human physiological noise caused by subject motion, especially motion of the head, on functional connectivity at rest detected with RS-fMRI. The aim of the present study was to review head motion artifact with RS-fMRI, individual and patient population differences in head motion, and correction methods for head motion artifact with RS-fMRI. Numerous reports have described new methods [e.g., scrubbing, regional displacement interaction (RDI)] for motion correction on RS-fMRI, many of which have been successful in reducing this negative influence. However, the influence of head motion could not be entirely excluded by any of these published techniques. Therefore, in performing RS-fMRI studies, head motion of the participants should be quantified with measurement technique (e.g., framewise displacement). Development of a more effective correction method would improve the accuracy of RS-fMRI analysis.

  20. Does diffusion MRI tell us anything about the white matter? An overview of methods and pitfalls

    PubMed Central

    O’Donnell, Lauren J.; Pasternak, Ofer

    2014-01-01

    One key pitfall in diffusion magnetic resonance imaging (dMRI) clinical neuroimaging research is the challenge of understanding and interpreting the results of a complex analysis pipeline. The sophisticated algorithms employed by the analysis software, combined with the relatively non-specific nature of many diffusion measurements, lead to challenges in interpretation of the results. This paper is aimed at an intended audience of clinical researchers who are learning about dMRI or trying to interpret dMRI results, and who may be wondering “Does dMRI tell us anything about the white matter?” We present a critical review of dMRI methods and measures used in clinical neuroimaging research, focusing on the most commonly used analysis methods and the most commonly reported measures. We describe important pitfalls in every section, and provide extensive references for the reader interested in more detail. PMID:25278106

  1. 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…

  2. 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…

  3. An iterative reconstruction method of complex images using expectation maximization for radial parallel MRI

    NASA Astrophysics Data System (ADS)

    Choi, Joonsung; Kim, Dongchan; Oh, Changhyun; Han, Yeji; Park, HyunWook

    2013-05-01

    In MRI (magnetic resonance imaging), signal sampling along a radial k-space trajectory is preferred in certain applications due to its distinct advantages such as robustness to motion, and the radial sampling can be beneficial for reconstruction algorithms such as parallel MRI (pMRI) due to the incoherency. For radial MRI, the image is usually reconstructed from projection data using analytic methods such as filtered back-projection or Fourier reconstruction after gridding. However, the quality of the reconstructed image from these analytic methods can be degraded when the number of acquired projection views is insufficient. In this paper, we propose a novel reconstruction method based on the expectation maximization (EM) method, where the EM algorithm is remodeled for MRI so that complex images can be reconstructed. Then, to optimize the proposed method for radial pMRI, a reconstruction method that uses coil sensitivity information of multichannel RF coils is formulated. Experiment results from synthetic and in vivo data show that the proposed method introduces better reconstructed images than the analytic methods, even from highly subsampled data, and provides monotonic convergence properties compared to the conjugate gradient based reconstruction method.

  4. 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.

  5. [Mechanical Shimming Method and Implementation for Permanent Magnet of MRI System].

    PubMed

    Xue, Tingqiang; Chen, Jinjun

    2015-03-01

    A mechanical shimming method and device for permanent magnet of MRI system has been developed to meet its stringent homogeneity requirement without time-consuming passive shimming on site, installation and adjustment efficiency has been increased.

  6. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. New Methods of Low-Field MRI for Application to Traumatic Brain Injury

    DTIC Science & Technology

    2014-04-01

    TITLE: New Methods of Low-Field MRI for Application to Traumatic Brain Injury PRINCIPAL INVESTIGATOR: Matthew S. Rosen, Ph.D...SUBTITLE New Methods of Low-Field MRI for Application to TBI 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-11-2-0076 5c. PROGRAM...imaging in a 100 lb scanner based on a rotating permanent magnet array, and free-radical imaging ex vivo as a path toward in vivo applications

  8. Comparison of early and late MRI in neonatal hypoxic-ischemic encephalopathy using three assessment methods.

    PubMed

    Charon, Valérie; Proisy, Maïa; Ferré, Jean-Christophe; Bruneau, Bertrand; Tréguier, Catherine; Beuchée, Alain; Chauvel, Jennifer; Rozel, Céline

    2015-12-01

    There is no consensus on the optimum timing of MRI in neonates with hypoxic-ischemic encephalopathy treated with hypothermia. Reliable early imaging assessment might help managing treatment. To assess non-random differences between early and late MRI that might influence intensive-care decisions. This single-center retrospective study included all asphyxiated term neonates eligible for hypothermia treatment November 2009-July 2012. MRI scans were systematically performed at day 4 (early MRI) and day 11 of life as part of routine protocol. Two experienced pediatric radiologists reviewed both scans according to three assessment methods: a pattern classification, a scoring system and a simplified classification. Agreement between early and late imaging findings was assessed using Cohen's kappa coefficients. Thirty-three neonates were included. Interobserver agreement was excellent. Early MRI detected all severe injuries. Agreement between early and late MRI was excellent for the simplified classification (κ = 0.82), good for the pattern classification (κ = 0.64), and good to excellent for 3 scores out of 4 in the scoring system (κ = 0.70-0.89). Early MRI may provide valuable information about brain injury to help parents and neonatologists in intensive-care decisions at the end of hypothermia treatment.

  9. Graphical programming interface: A development environment for MRI methods.

    PubMed

    Zwart, Nicholas R; Pipe, James G

    2015-11-01

    To introduce a multiplatform, Python language-based, development environment called graphical programming interface for prototyping MRI techniques. The interface allows developers to interact with their scientific algorithm prototypes visually in an event-driven environment making tasks such as parameterization, algorithm testing, data manipulation, and visualization an integrated part of the work-flow. Algorithm developers extend the built-in functionality through simple code interfaces designed to facilitate rapid implementation. This article shows several examples of algorithms developed in graphical programming interface including the non-Cartesian MR reconstruction algorithms for PROPELLER and spiral as well as spin simulation and trajectory visualization of a FLORET example. The graphical programming interface framework is shown to be a versatile prototyping environment for developing numeric algorithms used in the latest MR techniques. © 2014 Wiley Periodicals, Inc.

  10. A Kernel Machine-based fMRI Physiological Noise Removal Method

    PubMed Central

    Song, Xiaomu; Chen, Nan-kuei; Gaur, Pooja

    2013-01-01

    Functional magnetic resonance imaging (fMRI) technique with blood oxygenation level dependent (BOLD) contrast is a powerful tool for noninvasive mapping of brain function under task and resting states. The removal of cardiac- and respiration-induced physiological noise in fMRI data has been a significant challenge as fMRI studies seek to achieve higher spatial resolutions and characterize more subtle neuronal changes. The low temporal sampling rate of most multi-slice fMRI experiments often causes aliasing of physiological noise into the frequency range of BOLD activation signal. In addition, changes of heartbeat and respiration patterns also generate physiological fluctuations that have similar frequencies with BOLD activation. Most existing physiological noise-removal methods either place restrictive limitations on image acquisition or utilize filtering or regression based post-processing algorithms, which cannot distinguish the frequency-overlapping BOLD activation and the physiological noise. In this work, we address the challenge of physiological noise removal via the kernel machine technique, where a nonlinear kernel machine technique, kernel principal component analysis, is used with a specifically identified kernel function to differentiate BOLD signal from the physiological noise of the frequency. The proposed method was evaluated in human fMRI data acquired from multiple task-related and resting state fMRI experiments. A comparison study was also performed with an existing adaptive filtering method. The results indicate that the proposed method can effectively identify and reduce the physiological noise in fMRI data. The comparison study shows that the proposed method can provide comparable or better noise removal performance than the adaptive filtering approach. PMID:24321306

  11. A kernel machine-based fMRI physiological noise removal method.

    PubMed

    Song, Xiaomu; Chen, Nan-kuei; Gaur, Pooja

    2014-02-01

    Functional magnetic resonance imaging (fMRI) technique with blood oxygenation level dependent (BOLD) contrast is a powerful tool for noninvasive mapping of brain function under task and resting states. The removal of cardiac- and respiration-induced physiological noise in fMRI data has been a significant challenge as fMRI studies seek to achieve higher spatial resolutions and characterize more subtle neuronal changes. The low temporal sampling rate of most multi-slice fMRI experiments often causes aliasing of physiological noise into the frequency range of BOLD activation signal. In addition, changes of heartbeat and respiration patterns also generate physiological fluctuations that have similar frequencies with BOLD activation. Most existing physiological noise-removal methods either place restrictive limitations on image acquisition or utilize filtering or regression based post-processing algorithms, which cannot distinguish the frequency-overlapping BOLD activation and the physiological noise. In this work, we address the challenge of physiological noise removal via the kernel machine technique, where a nonlinear kernel machine technique, kernel principal component analysis, is used with a specifically identified kernel function to differentiate BOLD signal from the physiological noise of the frequency. The proposed method was evaluated in human fMRI data acquired from multiple task-related and resting state fMRI experiments. A comparison study was also performed with an existing adaptive filtering method. The results indicate that the proposed method can effectively identify and reduce the physiological noise in fMRI data. The comparison study shows that the proposed method can provide comparable or better noise removal performance than the adaptive filtering approach.

  12. 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

  13. Principles and methods for automatic and semi-automatic tissue segmentation in MRI data.

    PubMed

    Wang, Lei; Chitiboi, Teodora; Meine, Hans; Günther, Matthias; Hahn, Horst K

    2016-04-01

    The development of magnetic resonance imaging (MRI) revolutionized both the medical and scientific worlds. A large variety of MRI options have generated a huge amount of image data to interpret. The investigation of a specific tissue in 3D or 4D MR images can be facilitated by image processing techniques, such as segmentation and registration. In this work, we provide a brief review of the principles and methods that are commonly applied to achieve superior tissue segmentation results in MRI. The impacts of MR image acquisition on segmentation outcome and the principles of selecting and exploiting segmentation techniques tailored for specific tissue identification tasks are discussed. In the end, two exemplary applications, breast and fibroglandular tissue segmentation in MRI and myocardium segmentation in short-axis cine and real-time MRI, are discussed to explain the typical challenges that can be posed in practical segmentation tasks in MRI data. The corresponding solutions that are adopted to deal with these challenges of the two practical segmentation tasks are thoroughly reviewed.

  14. An atlas-based electron density mapping method for magnetic resonance imaging (MRI)-alone treatment planning and adaptive MRI-based prostate radiation therapy.

    PubMed

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

    2012-05-01

    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. 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. 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. The electron-density atlas method provides the ability to

  15. Feasibility for mapping cartilage t1 relaxation times in the distal metacarpus3/metatarsus3 of thoroughbred racehorses using delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC): normal cadaver study.

    PubMed

    Carstens, Ann; Kirberger, Robert M; Velleman, Mark; Dahlberg, Leif E; Fletcher, Lizelle; Lammentausta, Eveliina

    2013-01-01

    Osteoarthritis of the metacarpo/metatarsophalangeal joints is one of the major causes of poor performance in horses. Delayed gadolinium-enhanced magnetic resonance imaging of cartilage (dGEMRIC) may be a useful technique for noninvasively quantifying articular cartilage damage in horses. The purpose of this study was to describe dGEMRIC characteristics of the distal metacarpus3/metatarsus3 (Mc3/Mt3) articular cartilage in 20 cadaver specimens collected from normal Thoroughbred horses. For each specimen, T1 relaxation time was measured from scans acquired precontrast and at 30, 60, 120, and 180 min post intraarticular injection of Gd-DTPA(2-) (dGEMRIC series). For each scan, T1 relaxation times were calculated using five regions of interest (sites 1-5) in the cartilage. For all sites, a significant decrease in T1 relaxation times occurred between precontrast scans and 30, 60, 120, and 180 min scans of the dGEMRIC series (P < 0.0001). A significant increase in T1 relaxation times occurred between 60 and 180 min and between 120 and 180 min post Gd injection for all sites. For sites 1-4, a significant increase in T1 relaxation time occurred between 30 and 180 min postinjection (P < 0.05). Sites 1-5 differed significantly among one another for all times (P < 0.0001). Findings from this cadaver study indicated that dGEMRIC using intraarticular Gd-DTPA(2-) is a feasible technique for measuring and mapping changes in T1 relaxation times in equine metacarpo/metatarsophalangeal joint cartilage. Optimal times for postcontrast scans were 60-120 min. Future studies are needed to determine whether these findings are reproducible in live horses. © 2013 Veterinary Radiology & Ultrasound.

  16. 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.

  17. 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.

  18. 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

  19. fMRI capture of auditory hallucinations: Validation of the two-steps method.

    PubMed

    Leroy, Arnaud; Foucher, Jack R; Pins, Delphine; Delmaire, Christine; Thomas, Pierre; Roser, Mathilde M; Lefebvre, Stéphanie; Amad, Ali; Fovet, Thomas; Jaafari, Nemat; Jardri, Renaud

    2017-10-01

    Our purpose was to validate a reliable method to capture brain activity concomitant with hallucinatory events, which constitute frequent and disabling experiences in schizophrenia. Capturing hallucinations using functional magnetic resonance imaging (fMRI) remains very challenging. We previously developed a method based on a two-steps strategy including (1) multivariate data-driven analysis of per-hallucinatory fMRI recording and (2) selection of the components of interest based on a post-fMRI interview. However, two tests still need to be conducted to rule out critical pitfalls of conventional fMRI capture methods before this two-steps strategy can be adopted in hallucination research: replication of these findings on an independent sample and assessment of the reliability of the hallucination-related patterns at the subject level. To do so, we recruited a sample of 45 schizophrenia patients suffering from frequent hallucinations, 20 schizophrenia patients without hallucinations and 20 matched healthy volunteers; all participants underwent four different experiments. The main findings are (1) high accuracy in reporting unexpected sensory stimuli in an MRI setting; (2) good detection concordance between hypothesis-driven and data-driven analysis methods (as used in the two-steps strategy) when controlled unexpected sensory stimuli are presented; (3) good agreement of the two-steps method with the online button-press approach to capture hallucinatory events; (4) high spatial consistency of hallucinatory-related networks detected using the two-steps method on two independent samples. By validating the two-steps method, we advance toward the possible transfer of such technology to new image-based therapies for hallucinations. Hum Brain Mapp 38:4966-4979, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. A SVM-based quantitative fMRI method for resting-state functional network detection.

    PubMed

    Song, Xiaomu; Chen, Nan-kuei

    2014-09-01

    Resting-state functional magnetic resonance imaging (fMRI) aims to measure baseline neuronal connectivity independent of specific functional tasks and to capture changes in the connectivity due to neurological diseases. Most existing network detection methods rely on a fixed threshold to identify functionally connected voxels under the resting state. Due to fMRI non-stationarity, the threshold cannot adapt to variation of data characteristics across sessions and subjects, and generates unreliable mapping results. In this study, a new method is presented for resting-state fMRI data analysis. Specifically, the resting-state network mapping is formulated as an outlier detection process that is implemented using one-class support vector machine (SVM). The results are refined by using a spatial-feature domain prototype selection method and two-class SVM reclassification. The final decision on each voxel is made by comparing its probabilities of functionally connected and unconnected instead of a threshold. Multiple features for resting-state analysis were extracted and examined using an SVM-based feature selection method, and the most representative features were identified. The proposed method was evaluated using synthetic and experimental fMRI data. A comparison study was also performed with independent component analysis (ICA) and correlation analysis. The experimental results show that the proposed method can provide comparable or better network detection performance than ICA and correlation analysis. The method is potentially applicable to various resting-state quantitative fMRI studies. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Fusing DTI and fMRI data: a survey of methods and applications.

    PubMed

    Zhu, Dajiang; Zhang, Tuo; Jiang, Xi; Hu, Xintao; Chen, Hanbo; Yang, Ning; Lv, Jinglei; Han, Junwei; Guo, Lei; Liu, Tianming

    2014-11-15

    The relationship between brain structure and function has been one of the centers of research in neuroimaging for decades. In recent years, diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques have been widely available and popular in cognitive and clinical neurosciences for examining the brain's white matter (WM) micro-structures and gray matter (GM) functions, respectively. Given the intrinsic integration of WM/GM and the complementary information embedded in DTI/fMRI data, it is natural and well-justified to combine these two neuroimaging modalities together to investigate brain structure and function and their relationships simultaneously. In the past decade, there have been remarkable achievements of DTI/fMRI fusion methods and applications in neuroimaging and human brain mapping community. This survey paper aims to review recent advancements on methodologies and applications in incorporating multimodal DTI and fMRI data, and offer our perspectives on future research directions. We envision that effective fusion of DTI/fMRI techniques will play increasingly important roles in neuroimaging and brain sciences in the years to come.

  2. A Study of Long-Term fMRI Reproducibility Using Data-Driven Analysis Methods.

    PubMed

    Song, Xiaomu; Panych, Lawrence P; Chou, Ying-Hui; Chen, Nan-Kuei

    2014-12-01

    The reproducibility of functional magnetic resonance imaging (fMRI) is important for fMRI-based neuroscience research and clinical applications. Previous studies show considerable variation in amplitude and spatial extent of fMRI activation across repeated sessions on individual subjects even using identical experimental paradigms and imaging conditions. Most existing fMRI reproducibility studies were typically limited by time duration and data analysis techniques. Particularly, the assessment of reproducibility is complicated by a fact that fMRI results may depend on data analysis techniques used in reproducibility studies. In this work, the long-term fMRI reproducibility was investigated with a focus on the data analysis methods. Two spatial smoothing techniques, including a wavelet-domain Bayesian method and the Gaussian smoothing, were evaluated in terms of their effects on the long-term reproducibility. A multivariate support vector machine (SVM)-based method was used to identify active voxels, and compared to a widely used general linear model (GLM)-based method at the group level. The reproducibility study was performed using multisession fMRI data acquired from eight healthy adults over 1.5 years' period of time. Three regions-of-interest (ROI) related to a motor task were defined based upon which the long-term reproducibility were examined. Experimental results indicate that different spatial smoothing techniques may lead to different reproducibility measures, and the wavelet-based spatial smoothing and SVM-based activation detection is a good combination for reproducibility studies. On the basis of the ROIs and multiple numerical criteria, we observed a moderate to substantial within-subject long-term reproducibility. A reasonable long-term reproducibility was also observed from the inter-subject study. It was found that the short-term reproducibility is usually higher than the long-term reproducibility. Furthermore, the results indicate that brain

  3. 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

    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.

  4. 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.

  5. MRI Features of Mucinous Cancer of the Breast: Correlation With Pathologic Findings and Other Imaging Methods.

    PubMed

    Bitencourt, Almir G V; Graziano, Luciana; Osório, Cynthia A B T; Guatelli, Camila S; Souza, Juliana A; Mendonça, Maria Helena S; Marques, Elvira F

    2016-02-01

    Mucinous breast carcinoma is an uncommon histologic type of invasive breast carcinoma that can be differentiated in pure and mixed forms, which have different prognosis and treatment. MRI features of both types of mucinous breast carcinomas are discussed, illustrated, and compared with pathologic findings and with other imaging methods, including mammography, ultrasound, and PET/CT.

  6. Axial STIR MRI: a faster method for confirming femoral head reduction in DDH.

    PubMed

    Conroy, Eimear; Sproule, J; Timlin, M; McManus, F

    2009-06-01

    cases of femoral head dislocation, MRI is useful to confirm concentric reduction of the femoral head in a dysplastic acetabulum when examination under anaesthesia and radiographic screening have been uncertain. In our series, 1 in 20 cases needed MRI. This is a reliable, non-invasive method confirming definite reduction of the femoral head prior to discharge in all of our patients. In this initial series, all patients had axial and coronal STIR and proton density MRI. We now only use axial STIR images because they provide adequate information regarding the position of the femoral head relative to the acetabulum.

  7. 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).

  8. Robust activation detection methods for real-time and offline fMRI analysis.

    PubMed

    Oguz, Kaya; Cinsdikici, Muhammed G; Gonul, Ali Saffet

    2017-06-01

    We propose two contributions with novel approaches to fMRI activation analysis. The first is to apply confidence intervals to locate activations in real-time, and second is a new metric based on robust regression of fMRI signals. These contributions are implemented in our four proposed methods; Instantaneous Activation Method (IAM), Instantaneous Activation Method with Past Blocks (IAMP) for real-time analysis, Task Robust Regression Distance Method (TRRD) for the new metric with robust regression and Instantaneous Robust Regression Distance Method (IRRD) for both contributions. For comparison, a statistical offline method called Task Activation Method (TAM) and a correlation analysis method are also implemented. The methods are initially evaluated with synthetic data generated using two different approaches; first using varying hemodynamic response function signals to simulate a wide range of stimuli responses, along with a Gaussian white noise, and second using no activity state data of a real fMRI experiment, which removes the need to generate noise. The methods are also tested with real fMRI experiments and compared with the results obtained by the widely used SPM tool. The results show that instantaneous methods reveal activations that are lost statistically in an offline analysis. They also reveal further improvements by robust fitting application, which minimizes the outlier effect. TRRD has an area under the ROC curve of 0,7127 for very noisy synthetic images, is reaching up to 0,9608 as the noise decreases, while the instantaneous score is in the range of 0,6124 to 0,8019 in the same noise levels. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. A fast, accurate, and reliable reconstruction method of the lumbar spine vertebrae using positional MRI.

    PubMed

    Simons, Craig J; Cobb, Loren; Davidson, Bradley S

    2014-04-01

    In vivo measurement of lumbar spine configuration is useful for constructing quantitative biomechanical models. Positional magnetic resonance imaging (MRI) accommodates a larger range of movement in most joints than conventional MRI and does not require a supine position. However, this is achieved at the expense of image resolution and contrast. As a result, quantitative research using positional MRI has required long reconstruction times and is sensitive to incorrectly identifying the vertebral boundary due to low contrast between bone and surrounding tissue in the images. We present a semi-automated method used to obtain digitized reconstructions of lumbar vertebrae in any posture of interest. This method combines a high-resolution reference scan with a low-resolution postural scan to provide a detailed and accurate representation of the vertebrae in the posture of interest. Compared to a criterion standard, translational reconstruction error ranged from 0.7 to 1.6 mm and rotational reconstruction error ranged from 0.3 to 2.6°. Intraclass correlation coefficients indicated high interrater reliability for measurements within the imaging plane (ICC 0.97-0.99). Computational efficiency indicates that this method may be used to compile data sets large enough to account for population variance, and potentially expand the use of positional MRI as a quantitative biomechanics research tool.

  10. 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.

  11. 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

  12. An Adaptive MR-CT Registration Method for MRI-guided Prostate Cancer Radiotherapy

    PubMed Central

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

    2015-01-01

    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/cm3, 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 during

  13. 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

  14. EEG-fMRI Methods for the Study of Brain Networks during Sleep

    PubMed Central

    Duyn, Jeff H.

    2012-01-01

    Modern neuroimaging methods may provide unique insights into the mechanism and role of sleep, as well as into particular mechanisms of brain function in general. Many of the recent neuroimaging studies have used concurrent EEG and fMRI, which present unique technical challenges ranging from the difficulty of inducing sleep in the MRI environment to appropriate instrumentation and data processing methods to obtain artifact free data. In addition, the use of EEG-fMRI during sleep leads to unique data interpretation issues, as common approaches developed for the analysis of task-evoked activity do not apply to sleep. Reviewed are a variety of statistical approaches that can be used to characterize brain activity from fMRI data acquired during sleep, with an emphasis on approaches that investigate the presence of correlated activity between brain regions. Each of these approaches has advantages and disadvantages that must be considered in concert with the theoretical questions of interest. Specifically, fundamental theories of sleep control and function should be considered when designing these studies and when choosing the associated statistical approaches. For example, the notion that local brain activity during sleep may be triggered by local, use-dependent activity during wakefulness may be tested by analyzing sleep networks as statistically independent components. Alternatively, the involvement of regions in more global processes such as arousal may be investigated with correlation analysis. PMID:22783221

  15. 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.

  16. EEG-fMRI Methods for the Study of Brain Networks during Sleep.

    PubMed

    Duyn, Jeff H

    2012-01-01

    Modern neuroimaging methods may provide unique insights into the mechanism and role of sleep, as well as into particular mechanisms of brain function in general. Many of the recent neuroimaging studies have used concurrent EEG and fMRI, which present unique technical challenges ranging from the difficulty of inducing sleep in the MRI environment to appropriate instrumentation and data processing methods to obtain artifact free data. In addition, the use of EEG-fMRI during sleep leads to unique data interpretation issues, as common approaches developed for the analysis of task-evoked activity do not apply to sleep. Reviewed are a variety of statistical approaches that can be used to characterize brain activity from fMRI data acquired during sleep, with an emphasis on approaches that investigate the presence of correlated activity between brain regions. Each of these approaches has advantages and disadvantages that must be considered in concert with the theoretical questions of interest. Specifically, fundamental theories of sleep control and function should be considered when designing these studies and when choosing the associated statistical approaches. For example, the notion that local brain activity during sleep may be triggered by local, use-dependent activity during wakefulness may be tested by analyzing sleep networks as statistically independent components. Alternatively, the involvement of regions in more global processes such as arousal may be investigated with correlation analysis.

  17. 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.

  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. Comparison between MRI-based attenuation correction methods for brain PET in dementia patients.

    PubMed

    Cabello, Jorge; Lukas, Mathias; Rota Kops, Elena; Ribeiro, André; Shah, N Jon; Yakushev, Igor; Pyka, Thomas; Nekolla, Stephan G; Ziegler, Sibylle I

    2016-11-01

    The combination of Positron Emission Tomography (PET) with magnetic resonance imaging (MRI) in hybrid PET/MRI scanners offers a number of advantages in investigating brain structure and function. A critical step of PET data reconstruction is attenuation correction (AC). Accounting for bone in attenuation maps (μ-map) was shown to be important in brain PET studies. While there are a number of MRI-based AC methods, no systematic comparison between them has been performed so far. The aim of this work was to study the different performance obtained by some of the recent methods presented in the literature. To perform such a comparison, we focused on [(18)F]-Fluorodeoxyglucose-PET/MRI neurodegenerative dementing disorders, which are known to exhibit reduced levels of glucose metabolism in certain brain regions. Four novel methods were used to calculate μ-maps from MRI data of 15 patients with Alzheimer's dementia (AD). The methods cover two atlas-based methods, a segmentation method, and a hybrid template/segmentation method. Additionally, the Dixon-based and a UTE-based method, offered by a vendor, were included in the comparison. Performance was assessed at three levels: tissue identification accuracy in the μ-map, quantitative accuracy of reconstructed PET data in specific brain regions, and precision in diagnostic images at identifying hypometabolic areas. Quantitative regional errors of -20--10 % were obtained using the vendor's AC methods, whereas the novel methods produced errors in a margin of ±5 %. The obtained precision at identifying areas with abnormally low levels of glucose uptake, potentially regions affected by AD, were 62.9 and 79.5 % for the two vendor AC methods, the former ignoring bone and the latter including bone information. The precision increased to 87.5-93.3 % in average for the four new methods, exhibiting similar performances. We confirm that the AC methods based on the Dixon and UTE sequences provided by the vendor are inferior to

  20. EEG/fMRI fusion based on independent component analysis: integration of data-driven and model-driven methods.

    PubMed

    Lei, Xu; Valdes-Sosa, Pedro A; Yao, Dezhong

    2012-09-01

    Simultaneous electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) provide complementary noninvasive information of brain activity, and EEG/fMRI fusion can achieve higher spatiotemporal resolution than each modality separately. This focuses on independent component analysis (ICA)-based EEG/fMRI fusion. In order to appreciate the issues, we first describe the potential and limitations of the developed fusion approaches: fMRI-constrained EEG imaging, EEG-informed fMRI analysis, and symmetric fusion. We then outline some newly developed hybrid fusion techniques using ICA and the combination of data-/model-driven methods, with special mention of the spatiotemporal EEG/fMRI fusion (STEFF). Finally, we discuss the current trend in methodological development and the existing limitations for extrapolating neural dynamics.

  1. 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.

  2. [fMRI functional connectivity analysis of anxiety disease patients based on spatiotemporal Lyapunov exponent method].

    PubMed

    Wang, Zhikang; Lou, Haifang; Sun, Jianzhong

    2011-07-01

    Attempting to use nonlinear spatiotemporal Lyapunov exponent to characterize fMRI brain functional connectivity of anxiety disease patients, we adopted the methods of nonlinear spatiotemporal Lyapunov exponent and linear correlation coefficients to analyses fMRI datum of 11 anxiety disease patients and 11 healthy volunteers, respectively. The results show that there are significant normalized variance exponent (NVE) differences in Inferior Frontal Gyrus (rIFG) and Medial Frontal Gyrus (MFG) between the two groups (P<0.01). And correlation coefficients shows significant differences (P<0.05). The spatial-temporal Lyapunov exponent method had higher sensitivity than the correlation coefficient method in the characterization of functional connectivity; Anxiety disease patients have abnormal functional connectivity in rIFG and MFG during our experiment.

  3. A multichannel speech enhancement method for functional MRI systems using a distributed microphone array.

    PubMed

    Milani, Ali A; Kannan, Govind; Panahi, Issa M S; Briggs, Richard

    2009-01-01

    Multichannel speech enhancement has been shown to be an effective method to decrease speech distortion introduced during speech enhancement, especially in environments like MRI (magnetic resonance imaging) which have a distributed noise source. However, these methods suffer from high computational complexity which makes them almost impractical. The use of subband filtering has been suggested to reduce this complexity but the performance of the existing subband methods deteriorate as the number of subbands increases. In this paper we introduce a new multichannel speech enhancement algorithm based on subband adaptive filtering that works for higher number of subbands at a lower complexity. The real-world experiments demonstrate the performance of the new scheme in an MRI room.

  4. fMRI bold signal analysis using a novel nonparametric statistical method

    NASA Astrophysics Data System (ADS)

    De Mazière, Patrick A.; Van Hulle, Marc M.

    2007-03-01

    We present in this article a novel analytical method that enables the application of nonparametric rank-order statistics to fMRI data analysis, since it takes the omnipresent serial correlations (temporal autocorrelations) properly into account. Comparative simulations, using the common General Linear Model and the permutation test, confirm the validity and usefulness of our approach. Our simulations, which are performed with both synthetic and real fMRI data, show that our method requires significantly less computation time than permutation-based methods, while offering the same order of robustness and returning more information about the evoked response when combined with/compared to the results obtained with the common General Lineal Model approach.

  5. Cerebrovascular MRI: a review of state-of-the-art approaches, methods and techniques.

    PubMed

    MacDonald, Matthew Ethan; Frayne, Richard

    2015-07-01

    Cerebrovascular imaging is of great interest in the understanding of neurological disease. MRI is a non-invasive technology that can visualize and provide information on: (i) the structure of major blood vessels; (ii) the blood flow velocity in these vessels; and (iii) the microcirculation, including the assessment of brain perfusion. Although other medical imaging modalities can also interrogate the cerebrovascular system, MR provides a comprehensive assessment, as it can acquire many different structural and functional image contrasts whilst maintaining a high level of patient comfort and acceptance. The extent of examination is limited only by the practicalities of patient tolerance or clinical scheduling limitations. Currently, MRI methods can provide a range of metrics related to the cerebral vasculature, including: (i) major vessel anatomy via time-of-flight and contrast-enhanced imaging; (ii) blood flow velocity via phase contrast imaging; (iii) major vessel anatomy and tissue perfusion via arterial spin labeling and dynamic bolus passage approaches; and (iv) venography via susceptibility-based imaging. When designing an MRI protocol for patients with suspected cerebral vascular abnormalities, it is appropriate to have a complete understanding of when to use each of the available techniques in the 'MR angiography toolkit'. In this review article, we: (i) overview the relevant anatomy, common pathologies and alternative imaging modalities; (ii) describe the physical principles and implementations of the above listed methods; (iii) provide guidance on the selection of acquisition parameters; and (iv) describe the existing and potential applications of MRI to the cerebral vasculature and diseases. The focus of this review is on obtaining an understanding through the application of advanced MRI methodology of both normal and abnormal blood flow in the cerebrovascular arteries, capillaries and veins.

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

    PubMed

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

    2013-08-01

    Radiofrequency (RF) field (B 1) 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 B 1 and MRI homogeneity by using pre-emphasized non-uniform B 1 distribution. The intrinsic B 1 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 B 1 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 B 1 distribution generated by the MTL volume coil, relatively uniform B 1 distribution and homogeneous MR image (98% homogeneity) within the spherical phantom (15 cm diameter) were achieved with 4.5 mm thickness. The B 1 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 B 1 and MRI homogeneities within the phantom containing 125 mM saline. The overall results demonstrate an efficient B 1 shimming approach for improving high field MRI.

  7. Oral distension methods for small bowel MRI: comparison of different agents to optimize bowel distension.

    PubMed

    Schmidt, Stefan A; Baumann, Julia A; Stanescu-Siegmund, Nora; Froehlich, Eckhart; Brambs, Hans-Juergen; Juchems, Markus S

    2016-12-01

    Background Different methods for bowel distension prior to magnetic resonance imaging (MRI) examinations were described in recent years. Purpose To compare orally administered psyllium or locust bean gum / mannitol (LBM) with tylose administered through a duodenal catheter for bowel distension in patients undergoing MRI examination of the small bowel. Material and Methods Three different methods of bowel distension prior to MRI were compared: tylose applied through a duodenal catheter and orally administered psyllium and LBM in three groups with 15 patients each. Datasets were blinded and reviewed independently by two experienced radiologists, who assessed the diagnostic value and the maximum luminal diameter. Results Tylose was superior to psyllium and LBM in the examination of the duodenum and proximal jejunum. LBM was superior to the other methods for distension of the ileum and terminal ileum. The greatest luminal diameter of the duodenum was achieved after tylose and distension of the terminal ileum was the best in patients receiving LBM. The psyllium group was inferior to the other two groups in all segments. Conclusion By using LBM as an oral method of bowel distension, many patients can avoid the unpleasant placement of a duodenal catheter without compromising the diagnostic value of the examination.

  8. New cardiac MRI gating method using event-synchronous adaptive digital filter.

    PubMed

    Park, Hodong; Park, Youngcheol; Cho, Sungpil; Jang, Bongryoel; Lee, Kyoungjoung

    2009-11-01

    When imaging the heart using MRI, an artefact-free electrocardiograph (ECG) signal is not only important for monitoring the patient's heart activity but also essential for cardiac gating to reduce noise in MR images induced by moving organs. The fundamental problem in conventional ECG is the distortion induced by electromagnetic interference. Here, we propose an adaptive algorithm for the suppression of MR gradient artefacts (MRGAs) in ECG leads of a cardiac MRI gating system. We have modeled MRGAs by assuming a source of strong pulses used for dephasing the MR signal. The modeled MRGAs are rectangular pulse-like signals. We used an event-synchronous adaptive digital filter whose reference signal is synchronous to the gradient peaks of MRI. The event detection processor for the event-synchronous adaptive digital filter was implemented using the phase space method-a sort of topology mapping method-and least-squares acceleration filter. For evaluating the efficiency of the proposed method, the filter was tested using simulation and actual data. The proposed method requires a simple experimental setup that does not require extra hardware connections to obtain the reference signals of adaptive digital filter. The proposed algorithm was more effective than the multichannel approach.

  9. Liver segmentation in MRI: A fully automatic method based on stochastic partitions.

    PubMed

    López-Mir, F; Naranjo, V; Angulo, J; Alcañiz, M; Luna, L

    2014-04-01

    There are few fully automated methods for liver segmentation in magnetic resonance images (MRI) despite the benefits of this type of acquisition in comparison to other radiology techniques such as computed tomography (CT). Motivated by medical requirements, liver segmentation in MRI has been carried out. For this purpose, we present a new method for liver segmentation based on the watershed transform and stochastic partitions. The classical watershed over-segmentation is reduced using a marker-controlled algorithm. To improve accuracy of selected contours, the gradient of the original image is successfully enhanced by applying a new variant of stochastic watershed. Moreover, a final classifier is performed in order to obtain the final liver mask. Optimal parameters of the method are tuned using a training dataset and then they are applied to the rest of studies (17 datasets). The obtained results (a Jaccard coefficient of 0.91 ± 0.02) in comparison to other methods demonstrate that the new variant of stochastic watershed is a robust tool for automatic segmentation of the liver in MRI.

  10. Residual hip dysplasia at 1 year after treatment for neonatal hip instability is not related to degenerative joint disease in young adulthood: a 21-year follow-up study including dGEMRIC.

    PubMed

    Wenger, D; Siversson, C; Dahlberg, L E; Tiderius, C J

    2016-03-01

    Developmental dysplasia of the hip (DDH) is associated with an increased risk of early hip osteoarthritis (OA). We aimed to examine the outcome at the completion of growth in a cohort of children who had residual acetabular dysplasia at age 1 year following early treatment for neonatal instability of the hip (NIH). We examined 21 of 30 subjects who had been treated with the von Rosen splint neonatally for NIH and had residual acetabular dysplasia at age 1 year. Mean follow-up time was 21 years (range 17-24). Signs of OA and acetabular dysplasia were assessed by radiography. Cartilage quality was assessed by delayed Gadolinium Enhanced Magnetic Resonance Imaging of Cartilage (dGEMRIC), a tool for molecular imaging of cartilage quality, at 1.5 T. Patient reported outcome (PRO) was assessed by the 12-item WOMAC score. No study participant had radiographic OA (defined as Kellgren-Lawrence grade ≥2) or minimum joint space width (JSW) ≤2 mm. The mean dGEMRIC index was 630 ms (95% CI: 600-666, range: 516-825) suggesting good cartilage quality. The mean 12-item WOMAC score was 1.2. Two of three radiographic measurements of DDH correlated positively to the dGEMRIC index. Children treated neonatally for NIH have good hip function and no signs of cartilage degeneration at 21-year follow-up, despite residual dysplasia at age 1 year. Unexpectedly, radiographic signs of dysplasia were associated with better cartilage quality, as assessed with dGEMRIC. This may indicate cartilage adaptation to increased mechanical stress in mild hip dysplasia. Copyright © 2015 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

  11. An automatic method of brain tumor segmentation from MRI volume based on the symmetry of brain and level set method

    NASA Astrophysics Data System (ADS)

    Li, Xiaobing; Qiu, Tianshuang; Lebonvallet, Stephane; Ruan, Su

    2010-02-01

    This paper presents a brain tumor segmentation method which automatically segments tumors from human brain MRI image volume. The presented model is based on the symmetry of human brain and level set method. Firstly, the midsagittal plane of an MRI volume is searched, the slices with potential tumor of the volume are checked out according to their symmetries, and an initial boundary of the tumor in the slice, in which the tumor is in the largest size, is determined meanwhile by watershed and morphological algorithms; Secondly, the level set method is applied to the initial boundary to drive the curve evolving and stopping to the appropriate tumor boundary; Lastly, the tumor boundary is projected one by one to its adjacent slices as initial boundaries through the volume for the whole tumor. The experiment results are compared with hand tracking of the expert and show relatively good accordance between both.

  12. Resting state fMRI: A review of methods and clinical applications

    PubMed Central

    Lee, Megan H.; Smyser, Christopher D.; Shimony, Joshua S.

    2014-01-01

    Resting state fMRI measures spontaneous, low frequency fluctuations in the BOLD signal to investigate the functional architecture of the brain. Application of this technique has allowed for the identification of various RSNs, or spatially distinct areas of the brain that demonstrate synchronous BOLD fluctuations at rest. Various methods exist for analyzing resting state data, including seed based approaches, independent component analysis, graph methods, clustering algorithms, neural networks, and pattern classifiers. Clinical applications of resting state fMRI are at an early stage of development. However, its use in presurgical planning for brain tumor and epilepsy patients demonstrates early promise, and the technique may also have a future role in providing diagnostic and prognostic information for neurological and psychiatric diseases. PMID:22936095

  13. Numerical simulation of diffusion MRI signals using an adaptive time-stepping method

    NASA Astrophysics Data System (ADS)

    Li, Jing-Rebecca; Calhoun, Donna; Poupon, Cyril; Le Bihan, Denis

    2014-01-01

    The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch-Torrey partial differential equation. We present a method for the numerical solution of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization. The time discretization is done using the explicit Runge-Kutta-Chebyshev method, which is more efficient than the forward Euler time discretization for diffusive-type problems. We use this approach to simulate the diffusion MRI signal from the extra-cylindrical compartment in a tissue model of the brain gray matter consisting of cylindrical and spherical cells and illustrate the effect of cell membrane permeability.

  14. Numerical simulation of diffusion MRI signals using an adaptive time-stepping method.

    PubMed

    Li, Jing-Rebecca; Calhoun, Donna; Poupon, Cyril; Le Bihan, Denis

    2014-01-20

    The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch-Torrey partial differential equation. We present a method for the numerical solution of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization. The time discretization is done using the explicit Runge-Kutta-Chebyshev method, which is more efficient than the forward Euler time discretization for diffusive-type problems. We use this approach to simulate the diffusion MRI signal from the extra-cylindrical compartment in a tissue model of the brain gray matter consisting of cylindrical and spherical cells and illustrate the effect of cell membrane permeability.

  15. Evaluation of Femoral Head Necrosis Using a Volumetric Method Based on MRI

    DTIC Science & Technology

    2001-10-25

    hip hemi - arthroplasty . The specimens were trimmed and rounded-up with wax, to take the shape of a sphere. In order to simulate the affected...106 hips with osteonecrosis before treatment with vascularized fibular grafting. The hips were evaluated using the volumetric method. The follow up...Osteonecrosis, MRI, Volumetric Feature Extraction, Automated Diagnosis I.INTRODUCTION Femoral head osteonecrosis is responsible for a large number of hip

  16. Local perfusion and metabolic demand during exercise: a noninvasive MRI method of assessment.

    PubMed

    Richardson, R S; Haseler, L J; Nygren, A T; Bluml, S; Frank, L R

    2001-10-01

    A noninvasive magnetic resonance imaging (MRI) method to assess the distribution of perfusion and metabolic demand (Q/VO(2)) in exercising human skeletal muscle is described. This method combines two MRI techniques that can provide accurate multiple localized measurements of Q/VO(2) during steady-state plantar flexion exercise. The first technique, (31)P chemical shift imaging, permits the acquisition of comparable phosphorus spectra from multiple voxels simultaneously. Because phosphocreatine (PCr) depletion is directly proportional to ATP hydrolysis, its relative depletion can be used as an index of muscle O(2) uptake (VO(2)). The second MRI technique allows the measurement of both spatially and temporally resolved muscle perfusion in vivo by using arterial spin labeling. Promising validity and reliability data are presented for both MRI techniques. Initial results from the combined method provide evidence of a large variation in Q/VO(2), revealing areas of apparent under- and overperfusion for a given metabolic turnover. Analysis of these data in a similar fashion to that employed in the assessment of ventilation-to-perfusion matching in the lungs revealed a similar second moment of the perfusion distribution and PCr distribution on a log scale (log SD(Q) and log SD(PCr)) (0.47). Modeling the effect of variations in log SD(Q) and log SD(PCr) in terms of attainable VO(2), assuming no diffusion limits, indicates that the log SD(Q) and log SD(PCr) would allow only 92% of the target VO(2) to be achieved. This communication documents this novel, noninvasive method for assessing Q/VO(2), and initial data suggest that the mismatch in Q/VO(2) may play a significant role in determining O(2) transport and utilization during exercise.

  17. 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.

  18. MRI-based attenuation correction for whole-body PET/MRI: quantitative evaluation of segmentation- and atlas-based methods.

    PubMed

    Hofmann, Matthias; Bezrukov, Ilja; Mantlik, Frederic; Aschoff, Philip; Steinke, Florian; Beyer, Thomas; Pichler, Bernd J; Schölkopf, Bernhard

    2011-09-01

    PET/MRI is an emerging dual-modality imaging technology that requires new approaches to PET attenuation correction (AC). We assessed 2 algorithms for whole-body MRI-based AC (MRAC): a basic MR image segmentation algorithm and a method based on atlas registration and pattern recognition (AT&PR). Eleven patients each underwent a whole-body PET/CT study and a separate multibed whole-body MRI study. The MR image segmentation algorithm uses a combination of image thresholds, Dixon fat-water segmentation, and component analysis to detect the lungs. MR images are segmented into 5 tissue classes (not including bone), and each class is assigned a default linear attenuation value. The AT&PR algorithm uses a database of previously aligned pairs of MRI/CT image volumes. For each patient, these pairs are registered to the patient MRI volume, and machine-learning techniques are used to predict attenuation values on a continuous scale. MRAC methods are compared via the quantitative analysis of AC PET images using volumes of interest in normal organs and on lesions. We assume the PET/CT values after CT-based AC to be the reference standard. In regions of normal physiologic uptake, the average error of the mean standardized uptake value was 14.1% ± 10.2% and 7.7% ± 8.4% for the segmentation and the AT&PR methods, respectively. Lesion-based errors were 7.5% ± 7.9% for the segmentation method and 5.7% ± 4.7% for the AT&PR method. The MRAC method using AT&PR provided better overall PET quantification accuracy than the basic MR image segmentation approach. This better quantification was due to the significantly reduced volume of errors made regarding volumes of interest within or near bones and the slightly reduced volume of errors made regarding areas outside the lungs.

  19. Supervised methods for detection and segmentation of tissues in clinical lumbar MRI.

    PubMed

    Ghosh, Subarna; Chaudhary, Vipin

    2014-10-01

    Lower back pain (LBP) is widely prevalent all over the world and more than 80% of the people suffer from LBP at some point of their lives. Moreover, a shortage of radiologists is the most pressing cause for the need of CAD (computer-aided diagnosis) systems. Automatic localization and labeling of intervertebral discs from lumbar MRI is the first step towards computer-aided diagnosis of lower back ailments. Subsequently, for diagnosis and characterization (quantification and localization) of abnormalities like disc herniation and stenosis, a completely automatic segmentation of intervertebral discs and the dural sac is extremely important. Contribution of this paper towards clinical CAD systems is two-fold. First, we propose a method to automatically detect all visible intervertebral discs in clinical sagittal MRI using heuristics and machine learning techniques. We provide a novel end-to-end framework that outputs a tight bounding box for each disc, instead of simply marking the centroid of discs, as has been the trend in the recent past. Second, we propose a method to simultaneously segment all the tissues (vertebrae, intervertebral disc, dural sac and background) in a lumbar sagittal MRI, using an auto-context approach instead of any explicit shape features or models. Past work tackles the lumbar segmentation problem on a tissue/organ basis, and which tend to perform poorly in clinical scans due to high variability in appearance. We, on the other hand, train a series of robust classifiers (random forests) using image features and sparsely sampled context features, which implicitly represent the shape and configuration of the image. Both these methods have been tested on a huge clinical dataset comprising of 212 cases and show very promising results for both disc detection (98% disc localization accuracy and 2.08mm mean deviation) and sagittal MRI segmentation (dice similarity indices of 0.87 and 0.84 for the dural sac and the inter-vertebral disc, respectively

  20. 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.

  1. Developing an Appropriateness Criteria for Knee MRI Using the Rand Appropriateness Method (RAM)-2013.

    PubMed

    Ebrahimipour, Hossein; Mirfeizi, Seyedeh Zahra; Najar, Ali Vafaee; Kachooei, Amir Reza; Ariamanesh, Amir Shahriar; Ganji, Reza; Esmaeeli, Habibollah; Salari, Hedayat; Vejdani, Marjan

    2014-03-01

    Knee pain is one of the most common reasons patients visit their physician. In this regard Magnetic Resonance Imaging (MRI) is the tool of preference for diagnosis. The aim of this study was to determine appropriate guidelines for knee MRI administration using the RAND Appropriateness Method (RAM)-2013. This qualitative study was done in the Mashhad University of Medical Sciences in 2013. The most appropriate approved knee MRI administration clinical guidelines were evaluated using Guidelines Evaluation and Research Appraisal (AGREE). Panel members consisting of six orthopedic and three rheumatologic doctors gave scores ranging from 1 to 9 for each scenario. The indications were grouped as appropriate, equivocal and inappropriate. Data were analyzed by descriptive statistics and SPSS ver. 18 software. Sixty-three scenarios were extracted from the guidelines and then the scenarios were evaluated in 26 indications. Thirty-two (50.79%) cases were considered appropriate, 12 (19.04%) cases uncertain and 19 (30.1%) cases inappropriate. The RAND appropriateness method is helpful in identifying the opinion of stakeholders in health care systems. Moreover, making practical use of clinical guidelines can improve patients' quality of care and prevent unnecessary costs.

  2. A fully automatic lesion detection method for DCE-MRI fat-suppressed breast images

    NASA Astrophysics Data System (ADS)

    Vignati, Anna; Giannini, Valentina; Bert, Alberto; Deluca, Massimo; Morra, Lia; Persano, Diego; Martincich, Laura; Regge, Daniele

    2009-02-01

    Dynamic Contrast Enhanced MRI (DCE-MRI) has today a well-established role, complementary to routine imaging techniques for breast cancer diagnosis such as mammography. Despite its undoubted clinical advantages, DCE-MRI data analysis is time-consuming and Computer Aided Diagnosis (CAD) systems are required to help radiologists. Segmentation is one of the key step of every CAD image processing pipeline, but most techniques available require human interaction. We here present the preliminary results of a fully automatic lesion detection method, capable of dealing with fat suppression image acquisition sequences, which represents a challenge for image processing algorithms due to the low SNR. The method is based on four fundamental steps: registration to correct for motion artifacts; anatomical segmentation to discard anatomical structures located outside clinically interesting lesions; lesion detection to select enhanced areas and false positive reduction based on morphological and kinetic criteria. The testing set was composed by 13 cases and included 27 lesions (10 benign and 17 malignant) of diameter > 5 mm. The system achieves a per-lesion sensitivity of 93%, while yielding an acceptable number of false positives (26 on average). The results of our segmentation algorithm were verified by visual inspection, and qualitative comparison with a manual segmentation yielded encouraging results.

  3. 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.

  4. 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

  5. Constructing fMRI connectivity networks: a whole brain functional parcellation method for node definition.

    PubMed

    Maggioni, Eleonora; Tana, Maria Gabriella; Arrigoni, Filippo; Zucca, Claudio; Bianchi, Anna Maria

    2014-05-15

    Functional Magnetic Resonance Imaging (fMRI) is used for exploring brain functionality, and recently it was applied for mapping the brain connection patterns. To give a meaningful neurobiological interpretation to the connectivity network, it is fundamental to properly define the network framework. In particular, the choice of the network nodes may affect the final connectivity results and the consequent interpretation. We introduce a novel method for the intra subject topological characterization of the nodes of fMRI brain networks, based on a whole brain parcellation scheme. The proposed whole brain parcellation algorithm divides the brain into clusters that are homogeneous from the anatomical and functional point of view, each of which constitutes a node. The functional parcellation described is based on the Tononi's cluster index, which measures instantaneous correlation in terms of intrinsic and extrinsic statistical dependencies. The method performance and reliability were first tested on simulated data, then on a real fMRI dataset acquired on healthy subjects during visual stimulation. Finally, the proposed algorithm was applied to epileptic patients' fMRI data recorded during seizures, to verify its usefulness as preparatory step for effective connectivity analysis. For each patient, the nodes of the network involved in ictal activity were defined according to the proposed parcellation scheme and Granger Causality Analysis (GCA) was applied to infer effective connectivity. We showed that the algorithm 1) performed well on simulated data, 2) was able to produce reliable inter subjects results and 3) led to a detailed definition of the effective connectivity pattern. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

    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). Gycosaminoglycan (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

  7. Structure-seeking multilinear methods for the analysis of fMRI data.

    PubMed

    Andersen, Anders H; Rayens, William S

    2004-06-01

    In comprehensive fMRI studies of brain function, the data structures often contain higher-order ways such as trial, task condition, subject, and group in addition to the intrinsic dimensions of time and space. While multivariate bilinear methods such as principal component analysis (PCA) have been used successfully for extracting information about spatial and temporal features in data from a single fMRI run, the need to unfold higher-order data sets into bilinear arrays has led to decompositions that are nonunique and to the loss of multiway linkages and interactions present in the data. These additional dimensions or ways can be retained in multilinear models to produce structures that are unique and which admit interpretations that are neurophysiologically meaningful. Multiway analysis of fMRI data from multiple runs of a bilateral finger-tapping paradigm was performed using the parallel factor (PARAFAC) model. A trilinear model was fitted to a data cube of dimensions voxels by time by run. Similarly, a quadrilinear model was fitted to a higher-way structure of dimensions voxels by time by trial by run. The spatial and temporal response components were extracted and validated by comparison to results from traditional SVD/PCA analyses based on scenarios of unfolding into lower-order bilinear structures.

  8. Real-Time Compressive Sensing MRI Reconstruction Using GPU Computing and Split Bregman Methods.

    PubMed

    Smith, David S; Gore, John C; Yankeelov, Thomas E; Welch, E Brian

    2012-01-01

    Compressive sensing (CS) has been shown to enable dramatic acceleration of MRI acquisition in some applications. Being an iterative reconstruction technique, CS MRI reconstructions can be more time-consuming than traditional inverse Fourier reconstruction. We have accelerated our CS MRI reconstruction by factors of up to 27 by using a split Bregman solver combined with a graphics processing unit (GPU) computing platform. The increases in speed we find are similar to those we measure for matrix multiplication on this platform, suggesting that the split Bregman methods parallelize efficiently. We demonstrate that the combination of the rapid convergence of the split Bregman algorithm and the massively parallel strategy of GPU computing can enable real-time CS reconstruction of even acquisition data matrices of dimension 4096(2) or more, depending on available GPU VRAM. Reconstruction of two-dimensional data matrices of dimension 1024(2) and smaller took ~0.3 s or less, showing that this platform also provides very fast iterative reconstruction for small-to-moderate size images.

  9. A comparison of five standard methods for evaluating image intensity uniformity in partially parallel imaging MRI.

    PubMed

    Goerner, Frank L; Duong, Timothy; Stafford, R Jason; Clarke, Geoffrey D

    2013-08-01

    To investigate the utility of five different standard measurement methods for determining image uniformity for partially parallel imaging (PPI) acquisitions in terms of consistency across a variety of pulse sequences and reconstruction strategies. Images were produced with a phantom using a 12-channel head matrix coil in a 3T MRI system (TIM TRIO, Siemens Medical Solutions, Erlangen, Germany). Images produced using echo-planar, fast spin echo, gradient echo, and balanced steady state free precession pulse sequences were evaluated. Two different PPI reconstruction methods were investigated, generalized autocalibrating partially parallel acquisition algorithm (GRAPPA) and modified sensitivity-encoding (mSENSE) with acceleration factors (R) of 2, 3, and 4. Additionally images were acquired with conventional, two-dimensional Fourier imaging methods (R=1). Five measurement methods of uniformity, recommended by the American College of Radiology (ACR) and the National Electrical Manufacturers Association (NEMA) were considered. The methods investigated were (1) an ACR method and a (2) NEMA method for calculating the peak deviation nonuniformity, (3) a modification of a NEMA method used to produce a gray scale uniformity map, (4) determining the normalized absolute average deviation uniformity, and (5) a NEMA method that focused on 17 areas of the image to measure uniformity. Changes in uniformity as a function of reconstruction method at the same R-value were also investigated. Two-way analysis of variance (ANOVA) was used to determine whether R-value or reconstruction method had a greater influence on signal intensity uniformity measurements for partially parallel MRI. Two of the methods studied had consistently negative slopes when signal intensity uniformity was plotted against R-value. The results obtained comparing mSENSE against GRAPPA found no consistent difference between GRAPPA and mSENSE with regard to signal intensity uniformity. The results of the two

  10. Comparison of supervised MRI segmentation methods for tumor volume determination during therapy.

    PubMed

    Vaidyanathan, M; Clarke, L P; Velthuizen, R P; Phuphanich, S; Bensaid, A M; Hall, L O; Bezdek, J C; Greenberg, H; Trotti, A; Silbiger, M

    1995-01-01

    Two different multispectral pattern recognition methods are used to segment magnetic resonance images (MRI) of the brain for quantitative estimation of tumor volume and volume changes with therapy. A supervised k-nearest neighbor (kNN) rule and a semi-supervised fuzzy c-means (SFCM) method are used to segment MRI slice data. Tumor volumes as determined by the kNN and SFCM segmentation methods are compared with two reference methods, based on image grey scale, as a basis for an estimation of ground truth, namely: (a) a commonly used seed growing method that is applied to the contrast enhanced T1-weighted image, and (b) a manual segmentation method using a custom-designed graphical user interface applied to the same raw image (T1-weighted) dataset. Emphasis is placed on measurement of intra and inter observer reproducibility using the proposed methods. Intra- and interobserver variation for the kNN method was 9% and 5%, respectively. The results for the SFCM method was a little better at 6% and 4%, respectively. For the seed growing method, the intra-observer variation was 6% and the interobserver variation was 17%, significantly larger when compared with the multispectral methods. The absolute tumor volume determined by the multispectral segmentation methods was consistently smaller than that observed for the reference methods. The results of this study are found to be very patient case-dependent. The results for SFCM suggest that it should be useful for relative measurements of tumor volume during therapy, but further studies are required. This work demonstrates the need for minimally supervised or unsupervised methods for tumor volume measurements.

  11. A practical MRI-based reconstruction method for a new endocavitary and interstitial gynaecological template

    PubMed Central

    Richart, Jose; Otal, Antonio; Rodriguez, Silvia; Nicolás, Ana Isabel; DePiaggio, Marina; Santos, Manuel; Vijande, Javier; Perez-Calatayud, Jose

    2015-01-01

    Purpose There are perineal templates for interstitial implants such as MUPIT and Syed applicators. Their limitations are the intracavitary component deficit and the necessity to use computed tomography (CT) for treatment planning since both applicators are non-magnetic resonance imaging (MRI) compatibles. To overcome these problems, a new template named Template Benidorm (TB) has been recently developed. Titanium needles are usually reconstructed based on their own artifacts, mainly in T1-weighted sequence, using the void on the tip as the needle tip position. Nevertheless, patient tissues surrounding the needles present heterogeneities that complicate the accurate identification of these artifact patterns. The purpose of this work is to improve the titanium needle reconstruction uncertainty for the TB case using a simple method based on the free needle lengths and typical MRI pellets markers. Material and methods The proposed procedure consists on the inclusion of three small A-vitamin pellets (hyperintense on MRI images) compressed by both applicator plates defining the central plane of the plate's arrangement. The needles used are typically 20 cm in length. For each needle, two points are selected defining the straight line. From such line and the plane equations, the intersection can be obtained, and using the free length (knowing the offset distance), the coordinates of the needle tip can be obtained. The method is applied in both T1W and T2W acquisition sequences. To evaluate the inter-observer variation of the method, three implants of T1W and another three of T2W have been reconstructed by two different medical physicists with experience on these reconstructions. Results and conclusions The differences observed in the positioning were significantly smaller than 1 mm in all cases. The presented algorithm also allows the use of only T2W sequence either for contouring or reconstruction purposes. The proposed method is robust and independent of the visibility

  12. 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.

  13. 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.

  14. 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

  15. A Novel Method for Quantifying Scanner Instability in fMRI

    PubMed Central

    Greve, Douglas N.; Mueller, Bryon A.; Liu, Thomas; Turner, Jessica A.; Voyvodic, James; Yetter, Elizabeth; Diaz, Michele; McCarthy, Gregory; Wallace, Stuart; Roach, Brian J.; Ford, Judy M.; Mathalon, Daniel H.; Calhoun, Vince D.; Wible, Cynthia G.; Potkin, Stephen G.; Glover, Gary

    2010-01-01

    A method was developed to quantify the effect of scanner instability on fMRI data by comparing the instability noise to endogenous noise present when scanning a human. The instability noise was computed from agar phantom data collected with two flip angles, allowing for a separation of the instability from the background noise. This method was used on human data collected at four 3T scanners, allowing the physiological noise level to be extracted from the data. In a “well-operating” scanner, the instability noise is generally less than 10% of physiological noise in white matter and only about 2% of physiological noise in cortex. This indicates that instability in a well-operating scanner adds very little noise to fMRI results. This new method allows researchers to make informed decisions about the maximum instability level a scanner can have before it is taken off line for maintenance or rejected from a multisite consortium. This method also provides information about the background noise, which is generally larger in magnitude than the instability noise. PMID:21413069

  16. Using multivariate machine learning methods and structural MRI to classify childhood onset schizophrenia and healthy controls.

    PubMed

    Greenstein, Deanna; Malley, James D; Weisinger, Brian; Clasen, Liv; Gogtay, Nitin

    2012-01-01

    Multivariate machine learning methods can be used to classify groups of schizophrenia patients and controls using structural magnetic resonance imaging (MRI). However, machine learning methods to date have not been extended beyond classification and contemporaneously applied in a meaningful way to clinical measures. We hypothesized that brain measures would classify groups, and that increased likelihood of being classified as a patient using regional brain measures would be positively related to illness severity, developmental delays, and genetic risk. Using 74 anatomic brain MRI sub regions and Random Forest (RF), a machine learning method, we classified 98 childhood onset schizophrenia (COS) patients and 99 age, sex, and ethnicity-matched healthy controls. We also used RF to estimate the probability of being classified as a schizophrenia patient based on MRI measures. We then explored relationships between brain-based probability of illness and symptoms, premorbid development, and presence of copy number variation (CNV) associated with schizophrenia. Brain regions jointly classified COS and control groups with 73.7% accuracy. Greater brain-based probability of illness was associated with worse functioning (p = 0.0004) and fewer developmental delays (p = 0.02). Presence of CNV was associated with lower probability of being classified as schizophrenia (p = 0.001). The regions that were most important in classifying groups included left temporal lobes, bilateral dorsolateral prefrontal regions, and left medial parietal lobes. Schizophrenia and control groups can be well classified using RF and anatomic brain measures, and brain-based probability of illness has a positive relationship with illness severity and a negative relationship with developmental delays/problems and CNV-based risk.

  17. New coil positioning method for interleaved transcranial magnetic stimulation (TMS)/functional MRI (fMRI) and its validation in a motor cortex study.

    PubMed

    Moisa, Marius; Pohmann, Rolf; Ewald, Lars; Thielscher, Axel

    2009-01-01

    To develop and test a novel method for coil placement in interleaved transcranial magnetic stimulation (TMS)/functional MRI (fMRI) studies. Initially, a desired TMS coil position at the subject's head is recorded using a neuronavigation system. Subsequently, a custom-made holding device is used for coil placement inside the MR scanner. The parameters of the device corresponding to the prerecorded position are automatically determined from a fast structural image acquired directly before the experiment. The spatial accuracy of our method was verified on a phantom. Finally, in a study on five subjects, the coil was placed above the cortical representation of a hand muscle in M1 and the blood oxygenation level-dependent (BOLD) responses to short repetitive TMS (rTMS) trains were assessed using echo-planar imaging (EPI) recordings. The spatial accuracy of our method is in the range of 2.9 +/- 1.3 (SD) mm. Motor cortex stimulation resulted in robust BOLD activations in motor- and auditory related brain areas, with the activation in M1 being localized in the hand knob. We present a user-friendly method for TMS coil positioning in the MR scanner that exhibits good spatial accuracy and speeds up the setup of the experiment. The motor-cortex study proves the viability of the approach and validates our interleaved TMS/fMRI setup.

  18. A Hybrid Machine Learning Method for Fusing fMRI and Genetic Data: Combining both Improves Classification of Schizophrenia

    PubMed Central

    Yang, Honghui; Liu, Jingyu; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D.

    2010-01-01

    We demonstrate a hybrid machine learning method to classify schizophrenia patients and healthy controls, using functional magnetic resonance imaging (fMRI) and single nucleotide polymorphism (SNP) data. The method consists of four stages: (1) SNPs with the most discriminating information between the healthy controls and schizophrenia patients are selected to construct a support vector machine ensemble (SNP-SVME). (2) Voxels in the fMRI map contributing to classification are selected to build another SVME (Voxel-SVME). (3) Components of fMRI activation obtained with independent component analysis (ICA) are used to construct a single SVM classifier (ICA-SVMC). (4) The above three models are combined into a single module using a majority voting approach to make a final decision (Combined SNP-fMRI). The method was evaluated by a fully validated leave-one-out method using 40 subjects (20 patients and 20 controls). The classification accuracy was: 0.74 for SNP-SVME, 0.82 for Voxel-SVME, 0.83 for ICA-SVMC, and 0.87 for Combined SNP-fMRI. Experimental results show that better classification accuracy was achieved by combining genetic and fMRI data than using either alone, indicating that genetic and brain function representing different, but partially complementary aspects, of schizophrenia etiopathology. This study suggests an effective way to reassess biological classification of individuals with schizophrenia, which is also potentially useful for identifying diagnostically important markers for the disorder. PMID:21119772

  19. An efficient de-convolution reconstruction method for spatiotemporal-encoding single-scan 2D MRI.

    PubMed

    Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Li, Jing; Chen, Ying; Bao, Lijun; Chen, Zhong

    2013-03-01

    Spatiotemporal-encoding single-scan MRI method is relatively insensitive to field inhomogeneity compared to EPI method. Conjugate gradient (CG) method has been used to reconstruct super-resolved images from the original blurred ones based on coarse magnitude-calculation. In this article, a new de-convolution reconstruction method is proposed. Through removing the quadratic phase modulation from the signal acquired with spatiotemporal-encoding MRI, the signal can be described as a convolution of desired super-resolved image and a point spread function. The de-convolution method proposed herein not only is simpler than the CG method, but also provides super-resolved images with better quality. This new reconstruction method may make the spatiotemporal-encoding 2D MRI technique more valuable for clinic applications. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. 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.

  1. Nonlinear PET parametric image reconstruction with MRI information using kernel method

    NASA Astrophysics Data System (ADS)

    Gong, Kuang; Wang, Guobao; Chen, Kevin T.; Catana, Ciprian; Qi, Jinyi

    2017-03-01

    Positron Emission Tomography (PET) is a functional imaging modality widely used in oncology, cardiology, and neurology. It is highly sensitive, but suffers from relatively poor spatial resolution, as compared with anatomical imaging modalities, such as magnetic resonance imaging (MRI). With the recent development of combined PET/MR systems, we can improve the PET image quality by incorporating MR information. Previously we have used kernel learning to embed MR information in static PET reconstruction and direct Patlak reconstruction. Here we extend this method to direct reconstruction of nonlinear parameters in a compartment model by using the alternating direction of multiplier method (ADMM) algorithm. Simulation studies show that the proposed method can produce superior parametric images compared with existing methods.

  2. MRI measurement of blood-brain barrier transport with a rapid acquisition refocused echo (RARE) method

    PubMed Central

    Walton, Jeffrey H; Ng, Kit Fai; Anderson, Steven E; Rutledge, John C

    2015-01-01

    Dynamic Contrast Enhanced (DCE) MRI is increasingly being used to assess changes in capillary permeability. Most quantitative techniques used to measure capillary permeability are based on the Fick equation that requires measurement of signal reflecting both plasma and tissue concentrations of the solute being tested. To date, most Magnetic Resonance Imaging (MRI) methods for acquiring appropriate data quickly rely on gradient recalled echo (GRE) type acquisitions, which work well in clinical low field settings. However, acquiring this type of data on high field small animal preclinical MRIs is problematic due to geometrical distortions from susceptibility mismatch. This problem can be exacerbated when using small animal models to measure blood brain barrier (BBB) permeability, where precise sampling from the superior sagittal sinus (SSS) is commonly used to determine the plasma concentration of the contrast agent. Here we present results demonstrating that a standard saturation recovery rapid acquisition refocused echo (RARE) method is capable of acquiring T1 maps with good spatial and temporal resolution for Patlak analysis (Patlak, 1983) to assess changes in BBB Gd-DTPA permeability following middle cerebral artery occlusion with reperfusion in the rat. This method limits known problems with magnetic susceptibility mismatch and may thus allow greater accuracy in BBB permeability measurement in small animals. PMID:25998382

  3. The secret lives of experiments: methods reporting in the fMRI literature.

    PubMed

    Carp, Joshua

    2012-10-15

    Replication of research findings is critical to the progress of scientific understanding. Accordingly, most scientific journals require authors to report experimental procedures in sufficient detail for independent researchers to replicate their work. To what extent do research reports in the functional neuroimaging literature live up to this standard? The present study evaluated methods reporting and methodological choices across 241 recent fMRI articles. Many studies did not report critical methodological details with regard to experimental design, data acquisition, and analysis. Further, many studies were underpowered to detect any but the largest statistical effects. Finally, data collection and analysis methods were highly flexible across studies, with nearly as many unique analysis pipelines as there were studies in the sample. Because the rate of false positive results is thought to increase with the flexibility of experimental designs, the field of functional neuroimaging may be particularly vulnerable to false positives. In sum, the present study documented significant gaps in methods reporting among fMRI studies. Improved methodological descriptions in research reports would yield significant benefits for the field.

  4. Simple SPION Incubation as an Efficient Intracellular Labeling Method for Tracking Neural Progenitor Cells Using MRI

    PubMed Central

    D. M., Jayaseema; Lai, Jiann-Shiun; Hueng, Dueng-Yuan; Chang, Chen

    2013-01-01

    Cellular magnetic resonance imaging (MRI) has been well-established for tracking neural progenitor cells (NPC). Superparamagnetic iron oxide nanoparticles (SPIONs) approved for clinical application are the most common agents used for labeling. Conventionally, transfection agents (TAs) were added with SPIONs to facilitate cell labeling because SPIONs in the native unmodified form were deemed inefficient for intracellular labeling. However, compelling evidence also shows that simple SPION incubation is not invariably ineffective. The labeling efficiency can be improved by prolonged incubation and elevated iron doses. The goal of the present study was to establish simple SPION incubation as an efficient intracellular labeling method. To this end, NPCs derived from the neonatal subventricular zone were incubated with SPIONs (Feridex®) and then evaluated in vitro with regard to the labeling efficiency and biological functions. The results showed that, following 48 hours of incubation at 75 µg/ml, nearly all NPCs exhibited visible SPION intake. Evidence from light microscopy, electron microscopy, chemical analysis, and magnetic resonance imaging confirmed the effectiveness of the labeling. Additionally, biological assays showed that the labeled NPCs exhibited unaffected viability, oxidative stress, apoptosis and differentiation. In the demonstrated in vivo cellular MRI experiment, the hypointensities representing the SPION labeled NPCs remained observable throughout the entire tracking period. The findings indicate that simple SPION incubation without the addition of TAs is an efficient intracellular magnetic labeling method. This simple approach may be considered as an alternative approach to the mainstream labeling method that involves the use of TAs. PMID:23468856

  5. Simple SPION incubation as an efficient intracellular labeling method for tracking neural progenitor cells using MRI.

    PubMed

    Chen, Chiao-Chi V; Ku, Min-Chi; D M, Jayaseema; Lai, Jiann-Shiun; Hueng, Dueng-Yuan; Chang, Chen

    2013-01-01

    Cellular magnetic resonance imaging (MRI) has been well-established for tracking neural progenitor cells (NPC). Superparamagnetic iron oxide nanoparticles (SPIONs) approved for clinical application are the most common agents used for labeling. Conventionally, transfection agents (TAs) were added with SPIONs to facilitate cell labeling because SPIONs in the native unmodified form were deemed inefficient for intracellular labeling. However, compelling evidence also shows that simple SPION incubation is not invariably ineffective. The labeling efficiency can be improved by prolonged incubation and elevated iron doses. The goal of the present study was to establish simple SPION incubation as an efficient intracellular labeling method. To this end, NPCs derived from the neonatal subventricular zone were incubated with SPIONs (Feridex®) and then evaluated in vitro with regard to the labeling efficiency and biological functions. The results showed that, following 48 hours of incubation at 75 µg/ml, nearly all NPCs exhibited visible SPION intake. Evidence from light microscopy, electron microscopy, chemical analysis, and magnetic resonance imaging confirmed the effectiveness of the labeling. Additionally, biological assays showed that the labeled NPCs exhibited unaffected viability, oxidative stress, apoptosis and differentiation. In the demonstrated in vivo cellular MRI experiment, the hypointensities representing the SPION labeled NPCs remained observable throughout the entire tracking period. The findings indicate that simple SPION incubation without the addition of TAs is an efficient intracellular magnetic labeling method. This simple approach may be considered as an alternative approach to the mainstream labeling method that involves the use of TAs.

  6. Workflow sensitivity of post-processing methods in renal DCE-MRI.

    PubMed

    Hanson, Erik; Eikefjord, Eli; Rørvik, Jarle; Andersen, Erling; Lundervold, Arvid; Hodneland, Erlend

    2017-10-01

    Estimation of renal filtration using dynamic contrast-enhanced imaging (DCE-MRI) requires a series of analysis steps. The possible number of distinct post-processing chains is large and grows rapidly with increasing number of processing steps or options. In this study we introduce a framework for systematic evaluation of the post-processing chains. The framework is later used to highlight the workflow processing chain sensitivity towards accuracy in estimation of glomerular filtration rate (GFR). Twenty healthy volunteers underwent DCE-MRI examinations as well as iohexol clearance for reference GFR measurements. In total, 692 different combinations of post-processing steps were explored for analysis, including options for kidney segmentation, B1 inhomogeneity correction, placement of arterial input function, gadolinium concentration estimation as well as handling of motion-corrupted volumes and breathing motion. The evaluation of various processing chains is presented using a classification tree framework and random forest ensemble learning. Among the processing steps subject to testing, methods for calculating the gadolinium concentration as well as B1 inhomogeneity correction had the largest impact on accuracy of GFR estimations. Different segmentation methods did not play an important role in the post-processing of the MR data except from one processing chain where the automated segmentation outperformed the manual segmentation. The proposed classification trees were efficiently used as a statistical tool for visualization and communication of results to distinguish between important and less influential processing steps in renal DCE-MRI. We also identified several crucial factors in the processing chain. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Brain tumor segmentation in MRI by using the fuzzy connectedness method

    NASA Astrophysics Data System (ADS)

    Liu, Jian-Guo; Udupa, Jayaram K.; Hackney, David; Moonis, Gul

    2001-07-01

    The aim of this paper is the precise and accurate quantification of brain tumor via MRI. This is very useful in evaluating disease progression, response to therapy, and the need for changes in treatment plans. We use multiple MRI protocols including FLAIR, T1, and T1 with Gd enhancement to gather information about different aspects of the tumor and its vicinity- edema, active regions, and scar left over due to surgical intervention. We have adapted the fuzzy connectedness framework to segment tumor and to measure its volume. The method requires only limited user interaction in routine clinical MRI. The first step in the process is to apply an intensity normalization method to the images so that the same body region has the same tissue meaning independent of the scanner and patient. Subsequently, a fuzzy connectedness algorithm is utilized to segment the different aspects of the tumor. The system has been tested, for its precision, accuracy, and efficiency, utilizing 40 patient studies. The percent coefficient of variation (% CV) in volume due to operator subjectivity in specifying seeds for fuzzy connectedness segmentation is less than 1%. The mean operator and computer time taken per study is 3 minutes. The package is designed to run under operator supervision. Delineation has been found to agree with the operators' visual inspection most of the time except in some cases when the tumor is close to the boundary of the brain. In the latter case, the scalp is included in the delineation and an operator has to exclude this manually. The methodology is rapid, robust, consistent, yielding highly reproducible measurements, and is likely to become part of the routine evaluation of brain tumor patients in our health system.

  8. Value of MRI and MRS fat measurements to complement conventional screening methods for childhood obesity.

    PubMed

    Lange, Thomas; Buechert, Martin; Baumstark, Manfred W; Deibert, Peter; Gerner, Sarah; Rydén, Henric; Seufert, Jochen; Korsten-Reck, Ulrike

    2015-11-01

    To evaluate a protocol combining abdominal fat-water magnetic resonance imaging (MRI) and liver single voxel magnetic resonance spectroscopy (MRS) for studies of childhood obesity. Six obese male children and five age-matched normal-weight controls underwent abdominal fat-water Dixon MRI based on a gradient echo sequence with multiple echo times and single voxel liver MRS at a field strength of 3T. The MRI/MRS data were compared with data previously acquired from an obese adult cohort and with anthropometric and blood parameters that are typically acquired for screening in childhood obesity. There was a very strong correlation (r = 0.96) between the body mass index standard deviation score (BMI-SDS) and the subcutaneous fat volume fraction in the examined children, but only a moderate correlation (r = 0.62) between the BMI-SDS index and the intraabdominal fat volume fraction, which is much lower in the obese children (5.3 ± 1.1%) than in the obese adult cohort (19.4 ± 2.9%). Furthermore, a significant difference between the two child cohorts was observed in the intrahepatic lipid (IHL) content as obtained with MRS (P = 0.017). However, even the obese child cohort shows an IHL content that is 1-2 orders of magnitude lower (1.0 ± 0.5%) than in the obese adult cohort (17.0 ± 8.7%). The proposed method was successfully applied in children and may complement traditional clinical screening methods for childhood obesity such as anthropometry and laboratory tests to better characterize the obesity-associated metabolic risk. © 2015 Wiley Periodicals, Inc.

  9. 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

  10. 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.

  11. A method for localizing microelectrode trajectories in the macaque brain using MRI

    PubMed Central

    Kalwani, Rishi M.; Bloy, Luke; Elliott, Mark A.; Gold, Joshua I.

    2009-01-01

    Magnetic resonance imaging (MRI) is often used by electrophysiologists to target specific brain regions for placement of microelectrodes. However, the effectiveness of this technique has been limited by few methods to quantify in three dimensions the relative locations of brain structures, recording chambers and microelectrode trajectories. Here we present such a method. After surgical implantation, recording chambers are fitted with a plastic cylinder that is filled with a high-contrast agent to aid in the segmentation of the cylinder from brain matter in an MRI volume. The resulting images of the filled cylinder correspond to a virtual cylinder that is projected along its long axis – parallel to the trajectories of microelectrodes advanced through the recording chamber – through the three-dimensional image of the brain. This technique, which does not require a stereotaxic coordinate system, can be used to quantify the coverage of an implanted recording chamber relative to anatomical landmarks at any depth or orientation. We have used this technique in conjunction with Caret (Van Essen et al., 2001) and AFNI (Cox, 1996) brain mapping software to successfully localize several regions of macaque cortex, including the middle temporal area, the lateral intraparietal area and the frontal eye field, and one subcortical structure, the locus coeruleus, for electrophysiological recordings. PMID:18831988

  12. 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

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

    PubMed

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

    2014-04-15

    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. 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 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. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Magnetic wall decoupling method for monopole coil array in ultrahigh field MRI: a feasibility test.

    PubMed

    Yan, Xinqiang; Zhang, Xiaoliang; Wei, Long; Xue, Rong

    2014-04-01

    Ultrahigh field (UHF) MR imaging of deeply located target in high dielectric biological samples faces challenges due to the reduced penetration depth at the corresponding high frequencies. Radiative coils, e.g., dipole and monopole coils, have recently been applied for UHF MRI applications to obtain better signal-noise-ratio (SNR) in the area deep inside the human head and body. However, due to the unique structure of radiative coil elements, electromagnetic (EM) coupling between elements in radiative coil arrays cannot be readily addressed by using traditional decoupling methods such as element overlapping and L/C decoupling network. A new decoupling method based on induced current elimination (ICE) or magnetic wall technique has recently been proposed and has demonstrated feasibility in designing microstrip transmission line (MTL) arrays and L/C loop arrays. In this study, an array of two monopole elements decoupled using magnetic wall decoupling technique was designed, constructed and analyzed numerically and experimentally to investigate the feasibility of the decoupling technique in radiative coil array designs for MR imaging at 7 T. An L-shaped capacitive network was employed as the matching circuit and the reflection coefficients (S11) of the monopole element achieved -30 dB or better. Isolation between the two monopole elements was improved from about -10 dB (without decoupling treatment) to better than -30 dB with the ICE/magnetic wall decoupling method. B1 maps and MR images of the phantom were acquired and SNR maps were measured and calculated to evaluate the performance of the ICE/magnetic wall decoupling method. Compared with the monopole elements without decoupling methods, the ICE-decoupled array demonstrated more independent image profiles from each element and had a higher SNR in the peripheral area of the imaging subject. The experimental and simulation results indicate that the ICE/magnetic wall decoupling technique might be a promising solution

  15. Robustness of Automated Methods for Brain Volume Measurements across Different MRI Field Strengths

    PubMed Central

    Heinen, Rutger; Bouvy, Willem H.; Mendrik, Adrienne M.; Viergever, Max A.; Biessels, Geert Jan; de Bresser, Jeroen

    2016-01-01

    Introduction Pooling of multicenter brain imaging data is a trend in studies on ageing related brain diseases. This poses challenges to MR-based brain segmentation. The performance across different field strengths of three widely used automated methods for brain volume measurements was assessed in the present study. Methods Ten subjects (mean age: 64 years) were scanned on 1.5T and 3T MRI on the same day. We determined robustness across field strength (i.e., whether measured volumes between 3T and 1.5T scans in the same subjects were similar) for SPM12, Freesurfer 5.3.0 and FSL 5.0.7. As a frame of reference, 3T MRI scans from 20 additional subjects (mean age: 71 years) were segmented manually to determine accuracy of the methods (i.e., whether measured volumes corresponded with expert-defined volumes). Results Total brain volume (TBV) measurements were robust across field strength for Freesurfer and FSL (mean absolute difference as % of mean volume ≤ 1%), but less so for SPM (4%). Gray matter (GM) and white matter (WM) volume measurements were robust for Freesurfer (1%; 2%) and FSL (2%; 3%) but less so for SPM (5%; 4%). For intracranial volume (ICV), SPM was more robust (2%) than FSL (3%) and Freesurfer (9%). TBV measurements were accurate for SPM and FSL, but less so for Freesurfer. For GM volume, SPM was accurate, but accuracy was lower for Freesurfer and FSL. For WM volume, Freesurfer was accurate, but SPM and FSL were less accurate. For ICV, FSL was accurate, while SPM and Freesurfer were less accurate. Conclusion Brain volumes and ICV could be measured quite robustly in scans acquired at different field strengths, but performance of the methods varied depending on the assessed compartment (e.g., TBV or ICV). Selection of an appropriate method in multicenter brain imaging studies therefore depends on the compartment of interest. PMID:27798694

  16. The application of independent component analysis with projection method to two-task fMRI data over multiple subjects

    NASA Astrophysics Data System (ADS)

    Li, Rui; Hui, Mingqi; Yao, Li; Chen, Kewei; Long, Zhiying

    2011-03-01

    Spatial Independent component analysis (sICA) has been successfully used to analyze functional magnetic resonance (fMRI) data. However, the application of ICA was limited in multi-task fMRI data due to the potential spatial dependence between task-related components. Long et al. (2009) proposed ICA with linear projection (ICAp) method and demonstrated its capacity to solve the interaction among task-related components in multi-task fMRI data of single subject. However, it's unclear that how to perform ICAp over a group of subjects. In this study, we proposed a group analysis framework on multi-task fMRI data by combining ICAp with the temporal concatenation method reported by Calhoun (2001). The results of real fMRI experiment containing multiple visual processing tasks demonstrated the feasibility and effectiveness of the group ICAp method. Moreover, compared to the GLM method, the group ICAp method is more sensitive to detect the regions specific to each task.

  17. Hippocampal subfields at ultra high field MRI: An overview of segmentation and measurement methods.

    PubMed

    Giuliano, Alessia; Donatelli, Graziella; Cosottini, Mirco; Tosetti, Michela; Retico, Alessandra; Fantacci, Maria Evelina

    2017-02-11

    The hippocampus is one of the most interesting and studied brain regions because of its involvement in memory functions and its vulnerability in pathological conditions, such as neurodegenerative processes. In the recent years, the increasing availability of Magnetic Resonance Imaging (MRI) scanners that operate at ultra-high field (UHF), that is, with static magnetic field strength ≥7T, has opened new research perspectives. Compared to conventional high-field scanners, these systems can provide new contrasts, increased signal-to-noise ratio and higher spatial resolution, thus they may improve the visualization of very small structures of the brain, such as the hippocampal subfields. Studying the morphometry of the hippocampus is crucial in neuroimaging research because changes in volume and thickness of hippocampal subregions may be relevant in the early assessment of pathological cognitive decline and Alzheimer's Disease (AD). The present review provides an overview of the manual, semi-automated and fully automated methods that allow the assessment of hippocampal subfield morphometry at UHF MRI, focusing on the different hippocampal segmentation produced. © 2017 Wiley Periodicals, Inc.

  18. An orthogonal-based decoupling method for MRI phased array coil design.

    PubMed

    Li, Bing Keong; Wang, Hua; Trakic, Adnan; Engstrom, Craig; Weber, Ewald; Crozier, Stuart

    2012-06-01

    A new 2 T 3-element orthogonal knee coil array based on the three-dimensional orthogonality principle was designed, constructed and used in a series of pilot magnetic resonance imaging (MRI) studies on a standardized phantom, and human and pig knees. The coil elements within this new coil array are positioned orthogonal to one another allowing problematic mutual coupling effects to be minimized without the use of any passive mutual decoupling schemes. The proposed method is appropriate for the design of transmit, receive and/or transceive radiofrequency (RF) coil arrays for applications in animal/human MRI and spectroscopic studies. Experimental results demonstrated that the 3-element orthogonal knee coil array could be angled arbitrarily, including at 90°, relative to the main static magnetic field (B(0) ) whilst maintaining normal operation with minimal loss of efficiency and functionality. Initial trials with a pig knee specimen further showed that the greatest signal intensity in the patellar ligament (parallel collagen fibres) was observed when the orthogonal knee coil array and the pig knee specimen were angled at ~55° to B(0) , which may have potential uses in magic angle MR applications. Copyright © 2011 John Wiley & Sons, Ltd.

  19. A method for safety testing of radiofrequency/microwave-emitting devices using MRI.

    PubMed

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

    2015-11-01

    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. 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. 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. Information acquired using MR temperature mapping and thermal property measurements can assess RF/microwave safety with high resolution and fidelity. © 2014 Wiley Periodicals, Inc.

  20. A least angle regression method for fMRI activation detection in phase-encoded experimental designs.

    PubMed

    Li, Xingfeng; Coyle, Damien; Maguire, Liam; McGinnity, Thomas M; Watson, David R; Benali, Habib

    2010-10-01

    This paper presents a new regression method for functional magnetic resonance imaging (fMRI) activation detection. Unlike general linear models (GLM), this method is based on selecting models for activation detection adaptively which overcomes the limitation of requiring a predefined design matrix in GLM. This limitation is because GLM designs assume that the response of the neuron populations will be the same for the same stimuli, which is often not the case. In this work, the fMRI hemodynamic response model is selected from a series of models constructed online by the least angle regression (LARS) method. The slow drift terms in the design matrix for the activation detection are determined adaptively according to the fMRI response in order to achieve the best fit for each fMRI response. The LARS method is then applied along with the Moore-Penrose pseudoinverse (PINV) and fast orthogonal search (FOS) algorithm for implementation of the selected model to include the drift effects in the design matrix. Comparisons with GLM were made using 11 normal subjects to test method superiority. This paper found that GLM with fixed design matrix was inferior compared to the described LARS method for fMRI activation detection in a phased-encoded experimental design. In addition, the proposed method has the advantage of increasing the degrees of freedom in the regression analysis. We conclude that the method described provides a new and novel approach to the detection of fMRI activation which is better than GLM based analyses.

  1. Evaluation of left ventricular rotation by two-dimensional speckle tracking method and real-time three-dimensional echocardiography: comparison with MRI tagging method.

    PubMed

    Hayashi, Hidetaka; Izumi, Chisato; Takahashi, Shuichi; Uchikoshi, Masato; Yamazaki, Ryou; Asanuma, Toshihiko; Ishikura, Fuminobu; Beppu, Shintaro; Nakatani, Satoshi

    2011-09-01

    Recently, it has become possible to evaluate left ventricular (LV) torsion by two-dimensional (2D) speckle tracking images. However, LV torsion is a three-dimensional (3D) performance, which per se cannot be assessed by the 2D speckle tracking method. The present study investigated the accuracy of the 2D speckle tracking method and real-time 3D echocardiography in measuring LV rotation, comparing with the MRI tagging method. We assessed LV apical rotation using the 2D speckle tracking method, real-time 3D echocardiography, and MRI tagging method in 26 normal subjects, and compared the results of these three methods. LV apical rotation was measured just before the level in which the posterior papillary muscle was absorbed into the free wall. The degree of LV apical rotation evaluated by the 2D speckle tracking method (Δθ 2D) was significantly smaller than that evaluated by 3D echocardiography (Δθ 3D) and the MRI tagging method (Δθ MRI) (Δθ 2D 7.3 ± 2.8°; Δθ 3D 8.8 ± 3.4°; Δθ MRI 9.0 ± 3.4°; Δθ 2D vs. Δθ 3D, p = 0.0001; Δθ 2D vs. Δθ MRI, p < 0.0001). There were good correlations among Δθ 2D, Δθ 3D, and Δθ MRI, but agreement between Δθ 3D and Δθ MRI (mean difference 0.14 ± 1.43°) was better than that between Δθ 2D and Δθ MRI (mean difference 1.68 ± 1.89°). The degree of LV apical rotation was underestimated with the 2D speckle tracking method compared with the MRI tagging method, whereas it could be precisely measured by 3D echocardiography.

  2. 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

  3. 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

  4. 4D MRI for the Localization of Parathyroid Adenoma: A Novel Method in Evolution.

    PubMed

    Merchavy, Shlomo; Luckman, Judith; Guindy, Michal; Segev, Yoram; Khafif, Avi

    2016-03-01

    The sestamibi scan (MIBI) and ultrasound (US) are used for preoperative localization of parathyroid adenoma (PTA), with sensitivity as high as 90%. We developed 4-dimensional magnetic resonance imaging (4D MRI) as a novel tool for identifying PTAs. Eleven patients with PTA were enrolled. 4D MRI from the mandible to the aortic arch was used. Optimization of the timing of image acquisition was obtained by changing dynamic and static sequences. PTAs were identified in all except 1 patient. In 9 patients, there was a complete match between the 4D MRI and the US and MIBI, as well as with the operative finding. In 1 patient, the adenoma was correctly localized by 4D MRI, in contrast to the US and MIBI scan. The sensitivity of the 4D MRI was 90% and after optimization, 100%. Specificity was 100%. We concluded that 4D MRI is a reliable technique for identification of PTAs, although more studies are needed.

  5. An iterative method for coil sensitivity estimation in multi-coil MRI systems.

    PubMed

    Ling, Qiang; Li, Zhaohui; Song, Kaikai; Li, Feng

    2014-12-01

    This paper presents an iterative coil sensitivity estimation method for multi-coil MRI systems. The proposed method works with coil images in the magnitude image domain. It determines a region of support (RoS), a region being composed of the same type of tissues, by a region growing algorithm, which makes use of both intensities and intensity gradients of pixels. By repeating this procedure, it can determine multiple regions of support, which together cover most of the concerned image area. The union of these regions of support provides a rough estimate of the sensitivity of each coil through dividing the intensities of pixels by the average intensity inside every region of support. The obtained rough coil sensitivity estimate is further approached with the product of multiple low-order polynomials, rather than a single one. The product of these polynomials provides a smooth estimate of the sensitivity of each coil. With the obtained sensitivities of coils, it can produce a better reconstructed image, which determines more correct regions of support and yields preciser estimates of the sensitivities of coils. In other words, the method can be iteratively implemented to improve the estimation performance. The proposed method was verified through both simulated data and clinical data from different body parts. The experimental results confirm the superiority of our method to some conventional methods.

  6. 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.

  7. 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 ...

  8. Integration of multimodal neuroimaging methods: a rationale for clinical applications of simultaneous EEG-fMRI

    PubMed Central

    Vitali, Paolo; Di Perri, Carol; Vaudano, Anna Elisabetta; Meletti, Stefano; Villani, Flavio

    2015-01-01

    Summary Functional magnetic resonance imaging (fMRI), which has high spatial resolution, is increasingly used to evaluate cerebral functions in neurological and psychiatric diseases. The main limitation of fMRI is that it detects neural activity indirectly, through the associated slow hemodynamic variations. Because neurovascular coupling can be regionally altered by pathological conditions or drugs, fMRI responses may not truly reflect neural activity. Electroencephalography (EEG) recordings, which directly detect neural activity with optimal temporal resolution, can now be obtained during fMRI data acquisition. Therefore, there is a growing interest in combining the techniques to obtain simultaneous EEG-fMRI recordings. The EEG-fMRI approach has several promising clinical applications. The first is the detection of cortical areas involved in interictal and ictal epileptic activity. Second, combining evoked potentials with fMRI could be an accurate way to study eloquent cortical areas for the planning of neurosurgery or rehabilitation, circumventing the above-mentioned limitation of fMRI. Finally, the use of this approach to evaluate the functional connectivity of resting-state networks would extend the applications of EEG-fMRI to uncooperative or unconscious patients. PMID:26214023

  9. Skeletal muscle diffusion tensor-MRI fiber tracking: rationale, data acquisition and analysis methods, applications and future directions.

    PubMed

    Damon, Bruce M; Froeling, Martijn; Buck, Amanda K W; Oudeman, Jos; Ding, Zhaohua; Nederveen, Aart J; Bush, Emily C; Strijkers, Gustav J

    2017-03-01

    The mechanical functions of muscles involve the generation of force and the actuation of movement by shortening or lengthening under load. These functions are influenced, in part, by the internal arrangement of muscle fibers with respect to the muscle's mechanical line of action. This property is known as muscle architecture. In this review, we describe the use of diffusion tensor (DT)-MRI muscle fiber tracking for the study of muscle architecture. In the first section, the importance of skeletal muscle architecture to function is discussed. In addition, traditional and complementary methods for the assessment of muscle architecture (brightness-mode ultrasound imaging and cadaver analysis) are presented. Next, DT-MRI is introduced and the structural basis for the reduced and anisotropic diffusion of water in muscle is discussed. The third section discusses issues related to the acquisition of skeletal muscle DT-MRI data and presents recommendations for optimal strategies. The fourth section discusses methods for the pre-processing of DT-MRI data, the available approaches for the calculation of the diffusion tensor and the seeding and propagating of fiber tracts, and the analysis of the tracking results to measure structural properties pertinent to muscle biomechanics. Lastly, examples are presented of how DT-MRI fiber tracking has been used to provide new insights into how muscles function, and important future research directions are highlighted. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Method of Quantifying Three Dimensional Strain Distribution in Skeletal Muscle Using Cine Phase Contrast MRI

    PubMed Central

    Jensen, Elisabeth R.; Morrow, Duane A.; Felmlee, Joel P.; Murthy, Naveen S.; Kaufman, Kenton R.

    2016-01-01

    Intramuscular pressure (IMP), a correlate of muscle tension, may fill an important clinical testing void. A barrier to implementing this measure clinically is its non-uniform distribution, which is not fully understood. Pressure is generated by changes in fluid mass and volume, therefore 3D volumetric strain distribution may affect IMP distribution. The purpose of this study was to develop a method for quantifying 3D volumetric strain distribution in the human tibialis anterior (TA) during passive tension using cine Phase Contrast (CPC) MRI and to assess its accuracy and precision. Five healthy subjects each participated in three data collections. A custom MRI-compatible apparatus repeatedly rotated the subjects’ ankle between 0 and 26 degrees plantarflexion while CPC MRI data were collected. Additionally, T2-weighted images of the lower leg were collected both before and after the CPC data collection with the ankle stationary at both 0 and 26 degrees plantarflexion for TA muscle segmentation. A 3D hexahedral mesh was generated based on the TA surface before CPC data collection with the ankle at 0 degrees plantarflexion and the node trajectories were tracked using the CPC data. The volumetric strain of each element was quantified. Three tests were employed to assess the measure accuracy and precision. First, to quantify leg position drift, the TA segmentations were compared before and after CPC data collection. This error was 1.5±0.7 mm. Second, to assess the surface node trajectory accuracy, the deformed mesh surface was compared to the TA segmented at 26 degrees of ankle plantarflexion. This error was 0.6±0.2 mm. Third, the standard deviation of volumetric strain across the three data collections was calculated for each element and subject. The median between-day variability across subjects and mesh elements was 0.06 mm3/mm3 (95% confidence interval 0.01 to 0.18 mm3/mm3). Overall the results demonstrated excellent accuracy and precision. PMID:26595686

  11. Itch induced by a novel method leads to limbic deactivations a functional MRI study.

    PubMed

    Herde, Lina; Forster, Clemens; Strupf, Marion; Handwerker, Hermann O

    2007-10-01

    Functional brain imaging studies on itch usually use histamine as a stimulus and, in consequence, have to cope with the highly variable time course of this particular itch sensation. In this study, we describe a novel method of histamine application. To provoke itch, a mixture of histamine and codeine was applied through intradermally positioned microdialysis fiber. The itch was terminated by lidocaine application through the same fiber. During one fMRI session, this procedure was repeated four times in four different microdialysis fibers, including one placebo control. Itch ratings of the subjects were correlated with blood-oxygen-level-dependent (BOLD) effects. In a subsequent experiment performed in the same fMRI session, heat pain was provoked in the right forearm with a Peltier thermode. During both experiments, activation clusters were found in brain areas that have been described previously to be frequently activated in response to painful stimuli. This includes prefrontal areas, supplementary motor areas (SMA), premotor cortex, anterior insula, anterior midcingulate cortex, S1, S2, thalamus, basal ganglia, and cerebellum. In general, itch stimulation entailed more activation clusters, in particular on the contralateral brain side. Only on itch, but not on heat pain, negative BOLD signals were found in the subgenual anterior cingulate cortex and the amygdala. The latter results may be associated with the itch induced urge to scratch. Amygdala deactivation may be related to the preparation of scratching by aiming to dissolve the otherwise aversive effects of the noxious scratch stimuli. These negative BOLD effects may also be attributed to the stressful character of itch stimulation.

  12. Magnetic wall decoupling method for monopole coil array in ultrahigh field MRI: a feasibility test

    PubMed Central

    Yan, Xinqiang; Zhang, Xiaoliang; Wei, Long

    2014-01-01

    Ultrahigh field (UHF) MR imaging of deeply located target in high dielectric biological samples faces challenges due to the reduced penetration depth at the corresponding high frequencies. Radiative coils, e.g., dipole and monopole coils, have recently been applied for UHF MRI applications to obtain better signal-noise-ratio (SNR) in the area deep inside the human head and body. However, due to the unique structure of radiative coil elements, electromagnetic (EM) coupling between elements in radiative coil arrays cannot be readily addressed by using traditional decoupling methods such as element overlapping and L/C decoupling network. A new decoupling method based on induced current elimination (ICE) or magnetic wall technique has recently been proposed and has demonstrated feasibility in designing microstrip transmission line (MTL) arrays and L/C loop arrays. In this study, an array of two monopole elements decoupled using magnetic wall decoupling technique was designed, constructed and analyzed numerically and experimentally to investigate the feasibility of the decoupling technique in radiative coil array designs for MR imaging at 7 T. An L-shaped capacitive network was employed as the matching circuit and the reflection coefficients (S11) of the monopole element achieved –30 dB or better. Isolation between the two monopole elements was improved from about –10 dB (without decoupling treatment) to better than –30 dB with the ICE/magnetic wall decoupling method. B1 maps and MR images of the phantom were acquired and SNR maps were measured and calculated to evaluate the performance of the ICE/magnetic wall decoupling method. Compared with the monopole elements without decoupling methods, the ICE-decoupled array demonstrated more independent image profiles from each element and had a higher SNR in the peripheral area of the imaging subject. The experimental and simulation results indicate that the ICE/magnetic wall decoupling technique might be a promising

  13. A comparison study between the saturation-recovery-T1 and CASL MRI methods for quantitative CBF imaging.

    PubMed

    Wang, Xiao; Zhu, Xiao-Hong; Zhang, Yi; Divani, Afshin A; Murphy, Amanda J; Chen, Wei

    2017-04-01

    The saturation-recovery (SR)-T1 MRI method for quantitatively imaging cerebral blood flow (CBF) change (ΔCBF) concurrently with the blood oxygenation level dependence (BOLD) alteration has been recently developed and validated by simultaneous measurement of relative CBF change using laser Doppler flowmetry (LDF) in rats at 9.4T. In this study, ΔCBF induced by mildly transient hypercapnia and measured by the SR-T1 MRI method was rigorously compared with an established perfusion MRI method-continuous arterial spin labeling (CASL) approach in normal and preclinical middle cerebral artery occlusion (MCAo) rat models. The results show an excellent agreement between ΔCBF values measured with these two imaging methods. Moreover, the intrinsic longitudinal relaxation rate (R1(int)) was experimentally determined in vivo in normal rat brains at 9.4T by comparing two independent measures of the apparent longitudinal relaxation rate (R1(app)) and CBF measured by the CSAL approach across a wide range of perfusion. In turn, the R1(int) constant can be employed to calculate the CBF value based on the R1(app) measurement in healthy brain. This comparison study validates the fundamental relationship for linking brain tissue water R1(app) and cerebral perfusion, demonstrates the feasibility of imaging and quantifying both CBF and its change using the SR-T1 MRI method in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    PubMed

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

    2015-11-16

    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. The difference in performance between breast tomosynthesis and digital mammography was significant (p <0.001), while the difference between breast tomosynthesis and breast MRI was not significant (p=0.20).

  15. Use of Brain MRI Atlases to Determine Boundaries of Age-Related Pathology: The Importance of Statistical Method

    PubMed Central

    Dickie, David Alexander; Job, Dominic E.; Gonzalez, David Rodriguez; Shenkin, Susan D.; Wardlaw, Joanna M.

    2015-01-01

    Introduction Neurodegenerative disease diagnoses may be supported by the comparison of an individual patient’s brain magnetic resonance image (MRI) with a voxel-based atlas of normal brain MRI. Most current brain MRI atlases are of young to middle-aged adults and parametric, e.g., mean ±standard deviation (SD); these atlases require data to be Gaussian. Brain MRI data, e.g., grey matter (GM) proportion images, from normal older subjects are apparently not Gaussian. We created a nonparametric and a parametric atlas of the normal limits of GM proportions in older subjects and compared their classifications of GM proportions in Alzheimer’s disease (AD) patients. Methods Using publicly available brain MRI from 138 normal subjects and 138 subjects diagnosed with AD (all 55–90 years), we created: a mean ±SD atlas to estimate parametrically the percentile ranks and limits of normal ageing GM; and, separately, a nonparametric, rank order-based GM atlas from the same normal ageing subjects. GM images from AD patients were then classified with respect to each atlas to determine the effect statistical distributions had on classifications of proportions of GM in AD patients. Results The parametric atlas often defined the lower normal limit of the proportion of GM to be negative (which does not make sense physiologically as the lowest possible proportion is zero). Because of this, for approximately half of the AD subjects, 25–45% of voxels were classified as normal when compared to the parametric atlas; but were classified as abnormal when compared to the nonparametric atlas. These voxels were mainly concentrated in the frontal and occipital lobes. Discussion To our knowledge, we have presented the first nonparametric brain MRI atlas. In conditions where there is increasing variability in brain structure, such as in old age, nonparametric brain MRI atlases may represent the limits of normal brain structure more accurately than parametric approaches. Therefore, we

  16. Fast Electromagnetic Analysis of MRI Transmit RF Coils Based on Accelerated Integral Equation Methods.

    PubMed

    Villena, Jorge Fernandez; Polimeridis, Athanasios G; Eryaman, Yigitcan; Adalsteinsson, Elfar; Wald, Lawrence L; White, Jacob K; Daniel, Luca

    2016-11-01

    A fast frequency domain full-wave electromagnetic simulation method is introduced for the analysis of MRI coils loaded with the realistic human body models. The approach is based on integral equation methods decomposed into two domains: 1) the RF coil array and shield, and 2) the human body region where the load is placed. The analysis of multiple coil designs is accelerated by introducing the precomputed magnetic resonance Green functions (MRGFs), which describe how the particular body model used responds to the incident fields from external sources. These MRGFs, which are precomputed once for a given body model, can be combined with any integral equation solver and reused for the analysis of many coil designs. This approach provides a fast, yet comprehensive, analysis of coil designs, including the port S-parameters and the electromagnetic field distribution within the inhomogeneous body. The method solves the full-wave electromagnetic problem for a head array in few minutes, achieving a speed up of over 150 folds with root mean square errors in the electromagnetic field maps smaller than 0.4% when compared to the unaccelerated integral equation-based solver. This enables the characterization of a large number of RF coil designs in a reasonable time, which is a first step toward an automatic optimization of multiple parameters in the design of transmit arrays, as illustrated in this paper, but also receive arrays.

  17. Input permutation method to detect active voxels in fMRI study☆

    PubMed Central

    Lee, Sang H.; Lim, Johan; Park, DoHwan; Biswal, Bharat B.; Petkova, Eva

    2013-01-01

    Correctly identifying voxels or regions of interest (ROI) that actively respond to a given stimulus is often an important objective/step in many functional magnetic resonance imaging (fMRI) studies. In this article, we study a nonparametric method to detect active voxels, which makes minimal assumption about the distribution of blood oxygen level-dependent (BOLD) signals. Our proposal has several interesting features. It uses time lagged correlation to take into account the delay in response to the stimulus, due to hemodynamic variations. We introduce an input permutation method (IPM), a type of block permutation method, to approximate the null distribution of the test statistic. Also, we propose to pool the permutation-derived statistics of preselected voxels for a better approximation to the null distribution. Finally, we control multiple testing error rate using the local false discovery rate (FDR) by Efron [Correlation and large-scale simultaneous hypothesis testing. J Am Stat Assoc 102 (2007) 93–103] and Park et al. [Estimation of empirical null using a mixture of normals and its use in local false discovery rate. Comput Stat Data Anal 55 (2011) 2421–2432] to select the active voxels. PMID:22819177

  18. Materials and methods for higher performance screen-printed flexible MRI receive coils.

    PubMed

    Corea, Joseph R; Lechene, P Balthazar; Lustig, Michael; Arias, Ana C

    2017-08-01

    To develop methods for characterizing materials used in screen-printed MRI coils and improve signal-to-noise ratio (SNR) with new lower-loss materials. An experimental apparatus was created to characterize dielectric properties of plastic substrates used in receive coils. Coils were fabricated by screen printing conductive ink onto several plastic substrates. Unloaded and sample loaded quality factor (QUnloaded /QLoaded ) measurements and scans on a 3T scanner were used to characterize coil performance. An experimental method was developed to describe the relationship between a coil's QUnloaded and the SNR it provides in images of a phantom. In addition, 3T scans of a phantom and the head of a volunteer were obtained with a proof-of-concept printed eight-channel array, and the results were compared with a commercial 12-channel array. Printed coils with optimized substrates exhibited up to 97% of the image SNR when compared with a traditional coil on a loading phantom. QUnloaded and the SNR of coils were successfully correlated. The printed array resulted in images comparable to the quality given by the commercial array. Using the proposed methods and materials, the SNR of printed coils approached that of commercial coils while using a new fabrication technique that provided more flexibility and close contact with the patient's body. Magn Reson Med 78:775-783, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  19. Compressed sensing MRI via fast linearized preconditioned alternating direction method of multipliers.

    PubMed

    Chen, Shanshan; Du, Hongwei; Wu, Linna; Jin, Jiaquan; Qiu, Bensheng

    2017-04-27

    The challenge of reconstructing a sparse medical magnetic resonance image based on compressed sensing from undersampled k-space data has been investigated within recent years. As total variation (TV) performs well in preserving edge, one type of approach considers TV-regularization as a sparse structure to solve a convex optimization problem. Nevertheless, this convex optimization problem is both nonlinear and nonsmooth, and thus difficult to handle, especially for a large-scale problem. Therefore, it is essential to develop efficient algorithms to solve a very broad class of TV-regularized problems. In this paper, we propose an efficient algorithm referred to as the fast linearized preconditioned alternating direction method of multipliers (FLPADMM), to solve an augmented TV-regularized model that adds a quadratic term to enforce image smoothness. Because of the separable structure of this model, FLPADMM decomposes the convex problem into two subproblems. Each subproblem can be alternatively minimized by augmented Lagrangian function. Furthermore, a linearized strategy and multistep weighted scheme can be easily combined for more effective image recovery. The method of the present study showed improved accuracy and efficiency, in comparison to other methods. Furthermore, the experiments conducted on in vivo data showed that our algorithm achieved a higher signal-to-noise ratio (SNR), lower relative error (Rel.Err), and better structural similarity (SSIM) index in comparison to other state-of-the-art algorithms. Extensive experiments demonstrate that the proposed algorithm exhibits superior performance in accuracy and efficiency than conventional compressed sensing MRI algorithms.

  20. A semi-automatic method for developing an anthropomorphic numerical model of dielectric anatomy by MRI

    NASA Astrophysics Data System (ADS)

    Mazzurana, M.; Sandrini, L.; Vaccari, A.; Malacarne, C.; Cristoforetti, L.; Pontalti, R.

    2003-10-01

    Complex permittivity values have a dominant role in the overall consideration of interaction between radiofrequency electromagnetic fields and living matter, and in related applications such as electromagnetic dosimetry. There are still some concerns about the accuracy of published data and about their variability due to the heterogeneous nature of biological tissues. The aim of this study is to provide an alternative semi-automatic method by which numerical dielectric human models for dosimetric studies can be obtained. Magnetic resonance imaging (MRI) tomography was used to acquire images. A new technique was employed to correct nonuniformities in the images and frequency-dependent transfer functions to correlate image intensity with complex permittivity were used. The proposed method provides frequency-dependent models in which permittivity and conductivity vary with continuity—even in the same tissue—reflecting the intrinsic realistic spatial dispersion of such parameters. The human model is tested with an FDTD (finite difference time domain) algorithm at different frequencies; the results of layer-averaged and whole-body-averaged SAR (specific absorption rate) are compared with published work, and reasonable agreement has been found. Due to the short time needed to obtain a whole body model, this semi-automatic method may be suitable for efficient study of various conditions that can determine large differences in the SAR distribution, such as body shape, posture, fat-to-muscle ratio, height and weight.

  1. Use of brain MRI atlases to determine boundaries of age-related pathology: the importance of statistical method.

    PubMed

    Dickie, David Alexander; Job, Dominic E; Gonzalez, David Rodriguez; Shenkin, Susan D; Wardlaw, Joanna M

    2015-01-01

    Neurodegenerative disease diagnoses may be supported by the comparison of an individual patient's brain magnetic resonance image (MRI) with a voxel-based atlas of normal brain MRI. Most current brain MRI atlases are of young to middle-aged adults and parametric, e.g., mean ± standard deviation (SD); these atlases require data to be Gaussian. Brain MRI data, e.g., grey matter (GM) proportion images, from normal older subjects are apparently not Gaussian. We created a nonparametric and a parametric atlas of the normal limits of GM proportions in older subjects and compared their classifications of GM proportions in Alzheimer's disease (AD) patients. Using publicly available brain MRI from 138 normal subjects and 138 subjects diagnosed with AD (all 55-90 years), we created: a mean ± SD atlas to estimate parametrically the percentile ranks and limits of normal ageing GM; and, separately, a nonparametric, rank order-based GM atlas from the same normal ageing subjects. GM images from AD patients were then classified with respect to each atlas to determine the effect statistical distributions had on classifications of proportions of GM in AD patients. The parametric atlas often defined the lower normal limit of the proportion of GM to be negative (which does not make sense physiologically as the lowest possible proportion is zero). Because of this, for approximately half of the AD subjects, 25-45% of voxels were classified as normal when compared to the parametric atlas; but were classified as abnormal when compared to the nonparametric atlas. These voxels were mainly concentrated in the frontal and occipital lobes. To our knowledge, we have presented the first nonparametric brain MRI atlas. In conditions where there is increasing variability in brain structure, such as in old age, nonparametric brain MRI atlases may represent the limits of normal brain structure more accurately than parametric approaches. Therefore, we conclude that the statistical method used for

  2. Comparative Study of SVM Methods Combined with Voxel Selection for Object Category Classification on fMRI Data

    PubMed Central

    Song, Sutao; Zhan, Zhichao; Long, Zhiying; Zhang, Jiacai; Yao, Li

    2011-01-01

    Background Support vector machine (SVM) has been widely used as accurate and reliable method to decipher brain patterns from functional MRI (fMRI) data. Previous studies have not found a clear benefit for non-linear (polynomial kernel) SVM versus linear one. Here, a more effective non-linear SVM using radial basis function (RBF) kernel is compared with linear SVM. Different from traditional studies which focused either merely on the evaluation of different types of SVM or the voxel selection methods, we aimed to investigate the overall performance of linear and RBF SVM for fMRI classification together with voxel selection schemes on classification accuracy and time-consuming. Methodology/Principal Findings Six different voxel selection methods were employed to decide which voxels of fMRI data would be included in SVM classifiers with linear and RBF kernels in classifying 4-category objects. Then the overall performances of voxel selection and classification methods were compared. Results showed that: (1) Voxel selection had an important impact on the classification accuracy of the classifiers: in a relative low dimensional feature space, RBF SVM outperformed linear SVM significantly; in a relative high dimensional space, linear SVM performed better than its counterpart; (2) Considering the classification accuracy and time-consuming holistically, linear SVM with relative more voxels as features and RBF SVM with small set of voxels (after PCA) could achieve the better accuracy and cost shorter time. Conclusions/Significance The present work provides the first empirical result of linear and RBF SVM in classification of fMRI data, combined with voxel selection methods. Based on the findings, if only classification accuracy was concerned, RBF SVM with appropriate small voxels and linear SVM with relative more voxels were two suggested solutions; if users concerned more about the computational time, RBF SVM with relative small set of voxels when part of the principal

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

    PubMed

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

    2014-07-15

    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

  4. 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

  5. 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.

  6. Brain MRI atrophy quantification in MS: From methods to clinical application.

    PubMed

    Rocca, Maria A; Battaglini, Marco; Benedict, Ralph H B; De Stefano, Nicola; Geurts, Jeroen J G; Henry, Roland G; Horsfield, Mark A; Jenkinson, Mark; Pagani, Elisabetta; Filippi, Massimo

    2017-01-24

    Patients with the main clinical phenotypes of multiple sclerosis (MS) manifest varying degrees of brain atrophy beyond that of normal aging. Assessment of atrophy helps to distinguish clinically and cognitively deteriorating patients and predicts those who will have a less-favorable clinical outcome over the long term. Atrophy can be measured from brain MRI scans, and many technological improvements have been made over the last few years. Several software tools, with differing requirements on technical ability and levels of operator intervention, are currently available and have already been applied in research or clinical trial settings. Despite this, the measurement of atrophy in routine clinical practice remains an unmet need. After a short summary of the pathologic substrates of brain atrophy in MS, this review attempts to guide the clinician towards a better understanding of the methods currently used for quantifying brain atrophy in this condition. Important physiologic factors that affect brain volume measures are also considered. Finally, the most recent research on brain atrophy in MS is summarized, including whole brain and various compartments thereof (i.e., white matter, gray matter, selected CNS structures). Current methods provide sufficient precision for cohort studies, but are not adequate for confidently assessing changes in individual patients over the scale of months or a few years. © 2016 American Academy of Neurology.

  7. Evaluation of Field Map and Nonlinear Registration Methods for Correction of Susceptibility Artifacts in Diffusion MRI

    PubMed Central

    Wang, Sijia; Peterson, Daniel J.; Gatenby, J. C.; Li, Wenbin; Grabowski, Thomas J.; Madhyastha, Tara M.

    2017-01-01

    Correction of echo planar imaging (EPI)-induced distortions (called “unwarping”) improves anatomical fidelity for diffusion magnetic resonance imaging (MRI) and functional imaging investigations. Commonly used unwarping methods require the acquisition of supplementary images during the scanning session. Alternatively, distortions can be corrected by nonlinear registration to a non-EPI acquired structural image. In this study, we compared reliability using two methods of unwarping: (1) nonlinear registration to a structural image using symmetric normalization (SyN) implemented in Advanced Normalization Tools (ANTs); and (2) unwarping using an acquired field map. We performed this comparison in two different test-retest data sets acquired at differing sites (N = 39 and N = 32). In both data sets, nonlinear registration provided higher test-retest reliability of the output fractional anisotropy (FA) maps than field map-based unwarping, even when accounting for the effect of interpolation on the smoothness of the images. In general, field map-based unwarping was preferable if and only if the field maps were acquired optimally. PMID:28270762

  8. Effect of the nanoparticle synthesis method on dendronized iron oxides as MRI contrast agents.

    PubMed

    Basly, Brice; Popa, Gabriela; Fleutot, Solenne; Pichon, Benoit P; Garofalo, Antonio; Ghobril, Cynthia; Billotey, Claire; Berniard, Aurélie; Bonazza, Pauline; Martinez, Hervé; Felder-Flesch, Delphine; Begin-Colin, Sylvie

    2013-02-14

    Aqueous suspensions of dendronized iron oxide nanoparticles (NPs) have been obtained after functionalization, with two types of dendrons, of NPs synthesized either by coprecipitation (leading to naked NPs in water) or by thermal decomposition (NPs in situ coated by oleic acid in an organic solvent). Different grafting strategies have been optimized depending on the NPs synthetic method. The size distribution, the colloidal stability in isoosmolar media, the surface complex nature as well as the preliminary biokinetic studies performed with optical imaging, and the contrast enhancement properties evaluated through in vitro and in vivo MRI experiments, have been compared as a function of the nature of both dendrons and NPs. All functionalized NPs displayed good colloidal stability in water, however the ones bearing a peripheral carboxylic acid function gave the best results in isoosmolar media. Whereas the grafting rates were similar, the nature of the surface complex depended on the NPs synthetic method. The in vitro contrast enhancement properties were better than commercial products, with a better performance of the NPs synthesized by coprecipitation. On the other hand, the NPs synthesized by thermal decomposition were more efficient in vivo. Furthermore, they both displayed good biodistribution with renal and hepatobiliary elimination pathways and no consistent RES uptake.

  9. Bunched phase encoding (BPE): a new fast data acquisition method in MRI.

    PubMed

    Moriguchi, Hisamoto; Duerk, Jeffrey L

    2006-03-01

    A new fast data acquisition method, "Bunched Phase Encoding" (BPE), is presented. In conventional rectilinear data acquisition, only a readout gradient (and no phase encoding gradient) is applied when k-space data are acquired. Reduction of the number of phase encoding lines by increasing the phase encoding step size often leads to aliasing artifacts. Papoulis's generalized sampling theory asserts that in some cases aliasing artifact-free signals can be reconstructed even if the Nyquist criterion is violated in some regions of the Fourier domain. In this study, Papoulis's theoretical construct is exploited to reduce the number of acquired phase encoding lines. To achieve this, k-space data are sampled along a "zigzag" trajectory during each readout; samples are acquired at a sampling frequency higher than that of the normal rectilinear acquisition. The total number of TR cycles and, hence, the total scan time can be reduced. The resultant signal-to-noise ratio (SNR) often varies across the reconstructed image when using the BPE technique, and the image SNR depends on the reconstruction method. This work is comparable to a gradient based version of parallel imaging. Evidence suggests it may serve as the basis for new opportunities for fast data acquisition in MRI. Magn Reson Med, 2006. (c) 2006 Wiley-Liss, Inc.

  10. Evaluation of MRI acquisition workflow with lean six sigma method: case study of liver and knee examinations.

    PubMed

    Roth, Christopher J; Boll, Daniel T; Wall, Lisa K; Merkle, Elmar M

    2010-08-01

    The purpose of this investigation was to assess workflow for medical imaging studies, specifically comparing liver and knee MRI examinations by use of the Lean Six Sigma methodologic framework. The hypothesis tested was that the Lean Six Sigma framework can be used to quantify MRI workflow and to identify sources of inefficiency to target for sequence and protocol improvement. Audio-video interleave streams representing individual acquisitions were obtained with graphic user interface screen capture software in the examinations of 10 outpatients undergoing MRI of the liver and 10 outpatients undergoing MRI of the knee. With Lean Six Sigma methods, the audio-video streams were dissected into value-added time (true image data acquisition periods), business value-added time (time spent that provides no direct patient benefit but is requisite in the current system), and non-value-added time (scanner inactivity while awaiting manual input). For overall MRI table time, value-added time was 43.5% (range, 39.7-48.3%) of the time for liver examinations and 89.9% (range, 87.4-93.6%) for knee examinations. Business value-added time was 16.3% of the table time for the liver and 4.3% of the table time for the knee examinations. Non-value-added time was 40.2% of the overall table time for the liver and 5.8% for the knee examinations. Liver MRI examinations consume statistically significantly more non-value-added and business value-added times than do knee examinations, primarily because of respiratory command management and contrast administration. Workflow analyses and accepted inefficiency reduction frameworks can be applied with use of a graphic user interface screen capture program.

  11. 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.

  12. 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

  13. A Method for Multitask fMRI Data Fusion Applied to Schizophrenia

    PubMed Central

    Calhoun, Vince D.; Adali, Tulay; Kiehl, Kent A.; Astur, Robert; Pekar, James J.; Pearlson, Godfrey D.

    2009-01-01

    It is becoming common to collect data from multiple functional magnetic resonance imaging (fMRI) paradigms on a single individual. The data from these experiments are typically analyzed separately and sometimes directly subtracted from one another on a voxel-by-voxel basis. These comparative approaches, although useful, do not directly attempt to examine potential commonalities between tasks and between voxels. To remedy this we propose a method to extract maximally spatially independent maps for each task that are “coupled” together by a shared loading parameter. We first compute an activation map for each task and each individual as “features, ” which are then used to perform joint independent component analysis (jICA) on the group data. We demonstrate our approach on a data set derived from healthy controls and schizophrenia patients, each of which carried out an auditory oddball task and a Sternberg working memory task. Our analysis approach revealed two interesting findings in the data that were missed with traditional analyses. First, consistent with our hypotheses, schizophrenia patients demonstrate “decreased” connectivity in a joint network including portions of regions implicated in two prevalent models of schizophrenia. A second finding is that for the voxels identified by the jICA analysis, the correlation between the two tasks was significantly higher in patients than in controls. This finding suggests that schizophrenia patients activate “more similarly” for both tasks than do controls. A possible synthesis of both findings is that patients are activating less, but also activating with a less-unique set of regions for these very different tasks. Both of the findings described support the claim that examination of joint activation across multiple tasks can enable new questions to be posed about fMRI data. Our approach can also be applied to data using more than two tasks. It thus provides a way to integrate and probe brain networks

  14. A method for multitask fMRI data fusion applied to schizophrenia.

    PubMed

    Calhoun, Vince D; Adali, Tulay; Kiehl, Kent A; Astur, Robert; Pekar, James J; Pearlson, Godfrey D

    2006-07-01

    It is becoming common to collect data from multiple functional magnetic resonance imaging (fMRI) paradigms on a single individual. The data from these experiments are typically analyzed separately and sometimes directly subtracted from one another on a voxel-by-voxel basis. These comparative approaches, although useful, do not directly attempt to examine potential commonalities between tasks and between voxels. To remedy this we propose a method to extract maximally spatially independent maps for each task that are "coupled" together by a shared loading parameter. We first compute an activation map for each task and each individual as "features," which are then used to perform joint independent component analysis (jICA) on the group data. We demonstrate our approach on a data set derived from healthy controls and schizophrenia patients, each of which carried out an auditory oddball task and a Sternberg working memory task. Our analysis approach revealed two interesting findings in the data that were missed with traditional analyses. First, consistent with our hypotheses, schizophrenia patients demonstrate "decreased" connectivity in a joint network including portions of regions implicated in two prevalent models of schizophrenia. A second finding is that for the voxels identified by the jICA analysis, the correlation between the two tasks was significantly higher in patients than in controls. This finding suggests that schizophrenia patients activate "more similarly" for both tasks than do controls. A possible synthesis of both findings is that patients are activating less, but also activating with a less-unique set of regions for these very different tasks. Both of the findings described support the claim that examination of joint activation across multiple tasks can enable new questions to be posed about fMRI data. Our approach can also be applied to data using more than two tasks. It thus provides a way to integrate and probe brain networks using a variety of

  15. A multi-atlas based method for automated anatomical rat brain MRI segmentation and extraction of PET activity.

    PubMed

    Lancelot, Sophie; Roche, Roxane; Slimen, Afifa; Bouillot, Caroline; Levigoureux, Elise; Langlois, Jean-Baptiste; Zimmer, Luc; Costes, Nicolas

    2014-01-01

    Preclinical in vivo imaging requires precise and reproducible delineation of brain structures. Manual segmentation is time consuming and operator dependent. Automated segmentation as usually performed via single atlas registration fails to account for anatomo-physiological variability. We present, evaluate, and make available a multi-atlas approach for automatically segmenting rat brain MRI and extracting PET activies. High-resolution 7T 2DT2 MR images of 12 Sprague-Dawley rat brains were manually segmented into 27-VOI label volumes using detailed protocols. Automated methods were developed with 7/12 atlas datasets, i.e. the MRIs and their associated label volumes. MRIs were registered to a common space, where an MRI template and a maximum probability atlas were created. Three automated methods were tested: 1/registering individual MRIs to the template, and using a single atlas (SA), 2/using the maximum probability atlas (MP), and 3/registering the MRIs from the multi-atlas dataset to an individual MRI, propagating the label volumes and fusing them in individual MRI space (propagation & fusion, PF). Evaluation was performed on the five remaining rats which additionally underwent [18F]FDG PET. Automated and manual segmentations were compared for morphometric performance (assessed by comparing volume bias and Dice overlap index) and functional performance (evaluated by comparing extracted PET measures). Only the SA method showed volume bias. Dice indices were significantly different between methods (PF>MP>SA). PET regional measures were more accurate with multi-atlas methods than with SA method. Multi-atlas methods outperform SA for automated anatomical brain segmentation and PET measure's extraction. They perform comparably to manual segmentation for FDG-PET quantification. Multi-atlas methods are suitable for rapid reproducible VOI analyses.

  16. A method for fully automated measurement of neurological structures in MRI

    NASA Astrophysics Data System (ADS)

    Ashton, Edward A.; Riek, Jonathan K.; Molinelli, Larry; Berg, Michel J.; Parker, Kevin J.

    2003-05-01

    A method for fully automating the measurement of various neurological structures in MRI is presented. This technique uses an atlas-based trained maximum likelihood classifier. The classifier requires a map of prior probabilities, which is obtained by registering a large number of previously classified data sets to the atlas and calculating the resulting probability that each represented tissue type or structure will appear at each voxel in the data set. Classification is then carried out using the standard maximum likelihood discriminant function, assuming normal statistics. The results of this classification process can be used in three ways, depending on the type of structure that is being detected or measured. In the most straightforward case, measurement of a normal neural sub-structure such as the hippocampus, the results of the classifier provide a localization point for the initiation of a deformable template model, which is then optimized with respect to the original data. The detection and measurement of abnormal structures, such as white matter lesions in multiple sclerosis patients, requires a slightly different approach. Lesions are detected through the application of a spectral matched filter to areas identified by the classifier as white matter. Finally, detection of unknown abnormalities can be accomplished through anomaly detection.

  17. Sparse Reconstruction Techniques in MRI: Methods, Applications, and Challenges to Clinical Adoption

    PubMed Central

    Yang, Alice Chieh-Yu; Kretzler, Madison; Sudarski, Sonja; Gulani, Vikas; Seiberlich, Nicole

    2016-01-01

    The family of sparse reconstruction techniques, including the recently introduced compressed sensing framework, has been extensively explored to reduce scan times in Magnetic Resonance Imaging (MRI). While there are many different methods that fall under the general umbrella of sparse reconstructions, they all rely on the idea that a priori information about the sparsity of MR images can be employed to reconstruct full images from undersampled data. This review describes the basic ideas behind sparse reconstruction techniques, how they could be applied to improve MR imaging, and the open challenges to their general adoption in a clinical setting. The fundamental principles underlying different classes of sparse reconstructions techniques are examined, and the requirements that each make on the undersampled data outlined. Applications that could potentially benefit from the accelerations that sparse reconstructions could provide are described, and clinical studies using sparse reconstructions reviewed. Lastly, technical and clinical challenges to widespread implementation of sparse reconstruction techniques, including optimization, reconstruction times, artifact appearance, and comparison with current gold-standards, are discussed. PMID:27003227

  18. 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

  19. 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.

  20. A practical clinical method to quantify language lateralization in fMRI using whole-brain analysis.

    PubMed

    Jones, Stephen E; Mahmoud, Shamseldeen Y; Phillips, Micheal D

    2011-02-14

    Surgery is often the only effective treatment for intractable epilepsy, but its benefits must be balanced by potential disruption of eloquent cortical functions. Wada test is the standard technique to lateralize language before surgery; however, it is invasive and associated with complications. fMRI provides an attractive noninvasive alternative, which has been previously shown to correlate with Wada results. However this correlation is imperfect since standard fMRI laterality indices are dependent on a particular arbitrary statistical threshold used in the data processing. We report a novel automated, threshold-independent fMRI methodology to assess language lateralization, which we hypothesize provides a robust and unbiased pre-operative assessment. This hemispheric histogram analysis method can accurately interrogate language lateralization, as validated against the Wada test. Fifty-nine subjects with intractable epilepsy received preoperative evaluation for language lateralization using fMRI. fMRI data then were analyzed using a novel automated threshold-independent method for determining language lateralization. The methodology generated a lateralization score based on hemispheric activation of language areas and a quality index based on multiple factors, including patient motion and signal-to-noise characteristics. Lateralization scores were compared to Wada test results (51 patients), direct cortical stimulation (3 patients), and subdural grid stimulation (5 patients). Data sets were used to generate a probability score for language lateralization for each subject. The lateralization scores correlated well with the objective measures of language lateralization (r(2)=0.46). Cumulative historical data were utilized to prospectively determine probabilities of language lateralization for individual patients. In conclusion, hemispheric language lateralization can be accurately determined using a novel objective and automated methodology that calculates language

  1. Comparison of two exploratory data analysis methods for fMRI: unsupervised clustering versus independent component analysis.

    PubMed

    Meyer-Baese, A; Wismueller, Axel; Lange, Oliver

    2004-09-01

    Exploratory data-driven methods such as unsupervised clustering and independent component analysis (ICA) are considered to be hypothesis-generating procedures, and are complementary to the hypothesis-led statistical inferential methods in functional magnetic resonance imaging (fMRI). In this paper, we present a comparison between unsupervised clustering and ICA in a systematic fMRI study. The comparative results were evaluated by 1) task-related activation maps, 2) associated time-courses, and 3) receiver operating characteristic analysis. For the fMRI data, a comparative quantitative evaluation between the three clustering techniques, self-organizing map, "neural gas" network, and fuzzy clustering based on deterministic annealing, and the three ICA methods, FastICA, Infomax and topographic ICA was performed. The ICA methods proved to extract features relatively well for a small number of independent components but are limited to the linear mixture assumption. The unsupervised Clustering outperforms ICA in terms of classification results but requires a longer processing time than the ICA methods.

  2. Graph cut-based method for segmenting the left ventricle from MRI or echocardiographic images.

    PubMed

    Bernier, Michael; Jodoin, Pierre-Marc; Humbert, Olivier; Lalande, Alain

    2017-04-02

    In this paper, we present a fast and interactive graph cut method for 3D segmentation of the endocardial wall of the left ventricle (LV) adapted to work on two of the most widely used modalities: magnetic resonance imaging (MRI) and echocardiography. Our method accounts for the fundamentally different nature of both modalities: 3D echocardiographic images have a low contrast, a poor signal-to-noise ratio and frequent signal drop, while MR images are more detailed but also cluttered and contain highly anisotropic voxels. The main characteristic of our method is to work in a 3D Bezier coordinate system instead of the original Euclidean space. This comes with several advantages, including an implicit shape prior and a result guarantied not to have any holes in it. The proposed method is made of 4 steps. First, a 3D sampling of the LV cavity is made based on a Bezier coordinate system. This allows to warp the input 3D image to a Bezier space in which a plane corresponds to an anatomically plausible 3D Euclidean bullet shape. Second, a 3D graph is built and an energy term (which is based on the image gradient and a 3D probability map) is assigned to each edge of the graph, some of which being given an infinite energy to ensure the resulting 3D structure passes through key anatomical points. Third, a max-flow min-cut procedure is executed on the energy graph to delineate the endocardial surface. And fourth, the resulting surface is projected back to the Euclidean space where a post-processing convex hull algorithm is applied on every short axis slice to remove local concavities. Results obtained on two datasets reveal that our method takes between 2 and 5s to segment a 3D volume, it has better results overall than most state-of-the-art methods on the CETUS echocardiographic dataset and is statistically as good as a human operator on MR images.

  3. Physiological characterization of a robust survival rodent fMRI method.

    PubMed

    Brynildsen, Julia K; Hsu, Li-Ming; Ross, Thomas J; Stein, Elliot A; Yang, Yihong; Lu, Hanbing

    2017-01-01

    Anesthetics are commonly used in preclinical functional MRI studies. It is well-appreciated that proper choice of anesthetics is of critical importance for maintaining a physiologically normal range of autonomic functioning. A recent study, using a low dose of dexmedetomidine (active isomer of medetomidine) in combination with a low dose of isoflurane, suggested stable measurements across repeated fMRI experiments in individual animals with each session lasting up to several hours. The rat default mode network has been successfully identified using this preparation, indicating that this protocol minimally disturbs brain network functions. However, medetomidine is known to cause peripheral vasoconstriction, respiratory suppression, and bradycardia, each of which could independently confound the BOLD signal. The goal of this study was to systematically characterize physiological conditions for fMRI experiments under this anesthetic regimen. To this end, we acquired somatosensory stimulation "task-evoked" and resting-state fMRI to evaluate the integrity of neurovascular coupling and brain network function during three time windows (0-30min, 30-90min, and 90-150min) following dexmedetomidine initiation. Results demonstrate that both evoked BOLD response and resting-state fMRI signal remained stable during the 90-150min time window, while autonomic physiological parameters maintained near-normal conditions during this period. Our data suggest that using a spontaneously-inhaled, low dose of isoflurane in combination with a continuous low dose of dexmedetomidine is a viable option for longitudinal imaging studies in rats.

  4. A non-invasive method of quantifying pancreatic volume in mice using micro-MRI.

    PubMed

    Paredes, Jose L; Orabi, Abrahim I; Ahmad, Taimur; Benbourenane, Iman; Tobita, Kimimasa; Tadros, Sameh; Bae, Kyongtae T; Husain, Sohail Z

    2014-01-01

    In experimental models of pancreatic growth and recovery, changes in pancreatic size are assessed by euthanizing a large cohort of animals at varying time points and measuring organ mass. However, to ascertain this information in clinical practice, patients with pancreatic disorders routinely undergo non-invasive cross-sectional imaging of the pancreas using magnetic resonance imaging (MRI) or computed tomography (CT). The aim of the current study was to develop a thin-sliced, optimized sequence protocol using a high field MRI to accurately calculate pancreatic volumes in the most common experimental animal, the mouse. Using a 7 Telsa Bruker micro-MRI system, we performed abdominal imaging in whole-fixed mice in three standard planes: axial, sagittal, and coronal. The contour of the pancreas was traced using Vitrea software and then transformed into a 3-dimensional (3D) reconstruction, from which volumetric measurements were calculated. Images were optimized using heart perfusion-fixation, T1 sequence analysis, and 0.2 to 0.4 mm thick slices. As proof of principle, increases in pancreatic volume among mice of different ages correlated tightly with increasing body weight. In summary, this is the first study to measure pancreatic volumes in mice, using a high field 7 Tesla micro-MRI and a thin-sliced, optimized sequence protocol. We anticipate that micro-MRI will improve the ability to non-invasively quantify changes in pancreatic size and will dramatically reduce the number of animals required to serially assess pancreatic growth and recovery.

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

    PubMed

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

    2016-05-18

    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.

  6. 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

  7. Cartilage repair surgery: outcome evaluation by using noninvasive cartilage biomarkers based on quantitative MRI techniques?

    PubMed

    Jungmann, Pia M; Baum, Thomas; Bauer, Jan S; Karampinos, Dimitrios C; Erdle, Benjamin; Link, Thomas M; Li, Xiaojuan; Trattnig, Siegfried; Rummeny, Ernst J; Woertler, Klaus; Welsch, Goetz H

    2014-01-01

    New quantitative magnetic resonance imaging (MRI) techniques are increasingly applied as outcome measures after cartilage repair. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), and diffusion weighted imaging (DWI) are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair.

  8. An efficient calculation method for pharmacokinetic parameters in brain permeability study using dynamic contrast-enhanced MRI.

    PubMed

    Wang, Chunhao; Yin, Fang-Fang; Chang, Zheng

    2016-02-01

    To develop an efficient method for calculating pharmacokinetic (PK) parameters in brain DCE-MRI permeability studies. A linear least-squares fitting algorithm based on a derivative expression of the two-compartment PK model was proposed to analytically solve for the PK parameters. Noise in the expression was minimized through low-pass filtering. Simulation studies were conducted in which the proposed method was compared with two existing methods in terms of accuracy and efficiency. Five in vivo brain studies were demonstrated for potential clinical application. In the simulation studies using chosen parameter values, the calculated percent difference of K(trans) by the proposed method was <5.0% with a temporal resolution (Δt) < 5 s, and the accuracies of all parameter results were better or comparable to existing methods. When analyzed within certain parameter intensity ranges, the proposed method was more accurate than the existing methods and improved the efficiency by a factor of up to 458 for a Δt = 1 s and up to 38 for a Δt = 5 s. In the in vivo study, the calculated parameters using the proposed method were comparable to those using the existing methods with improved efficiencies. An efficient method was developed for the accurate and efficient calculation of parameters in brain DCE-MRI permeability studies. © 2015 Wiley Periodicals, Inc.

  9. Teaching Dental Students to Understand the Temporomandibular Joint Using MRI: Comparison of Conventional and Digital Learning Methods.

    PubMed

    Arús, Nádia A; da Silva, Átila M; Duarte, Rogério; da Silveira, Priscila F; Vizzotto, Mariana B; da Silveira, Heraldo L D; da Silveira, Heloisa E D

    2017-06-01

    The aims of this study were to evaluate and compare the performance of dental students in interpreting the temporomandibular joint (TMJ) with magnetic resonance imaging (MRI) scans using two learning methods (conventional and digital interactive learning) and to examine the usability of the digital learning object (DLO). The DLO consisted of tutorials about MRI and anatomic and functional aspects of the TMJ. In 2014, dental students in their final year of study who were enrolled in the elective "MRI Interpretation of the TMJ" course comprised the study sample. After exclusions for nonattendance and other reasons, 29 of the initial 37 students participated in the study, for a participation rate of 78%. The participants were divided into two groups: a digital interactive learning group (n=14) and a conventional learning group (n=15). Both methods were assessed by an objective test applied before and after training and classes. Aspects such as support and training requirements, complexity, and consistency of the DLO were also evaluated using the System Usability Scale (SUS). A significant between-group difference in the posttest results was found, with the conventional learning group scoring better than the DLO group, indicated by mean scores of 9.20 and 8.11, respectively, out of 10. However, when the pretest and posttest results were compared, both groups showed significantly improved performance. The SUS score was 89, which represented a high acceptance of the DLO by the users. The students who used the conventional method of learning showed superior performance in interpreting the TMJ using MRI compared to the group that used digital interactive learning.

  10. Activated region fitting: a robust high-power method for fMRI analysis using parameterized regions of activation.

    PubMed

    Weeda, Wouter D; Waldorp, Lourens J; Christoffels, Ingrid; Huizenga, Hilde M

    2009-08-01

    An important issue in the analysis of fMRI is how to account for the spatial smoothness of activated regions. In this article a method is proposed to accomplish this by modeling activated regions with Gaussian shapes. Hypothesis tests on the location, spatial extent, and amplitude of these regions are performed instead of hypothesis tests of individual voxels. This increases power and eases interpretation. Simulation studies show robust hypothesis tests under misspecification of the shape model, and increased power over standard techniques especially at low signal-to-noise ratios. An application to real single-subject data also indicates that the method has increased power over standard methods.

  11. SU-D-207A-06: Pediatric Abdominal Organ Motion Quantified Via a Novel 4D MRI Method

    SciTech Connect

    Uh, J; Krasin, MJ; Lucas, JT; Tinkle, C; Merchant, TE; Hua, C

    2016-06-15

    Purpose: To develop a 4D MRI method for assessing respiration-induced abdominal organ motion in children receiving radiation therapy. Methods: A 4D MRI using internal image-based respiratory surrogate has been developed and implemented on a clinical scanner (1.5T Siemens Avanto). Ten patients (younger group: N=6, 2–5 years, anesthetized; older group: N=4, 11–15 years) with neuroblastoma, Wilm’s tumor rhabdomyosarcoma, or desmoplastic small round cell tumor received free breathing 4D MRI scans for treatment planning. Coronal image slices of the entire abdomen were retrospectively constructed in 10 respiratory phases. A B-spline deformable registration (Metz et al. 2011) was performed on 4D datasets to automatically derive motion trajectories of selected anatomical landmarks, including the dome and the center of the liver, and the superior edges of kidneys and spleen. The extents of the motion in three dimensions (anteroposterior, AP; mediolateral, ML; superoinferior, SI) and the correlations between organ motion trajectories were quantified. Results: The 4D MRI scans were successfully performed in <20 minutes for all patients without the use of any external device. Organ motion extents were larger in adolescents (kidneys: 3–13 mm SI, liver and spleen: 6–18 mm SI) than in younger children (kidneys:<3mm in all directions; liver and spleen: 1–8 mm SI, 1–5 mm ML and AP). The magnitude of respiratory motion in some adolescents may warrant special motion management. Motion trajectories were not synchronized across selected anatomical landmarks, particularly in the ML and AP directions, indicating inter- and intra-organ variations of the respiratory-induced motion. Conclusion: The developed 4D MRI acquisition and motion analysis methods provide a non-ionizing, non-invasive approach to automatically measure the organ motion trajectory in the pediatric abdomen. It is useful for defining ITV and PRV, monitoring changes in target motion patterns during the

  12. A Non-Local Fuzzy Segmentation Method: Application to Brain MRI

    NASA Astrophysics Data System (ADS)

    Caldairou, Benoît; Rousseau, François; Passat, Nicolas; Habas, Piotr; Studholme, Colin; Heinrich, Christian

    The Fuzzy C-Means algorithm is a widely used and flexible approach for brain tissue segmentation from 3D MRI. Despite its recent enrichment by addition of a spatial dependency to its formulation, it remains quite sensitive to noise. In order to improve its reliability in noisy contexts, we propose a way to select the most suitable example regions for regularisation. This approach inspired by the Non-Local Mean strategy used in image restoration is based on the computation of weights modelling the grey-level similarity between the neighbourhoods being compared. Experiments were performed on MRI data and results illustrate the usefulness of the approach in the context of brain tissue classification.

  13. Methods of MRI-Based Structural Imaging in the Aging Monkey

    PubMed Central

    Makris, N.; Kennedy, D. N.; Boriel, D.L.; Rosene, D. L.

    2013-01-01

    Rhesus monkeys, whose typical lifespan can be as long as 30 years in the presence of veterinary care, undergo a cognitive decline as a function of age. While cortical neurons are largely preserved in the cerebral cortex, including primary motor and visual cortex as well as prefrontal association cortex there is marked breakdown of axonal myelin and an overall reduction in white matter predominantly in the frontal and temporal lobes. Whether the myelin breakdown is diffuse or specific to individual white matter fiber pathways is important to be known with certainty. To this end the delineation and quantification of specific frontotemporal fiber pathways within the frontal and temporal lobes is essential to determine which structures are altered and the extent to which these alterations correlate with behavioral findings. The capability of studying the living brain non-invasively with MRI opens up a new window in structural-functional and anatomic-clinical relationships allowing the integration of information derived from different scanning modalities in the same subject. For instance, for any particular voxel in the cerebrum we can obtain structural T1-, diffusion- and magnetization transfer-magnetic resonance imaging (MRI) based information. Moreover, it is thus possible to follow any observed changes longitudinally over time. These acquisitions of multidimensional data in the same individual within the same MRI experimental setting would enable the creation of a data base of integrated structural MRI-behavioral correlations for normal aging monkeys to elucidate the underlying neurobiological mechanisms of functional senescence in the aging non-human primate. PMID:19577648

  14. 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.

  15. Spatially constrained incoherent motion method improves diffusion-weighted MRI signal decay analysis in the liver and spleen

    PubMed Central

    Taimouri, Vahid; Afacan, Onur; Perez-Rossello, Jeannette M.; Callahan, Michael J.; Mulkern, Robert V.; Warfield, Simon K.; Freiman, Moti

    2015-01-01

    Purpose: To evaluate the effect of the spatially constrained incoherent motion (SCIM) method on improving the precision and robustness of fast and slow diffusion parameter estimates from diffusion-weighted MRI in liver and spleen in comparison to the independent voxel-wise intravoxel incoherent motion (IVIM) model. Methods: We collected diffusion-weighted MRI (DW-MRI) data of 29 subjects (5 healthy subjects and 24 patients with Crohn’s disease in the ileum). We evaluated parameters estimates’ robustness against different combinations of b-values (i.e., 4 b-values and 7 b-values) by comparing the variance of the estimates obtained with the SCIM and the independent voxel-wise IVIM model. We also evaluated the improvement in the precision of parameter estimates by comparing the coefficient of variation (CV) of the SCIM parameter estimates to that of the IVIM. Results: The SCIM method was more robust compared to IVIM (up to 70% in liver and spleen) for different combinations of b-values. Also, the CV values of the parameter estimations using the SCIM method were significantly lower compared to repeated acquisition and signal averaging estimated using IVIM, especially for the fast diffusion parameter in liver (CVIV IM = 46.61 ± 11.22, CVSCIM = 16.85 ± 2.160, p < 0.001) and spleen (CVIV IM = 95.15 ± 19.82, CVSCIM = 52.55 ± 1.91, p < 0.001). Conclusions: The SCIM method characterizes fast and slow diffusion more precisely compared to the independent voxel-wise IVIM model fitting in the liver and spleen. PMID:25832079

  16. Multi-method analysis of MRI images in early diagnostics of Alzheimer's disease.

    PubMed

    Wolz, Robin; Julkunen, Valtteri; Koikkalainen, Juha; Niskanen, Eini; Zhang, Dong Ping; Rueckert, Daniel; Soininen, Hilkka; Lötjönen, Jyrki

    2011-01-01

    The role of structural brain magnetic resonance imaging (MRI) is becoming more and more emphasized in the early diagnostics of Alzheimer's disease (AD). This study aimed to assess the improvement in classification accuracy that can be achieved by combining features from different structural MRI analysis techniques. Automatically estimated MR features used are hippocampal volume, tensor-based morphometry, cortical thickness and a novel technique based on manifold learning. Baseline MRIs acquired from all 834 subjects (231 healthy controls (HC), 238 stable mild cognitive impairment (S-MCI), 167 MCI to AD progressors (P-MCI), 198 AD) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database were used for evaluation. We compared the classification accuracy achieved with linear discriminant analysis (LDA) and support vector machines (SVM). The best results achieved with individual features are 90% sensitivity and 84% specificity (HC/AD classification), 64%/66% (S-MCI/P-MCI) and 82%/76% (HC/P-MCI) with the LDA classifier. The combination of all features improved these results to 93% sensitivity and 85% specificity (HC/AD), 67%/69% (S-MCI/P-MCI) and 86%/82% (HC/P-MCI). Compared with previously published results in the ADNI database using individual MR-based features, the presented results show that a comprehensive analysis of MRI images combining multiple features improves classification accuracy and predictive power in detecting early AD. The most stable and reliable classification was achieved when combining all available features.

  17. Comparison of BCG artifact removal methods for evoked responses in simultaneous EEG-fMRI.

    PubMed

    Shams, Nasim; Alain, Claude; Strother, Stephen

    2015-04-30

    Simultaneous recording of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) has gained attention due to the complimentary properties of the two imaging modalities. Their combined recording enables the study of brain function while taking advantage of the high temporal resolution of EEG and high spatial resolution of fMRI. However EEG data recorded inside the MR scanner is significantly contaminated by two main sources of artifacts: MR gradient artifacts and ballistocardiogram (BCG) artifacts. Most existing removal approaches for these artifacts fall into two main categories: average artifact subtraction (AAS) and optimal basis selection (OBS). While these techniques can improve the data quality significantly, highly effective removal of artifacts - particularly the BCG artifact - from the data is still lacking. Here, we compared two of the most commonly used algorithms for BCG artifact removal (OBS and AAS) based on the estimated signal-to-noise ratio (SNR) of auditory and visual evoked responses recorded during fMRI acquisition. We also further compared optimization of OBS for groups, and at the individual subject and run level. The results suggest that performance of the OBS algorithm can be significantly improved by choosing the optimum number of principal components. Furthermore, optimizing the number of principal components at the individual participant and run level results in significant improvements in the SNR of evoked responses compared to group optimization.

  18. 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.

  19. A comprehensive testing protocol for MRI neuroanatomical segmentation techniques: Evaluation of a novel lateral ventricle segmentation method.

    PubMed

    Kempton, Matthew J; Underwood, Tracy S A; Brunton, Simon; Stylios, Floris; Schmechtig, Anne; Ettinger, Ulrich; Smith, Marcus S; Lovestone, Simon; Crum, William R; Frangou, Sophia; Williams, Steven C R; Simmons, Andrew

    2011-10-15

    Although a wide range of approaches have been developed to automatically assess the volume of brain regions from MRI, the reproducibility of these algorithms across different scanners and pulse sequences, their accuracy in different clinical populations and sensitivity to real changes in brain volume have not always been comprehensively examined. Firstly we present a comprehensive testing protocol which comprises 312 freely available MR images to assess the accuracy, reproducibility and sensitivity of automated brain segmentation techniques. Accuracy is assessed in infants, young adults and patients with Alzheimer's disease in comparison to gold standard measures by expert observers using a manual technique based on Cavalieri's principle. The protocol determines the reliability of segmentation between scanning sessions, different MRI pulse sequences and 1.5T and 3T field strengths and examines their sensitivity to small changes in volume using a large longitudinal dataset. Secondly we apply this testing protocol to a novel algorithm for segmenting the lateral ventricles and compare its performance to the widely used FSL FIRST and FreeSurfer methods. The testing protocol produced quantitative measures of accuracy, reliability and sensitivity of lateral ventricle volume estimates for each segmentation method. The novel algorithm showed high accuracy in all populations (intraclass correlation coefficient, ICC>0.95), good reproducibility between MRI pulse sequences (ICC>0.99) and was sensitive to age related changes in longitudinal data. FreeSurfer demonstrated high accuracy (ICC>0.95), good reproducibility (ICC>0.99) and sensitivity whilst FSL FIRST showed good accuracy in young adults and infants (ICC>0.90) and good reproducibility (ICC=0.98), but was unable to segment ventricular volume in patients with Alzheimer's disease or healthy subjects with large ventricles. Using the same computer system, the novel algorithm and FSL FIRST processed a single MRI image in less

  20. A Method for Handling Intensity Inhomogenieties in fMRI Sequences of Moving Anatomy of the Early Developing Brain

    PubMed Central

    Seshamani, Sharmishtaa; Cheng, Xi; Fogtmann, Mads; Thomason, Moriah E.; Studholme, Colin

    2014-01-01

    This paper presents a method for intensity inhomogeniety removal in fMRI studies of a moving subject. In such studies, subtle changes in signal as the subject moves in the presence of a bias field can be a significant confound for BOLD signal analysis. The proposed method avoids the need for a specific tissue model or assumptions about tissue homogeneity by making use of the multiple views of the underlying bias field provided by the subject's motion. A parametric bias field model is assumed and a regression model is used to estimate the basis function weights of this model. Quantitative evaluation of the effects of motion and noise in motion estimates are performed using simulated data. Results demonstrate the strength and robustness of the new method compared to explicit segmentation based methods that estimate bias within individual timeframes, as well as the state of the art 4D nonparametric bias estimator (N4ITK). We also qualitatively demonstrate the impact of the method on resting state neuroimage analysis of a moving adult brain with simulated motion and bias fields, as well as on in-vivo moving fetal fMRI. PMID:24317121

  1. A real-time method to reduce ballistocardiogram artifacts from EEG during fMRI based on optimal basis sets (OBS).

    PubMed

    Wu, Xia; Wu, Tong; Zhan, Zhichao; Yao, Li; Wen, Xiaotong

    2016-04-01

    The simultaneous acquisition of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) provides both high temporal and spatial resolution when measuring brain activity. A real-time analysis during a simultaneous EEG-fMRI acquisition is essential when studying neurofeedback and conducting effective brain activity monitoring. However, the ballistocardiogram (BCG) artifacts which are induced by heartbeat-related electrode movements in an MRI scanner severely contaminate the EEG signals and hinder a reliable real-time analysis. The optimal basis sets (OBS) method is an effective candidate for removing BCG artifacts in a traditional offline EEG-fMRI analysis, but has yet to be applied to a real-time EEG-fMRI analysis. Here, a novel real-time technique based on OBS method (rtOBS) is proposed to remove BCG artifacts on a moment-to-moment basis. Real-time electrocardiogram R-peak detection procedure and sliding window OBS method were adopted. A series of simulated data was constructed to verify the feasibility of the rtOBS technique. Furthermore, this method was applied to real EEG-fMRI data to remove BCG artifacts. The results of both simulated data and real EEG-fMRI data from eight healthy human subjects demonstrate the effectiveness of rtOBS in both the time and frequency domains. A comparison between rtOBS and real-time averaged artifact subtraction (rtAAS) was conducted. The results suggest the efficacy and advantage of rtOBS in the real-time removal of BCG artifacts. In this study, a novel real-time OBS technique was proposed for the real-time removal of BCG artifacts. The proposed method was tested using simulated data and applied to real simultaneous EEG-fMRI data. The results suggest the effectiveness of this method. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. A component based noise correction method (CompCor) for BOLD and perfusion based fMRI.

    PubMed

    Behzadi, Yashar; Restom, Khaled; Liau, Joy; Liu, Thomas T

    2007-08-01

    A component based method (CompCor) for the reduction of noise in both blood oxygenation level-dependent (BOLD) and perfusion-based functional magnetic resonance imaging (fMRI) data is presented. In the proposed method, significant principal components are derived from noise regions-of-interest (ROI) in which the time series data are unlikely to be modulated by neural activity. These components are then included as nuisance parameters within general linear models for BOLD and perfusion-based fMRI time series data. Two approaches for the determination of the noise ROI are considered. The first method uses high-resolution anatomical data to define a region of interest composed primarily of white matter and cerebrospinal fluid, while the second method defines a region based upon the temporal standard deviation of the time series data. With the application of CompCor, the temporal standard deviation of resting-state perfusion and BOLD data in gray matter regions was significantly reduced as compared to either no correction or the application of a previously described retrospective image based correction scheme (RETROICOR). For both functional perfusion and BOLD data, the application of CompCor significantly increased the number of activated voxels as compared to no correction. In addition, for functional BOLD data, there were significantly more activated voxels detected with CompCor as compared to RETROICOR. In comparison to RETROICOR, CompCor has the advantage of not requiring external monitoring of physiological fluctuations.

  3. 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. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. A method for handling intensity inhomogenieties in fMRI sequences of moving anatomy of the early developing brain.

    PubMed

    Seshamani, Sharmishtaa; Cheng, Xi; Fogtmann, Mads; Thomason, Moriah E; Studholme, Colin

    2014-02-01

    This paper presents a method for intensity inhomogeniety removal in fMRI studies of a moving subject. In such studies, subtle changes in signal as the subject moves in the presence of a bias field can be a significant confound for BOLD signal analysis. The proposed method avoids the need for a specific tissue model or assumptions about tissue homogeneity by making use of the multiple views of the underlying bias field provided by the subject's motion. A parametric bias field model is assumed and a regression model is used to estimate the basis function weights of this model. Quantitative evaluation of the effects of motion and noise in motion estimates are performed using simulated data. Results demonstrate the strength and robustness of the new method compared to the state of the art 4D nonparametric bias estimator (N4ITK). We also qualitatively demonstrate the impact of the method on resting state neuroimage analysis of a moving adult brain with simulated motion and bias fields, as well as on in vivo moving fetal fMRI.

  5. Sodium MRI.

    PubMed

    Ouwerkerk, Ronald

    2011-01-01

    Sodium ((23)Na) imaging has a place somewhere between (1)H-MRI and MR spectroscopy (MRS). Like MRS it potentially provides information on metabolic processes, but only one single resonance of ionic (23)Na is observed. Therefore pulse sequences do not need to code for a chemical shift dimension, allowing (23)Na images to be obtained at high resolutions as compared to MRS. In this chapter the biological significance of sodium in the brain will be discussed, as well as methods for observing it with (23)Na-MRI. Many vital cellular processes and interactions in excitable tissues depend on the maintenance of a low intracellular and high extracellular sodium concentration. Healthy cells maintain this concentration gradient at the cost of energy. Leaky cell membranes or an impaired energy metabolism immediately leads to an increase in cytosolic total tissue sodium. This makes sodium a biomarker for ischemia, cancer, excessive tissue activation, or tissue damage as might be caused by ablation therapy. Special techniques allow quantification of tissue sodium for the monitoring of disease or therapy in longitudinal studies or preferential observation of the intracellular component of the tissue sodium. New methods and high-field magnet technology provide new opportunities for (23)Na-MRI in clinical and biomedical research.

  6. A method for detecting the temporal sequence of muscle activation during cycling using MRI.

    PubMed

    Elder, Christopher P; Cook, Ryan N; Wilkens, Kenneth L; Chance, Marti A; Sanchez, Otto A; Damon, Bruce M

    2011-03-01

    Surface electromyography (EMG) can assess muscle recruitment patterns during cycling, but has limited applicability to studies of deep muscle recruitment and electrically stimulated contractions. We determined whether muscle recruitment timing could be inferred from MRI-measured transverse relaxation time constant (T(2)) changes and a cycle ergometer modified to vary power as a function of pedal angle. Six subjects performed 6 min of single-leg cycling under two conditions (E0°-230° and E90°-230°), which increased the power from 0°-230° and 90-230° of the pedal cycle, respectively. The difference condition produced a virtual power output from 0-180° (V0°-180°). Recruitment was assessed by integrating EMG over the pedal cycle (IEMG) and as the (post-pre) exercise T(2) change (ΔT(2)). For E0°-230°, the mean IEMG for vastus medialis and lateralis (VM/VL; 49.3 ± 3.9 mV·s; mean ± SE) was greater (P < 0.05) than that for E90°-230° (17.9 ± 1.9 mV·s); the corresponding ΔT(2) values were 8.7 ± 1.0 and 1.4 ± 0.5 ms (P < 0.05). For E0°-230° and E90°-230°, the IEMG values for biceps femoris/long head (BF(L)) were 37.7 ± 5.4 and 27.1 ± 5.6 mV·s (P > 0.05); the corresponding ΔT(2) values were 0.9 ± 0.9 and 1.5 ± 0.9 ms (P > 0.05). MRI data indicated activation of the semitendinosus and BF/short head for E0°-230° and E90°-230°. For V0°-180°, ΔT(2) was 7.2 ± 0.9 ms for VM/VL and -0.6 ± 0.6 ms for BF(L); IEMG was 31.5 ± 3.7 mV·s for VM/VL and 10.6 ± 7.0 mV·s for BF(L). MRI and EMG data indicate VM/VL activity from 0 to 180° and selected hamstring activity from 90 to 230°. Combining ΔT(2) measurements with variable loading allows the spatial and temporal patterns of recruitment during cycling to be inferred from MRI data.

  7. An improved cylindrical FDTD method and its application to field-tissue interaction study in MRI.

    PubMed

    Chi, Jieru; Liu, Feng; Xia, Ling; Shao, Tingting; Mason, David G; Crozier, Stuart

    2010-01-01

    This paper presents a three dimensional finite-difference time-domain (FDTD) scheme in cylindrical coordinates with an improved algorithm for accommodating the numerical singularity associated with the polar axis. The regularization of this singularity problem is entirely based on Ampere's law. The proposed algorithm has been detailed and verified against a problem with a known solution obtained from a commercial electromagnetic simulation package. The numerical scheme is also illustrated by modeling high-frequency RF field-human body interactions in MRI. The results demonstrate the accuracy and capability of the proposed algorithm.

  8. Simple diagrammatic method to delineate male urethra in prostate cancer radiotherapy: an MRI based approach.

    PubMed

    Kataria, Tejinder; Gupta, Deepak; Goyal, Shikha; Bisht, Shyam S; Chaudhary, Ravi; Narang, Kushal; Banerjee, Susovan; Basu, Trinanjan; Abhishek, Ashu; Sambasivam, Sasikumar; Vishnu, Nisha T

    2016-12-01

    Stereotactic body radiotherapy (SBRT) is being increasingly utilized in the treatment of prostate cancer. With the advent of high-precision radiosurgery systems, it is possible to obtain dose distributions akin to high-dose rate brachytherapy with SBRT. However, urethral toxicity has a significant impact on the quality of life in patients with prostate cancer. Contouring the male urethra on a CT scan is difficult in the absence of an indwelling catheter. In this pictorial essay, we have used the MRI obtained for radiotherapy planning to aid in the delineation of the male urethra and have attempted to define guidelines for the same.

  9. A progressive processing method for breast cancer detection via UWB based on an MRI-derived model

    NASA Astrophysics Data System (ADS)

    Xiao, Xia; Song, Hang; Wang, Zong-Jie; Wang, Liang

    2014-07-01

    Ultra-wideband (UWB) microwave imaging is a promising method for breast cancer detection based on the large contrast of electric parameters between the malignant tumor and its surrounded normal breast organisms. In the case of multiple tumors being present, the conventional imaging approaches may be ineffective to detect all the tumors clearly. In this paper, a progressive processing method is proposed for detecting more than one tumor. The method is divided into three stages: primary detection, refocusing and image optimization. To test the feasibility of the approach, a numerical breast model is developed based on the realistic magnetic resonance image (MRI). Two tumors are assumed embedded in different positions. Successful detection of a 3.6 mm-diameter tumor at a depth of 42 mm is achieved. The correct information of both tumors is shown in the reconstructed image, suggesting that the progressive processing method is promising for multi-tumor detection.

  10. A five-colour colour-coded mapping method for DCE-MRI analysis of head and neck tumours.

    PubMed

    Yuan, J; Chow, S K K; Yeung, D K W; King, A D

    2012-03-01

    To devise a method to convert the time-intensity curves (TICs) of head and neck dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) data into a pixel-by-pixel colour-coded map for identifying normal tissues and tumours. Twenty-three patients with head and neck squamous cell carcinoma (HNSCC) underwent DCE-MRI. TIC patterns of primary tumours, metastatic nodes, and normal tissues were assessed and a program was devised to convert the patterns into a classified colour-coded map. The enhancement patterns of tumours and normal tissue structures were evaluated and categorized into nine grades (0-8) based on the predominance of coloured pixels on maps. Five identified TIC patterns were converted into a colour-coded map consisting of red (maximum enhancement), brown (continuous slow rise-up), yellow (rapid wash-in and wash-out), green (rapid wash-in and plateau), and blue (rapid wash-in and rise-up). The colour-coded map distinguished all 21 primary tumours and 15 metastatic nodes from normal structures. Primary tumours and metastatic nodes were colour coded as predominantly yellow (grades 1-2) in 17/21 and 6/15, green (grades 3-5) in 3/21 and 5/15, and blue (grades 6-7) in 1/21 and 4/15, respectively. Vessels were coded red in 46/46 (grade 0) and muscles were coded brown in 23/23 (grade 8). Salivary glands, thyroid glands, and palatine tonsils were coded into predominantly yellow (grade 1) in 46/46 and 10/10 and 18/22, respectively. DCE-MRI derived five-colour-coded mapping provides an objective easy-to-interpret method to assess the dynamic enhancement pattern of head and neck cancers. Copyright © 2011 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

  11. A Method to Convert MRI Images of Temperature Change Into Images of Absolute Temperature in Solid Tumors

    PubMed Central

    Davis, Ryan M.; Viglianti, Benjamin L.; Yarmolenko, Pavel; Park, Ji-Young; Stauffer, Paul; Needham, David; Dewhirst, Mark W.

    2013-01-01

    Purpose During hyperthermia (HT), the therapeutic response of tumors varies substantially within the target temperature range (39–43°C). Current thermometry methods are either invasive or measure only temperature change, which limits the ability to study tissue responses to HT. This study combines manganese-containing low-temperature sensitive liposomes (Mn-LTSL) with proton resonance frequency shift (PRFS) thermometry to measure absolute temperature in tumors with high spatial and temporal resolution using MRI. Methods Liposomes were loaded with 300mM MnSO4. The phase transition temperature (Tm) of Mn-LTSL samples was measured by differential scanning calorimetry (DSC). The release of manganese from Mn-LTSL in saline was characterized with inductively-coupled plasma atomic emission spectroscopy. A 2T GE small animal scanner was used to acquire dynamic T1-weighted images and temperature change images of Mn-LTSL in saline phantoms and fibrosarcoma-bearing Fisher 344 rats receiving hyperthermia after Mn-LTSL injection. Results The Tm of Mn-LTSL in rat blood was 42.9 ± 0.2 °C (DSC). For Mn-LTSL samples (0.06mM – 0.5mM Mn2+ in saline) heated monotonically from 30°C to 50°C, a peak in the rate of MRI signal enhancement occurred at 43.1 ± 0.3 °C. The same peak in signal enhancement rate was observed during heating of fibrosarcoma tumors (N=3) after injection of Mn-LTSL, and the peak was used to convert temperature change images into absolute temperature. Accuracies of calibrated temperature measurements were in the range 0.9 – 1.8°C. Conclusion The release of Mn2+ from Mn-LTSL affects the rate of MR signal enhancement which enables conversion of MRI-based temperature change images to absolute temperature. PMID:23957326

  12. An extension of olfactometry methods: An expandable, fully automated, mobile, MRI-compatible olfactometer.

    PubMed

    Bestgen, Anne-Kathrin; Schulze, Patrick; Kuchinke, Lars; Suchan, Boris; Derdak, Thilo; Otto, Tobias; Jettkant, Birger; Sucker, Kirsten

    2016-03-01

    fMRI experiments on olfaction offer new insights into the complex, but in contrast to other sensory systems, less studied cognition of odors. To perform these experiments is still a challenge. To address the challenge posed by MR settings, an olfactometer design is presented including specific improvements to the limited number of already existing olfactometers. Innovative features such as pneumatically controlled pinch valves, useable in the scanner and providing exact stimulus timing as well as a 3D-printed nasal mask inlet for common sleep laboratory masks that can be used for lateral divided stimulus presentation are introduced. To ensure a fully automated and mobile system, the use of a flexible and easily-adapted Matlab-Code and a portable adaptable container system are presented. The functional efficiency of these features are proven by results of an fMRI study as well as testing temporal resolution and concentration stability with a mass spectrometer. The 24-channel olfactometer design presented here provides an inexpensive alternative to the currently available olfactometers including the achievement of fast onset times, lateral divided stimulus presentation and high flexibility and adaptability to different scientific questions. The olfactometer design presented in this paper can be seen as a realistic and feasible solution to overcome the challenges of presenting olfactory stimuli within the MR setting. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. MRI-Guided Focused Ultrasound as a New Method of Drug Delivery

    PubMed Central

    Thanou, M.; Gedroyc, W.

    2013-01-01

    Ultrasound-mediated drug delivery under the guidance of an imaging modality can improve drug disposition and achieve site-specific drug delivery. The term focal drug delivery has been introduced to describe the focal targeting of drugs in tissues with the help of imaging and focused ultrasound. Focal drug delivery aims to improve the therapeutic profile of drugs by improving their specificity and their permeation in defined areas. Focused-ultrasound- (FUS-) mediated drug delivery has been applied with various molecules to improve their local distribution in tissues. FUS is applied with the aid of microbubbles to enhance the permeability of bioactive molecules across BBB and improve drug distribution in the brain. Recently, FUS has been utilised in combination with MRI-labelled liposomes that respond to temperature increase. This strategy aims to “activate” nanoparticles to release their cargo locally when triggered by hyperthermia induced by FUS. MRI-guided FUS drug delivery provides the opportunity to improve drug bioavailability locally and therefore improve the therapeutic profiles of drugs. This drug delivery strategy can be directly translated to clinic as MRg FUS is a promising clinically therapeutic approach. However, more basic research is required to understand the physiological mechanism of FUS-enhanced drug delivery. PMID:23738076

  14. In vitro determination of biomechanical properties of human articular cartilage in osteoarthritis using multi-parametric MRI

    NASA Astrophysics Data System (ADS)

    Juras, Vladimir; Bittsansky, Michal; Majdisova, Zuzana; Szomolanyi, Pavol; Sulzbacher, Irene; Gäbler, Stefan; Stampfl, Jürgen; Schüller, Georg; Trattnig, Siegfried

    2009-03-01

    The objective of this study was to evaluate the correlations between MR parameters and the biomechanical properties of naturally degenerated human articular cartilage. Human cartilage explants from the femoral condyles of patients who underwent total knee replacement were evaluated on a micro-imaging system at 3 T. To quantify glycosaminoglycan (GAG) content, delayed gadolinium-enhanced MRI of the cartilage (dGEMRIC) was used. T2 maps were created by using multi-echo, multi-slice spin echo sequences with six echoes: 15, 30, 45, 60, 75, and 90 ms. Data for apparent diffusion constant (ADC) maps were obtained from pulsed gradient spin echo (PGSE) sequences with five b-values: 10.472, 220.0, 627.0, 452.8, 724.5, and 957.7. MR parameters were correlated with mechanical parameters (instantaneous ( I) and equilibrium ( Eq) modulus and relaxation time ( τ)), and the OA stage of each cartilage specimen was determined by histological evaluation of hematoxylin-eosin stained slices. For some parameters, a high correlation was found: the correlation of T1Gd vs Eq ( r = 0.8095), T1Gd vs I/ Eq ( r = -0.8441) and T1Gd vs τ ( r = 0.8469). The correlation of T2 and ADC with selected biomechanical parameters was not statistically significant. In conclusion, GAG content measured by dGEMRIC is highly related to the selected biomechanical properties of naturally degenerated articular cartilage. In contrast, T2 and ADC were unable to estimate these properties. The results of the study imply that some MR parameters can non-invasively predict the biomechanical properties of degenerated articular cartilage.

  15. Semi-automatic 10/20 Identification Method for MRI-Free Probe Placement in Transcranial Brain Mapping Techniques.

    PubMed

    Xiao, Xiang; Zhu, Hao; Liu, Wei-Jie; Yu, Xiao-Ting; Duan, Lian; Li, Zheng; Zhu, Chao-Zhe

    2017-01-01

    The International 10/20 system is an important head-surface-based positioning system for transcranial brain mapping techniques, e.g., fNIRS and TMS. As guidance for probe placement, the 10/20 system permits both proper ROI coverage and spatial consistency among multiple subjects and experiments in a MRI-free context. However, the traditional manual approach to the identification of 10/20 landmarks faces problems in reliability and time cost. In this study, we propose a semi-automatic method to address these problems. First, a novel head surface reconstruction algorithm reconstructs head geometry from a set of points uniformly and sparsely sampled on the subject's head. Second, virtual 10/20 landmarks are determined on the reconstructed head surface in computational space. Finally, a visually-guided real-time navigation system guides the experimenter to each of the identified 10/20 landmarks on the physical head of the subject. Compared with the traditional manual approach, our proposed method provides a significant improvement both in reliability and time cost and thus could contribute to improving both the effectiveness and efficiency of 10/20-guided MRI-free probe placement.

  16. Semi-automatic 10/20 Identification Method for MRI-Free Probe Placement in Transcranial Brain Mapping Techniques

    PubMed Central

    Xiao, Xiang; Zhu, Hao; Liu, Wei-Jie; Yu, Xiao-Ting; Duan, Lian; Li, Zheng; Zhu, Chao-Zhe

    2017-01-01

    The International 10/20 system is an important head-surface-based positioning system for transcranial brain mapping techniques, e.g., fNIRS and TMS. As guidance for probe placement, the 10/20 system permits both proper ROI coverage and spatial consistency among multiple subjects and experiments in a MRI-free context. However, the traditional manual approach to the identification of 10/20 landmarks faces problems in reliability and time cost. In this study, we propose a semi-automatic method to address these problems. First, a novel head surface reconstruction algorithm reconstructs head geometry from a set of points uniformly and sparsely sampled on the subject's head. Second, virtual 10/20 landmarks are determined on the reconstructed head surface in computational space. Finally, a visually-guided real-time navigation system guides the experimenter to each of the identified 10/20 landmarks on the physical head of the subject. Compared with the traditional manual approach, our proposed method provides a significant improvement both in reliability and time cost and thus could contribute to improving both the effectiveness and efficiency of 10/20-guided MRI-free probe placement. PMID:28190997

  17. A method for independent component graph analysis of resting-state fMRI.

    PubMed

    Ribeiro de Paula, Demetrius; Ziegler, Erik; Abeyasinghe, Pubuditha M; Das, Tushar K; Cavaliere, Carlo; Aiello, Marco; Heine, Lizette; di Perri, Carol; Demertzi, Athena; Noirhomme, Quentin; Charland-Verville, Vanessa; Vanhaudenhuyse, Audrey; Stender, Johan; Gomez, Francisco; Tshibanda, Jean-Flory L; Laureys, Steven; Owen, Adrian M; Soddu, Andrea

    2017-03-01

    Independent component analysis (ICA) has been extensively used for reducing task-free BOLD fMRI recordings into spatial maps and their associated time-courses. The spatially identified independent components can be considered as intrinsic connectivity networks (ICNs) of non-contiguous regions. To date, the spatial patterns of the networks have been analyzed with techniques developed for volumetric data. Here, we detail a graph building technique that allows these ICNs to be analyzed with graph theory. First, ICA was performed at the single-subject level in 15 healthy volunteers using a 3T MRI scanner. The identification of nine networks was performed by a multiple-template matching procedure and a subsequent component classification based on the network "neuronal" properties. Second, for each of the identified networks, the nodes were defined as 1,015 anatomically parcellated regions. Third, between-node functional connectivity was established by building edge weights for each networks. Group-level graph analysis was finally performed for each network and compared to the classical network. Network graph comparison between the classically constructed network and the nine networks showed significant differences in the auditory and visual medial networks with regard to the average degree and the number of edges, while the visual lateral network showed a significant difference in the small-worldness. This novel approach permits us to take advantage of the well-recognized power of ICA in BOLD signal decomposition and, at the same time, to make use of well-established graph measures to evaluate connectivity differences. Moreover, by providing a graph for each separate network, it can offer the possibility to extract graph measures in a specific way for each network. This increased specificity could be relevant for studying pathological brain activity or altered states of consciousness as induced by anesthesia or sleep, where specific networks are known to be altered in

  18. 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.

  19. Subject-specific real-time respiratory liver motion compensation method for ultrasound-MRI/CT fusion imaging.

    PubMed

    Yang, Minglei; Ding, Hui; Kang, Jingang; Zhu, Lei; Wang, Guangzhi

    2015-05-01

    Ultrasound-MRI/CT fusion imaging is widely used in minimal invasive surgeries, such as liver biopsy and tumor ablation. However, respiration-induced quasi-periodic liver motion and deformation cause unacceptable misalignment of the fusion images (i.e., fusion error). A subject-specific liver motion model based on skin-mounted position sensor and corresponding ultrasound liver image sequence was developed to compensate for liver motion. External surrogate respiratory motion signal is used to predict internal liver motion. An electromagnetic position sensor fixed on abdominal skin is introduced to track the respiratory motion, and 2D ultrasound images are used to track the liver motion synchronously. Based on these measurements, a subject-specific model describing the relationship of respiratory skin motion and internal liver motion is built and applied in real time (ultrasound-MRI/CT fusion imaging system) to predict and to compensate for the liver motion due to respiratory movement. Feasibility experiments and clinical trials were carried out on a phantom and eight volunteers. Qualitative and quantitative analyses and visual inspections performed by experienced clinicians show that the proposed model could effectively compensate for the liver motion, and the ratio of motion-compensated fusion error to the original varied from 10 % (0.96/9.40 mm) to 28 % (2.90/10.22 mm). An online liver motion modeling and compensation method was developed that provides surgeons with stable and accurate multimodality fusion images in real time.

  20. Clinical language fMRI with real-time monitoring in temporal lobe epilepsy: Online processing methods

    PubMed Central

    Williams, E.J.; Stretton, J.; Centeno, M.; Bartlett, P.; Burdett, J.; Symms, M.; Duncan, J.S.; Micallef, C.

    2012-01-01

    The increasing demand for clinical fMRI data has resulted in a need to translate research methods to clinical use. Referrals for language lateralization prior to epilepsy surgery are becoming more common, but time constraints make this unachievable in many busy neuroimaging departments. This study examines whether a single covert verbal fluency paradigm with real-time monitoring and online processing (BrainWave) could replace conventional offline processing (SPM) for the purpose of establishing expressive language dominance prior to epilepsy surgery. We analyzed language fMRI results of 30 patients (17 female; 24 right‐handed; median age: 30.5) with temporal lobe epilepsy. Concordance between visual assessment of SPM and BrainWave was 92.8%. Lateralization indices correlated closely with visual assessments of lateralization with a concordance of 85.7%. BrainWave provided a real-time, fast and accurate display of language lateralization easily applied in a clinical setting using only online image processing. PMID:22841424

  1. Evaluation of Tissue Sampling Methods Used for MRI-Detected Contralateral Breast Lesions in the American College of Radiology Imaging Network 6667 Trial

    PubMed Central

    DeMartini, Wendy B.; Hanna, Lucy; Gatsonis, Constantine; Mahoney, Mary C.; Lehman, Constance D.

    2013-01-01

    OBJECTIVE The purpose of our study was to evaluate tissue sampling methods used for MRI-detected suspicious contralateral breast lesions in the American College of Radiology Imaging Network (ACRIN) 6667 trial. MATERIALS AND METHODS Breast MRI was performed at 25 institutions in 969 women who had a recent diagnosis of unilateral breast cancer and negative contralateral mammography and clinical breast examinations. Biopsy was recommended for MRI findings in 135 women, and 121 underwent sampling. Frequencies and positive biopsy rates of sampling methods used for initial diagnosis and imaging guidance techniques were calculated and compared. RESULTS Sampling yielded 30 malignant and 91 benign results. Initial sampling used needle biopsy in 88 of 121 (72.7%) and surgical biopsy in 30 of 121 (24.8%) women. Surgical biopsy was excisional biopsy in 28 of 30 (93.3%) and mastectomy in two of 30 (6.7%). The remaining three of 121 (2.5%) women underwent mastectomy, but it was not documented whether this represented initial tissue sampling. Of imaging-guided procedures, 56 of 106 (52.8%) used MRI; 49 of 106 (46.2%), ultrasound; and one of 106 (1.0%), stereotaxis. MRI-guided sampling was with needle biopsy rather than wire-localized surgical biopsy in 33 of 56 (58.9%) women, whereas ultrasound used needle biopsy in 47 of 49 (95.9%). Positive biopsy rates of sampling methods were 20.5% for needle biopsy, 46.2% for excisional biopsy, and 0% for mastectomy. CONCLUSION The majority of initial biopsies for MRI-detected contralateral breast lesions used needle biopsy rather than surgical biopsy. Contralateral surgery could have been avoided in most cases had needle biopsy been performed because most excisional biopsy and all mastectomy results were benign. MRI-guided biopsy was significantly more likely than ultrasound-guided sampling to use wire-localized surgical biopsy rather than needle biopsy. PMID:22915431

  2. 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

  3. Evaluation of tissue sampling methods used for MRI-detected contralateral breast lesions in the American College of Radiology Imaging Network 6667 trial.

    PubMed

    DeMartini, Wendy B; Hanna, Lucy; Gatsonis, Constantine; Mahoney, Mary C; Lehman, Constance D

    2012-09-01

    The purpose of our study was to evaluate tissue sampling methods used for MRI-detected suspicious contralateral breast lesions in the American College of Radiology Imaging Network (ACRIN) 6667 trial. Breast MRI was performed at 25 institutions in 969 women who had a recent diagnosis of unilateral breast cancer and negative contralateral mammography and clinical breast examinations. Biopsy was recommended for MRI findings in 135 women, and 121 underwent sampling. Frequencies and positive biopsy rates of sampling methods used for initial diagnosis and imaging guidance techniques were calculated and compared. Sampling yielded 30 malignant and 91 benign results. Initial sampling used needle biopsy in 88 of 121 (72.7%) and surgical biopsy in 30 of 121 (24.8%) women. Surgical biopsy was excisional biopsy in 28 of 30 (93.3%) and mastectomy in two of 30 (6.7%). The remaining three of 121 (2.5%) women underwent mastectomy, but it was not documented whether this represented initial tissue sampling. Of imaging-guided procedures, 56 of 106 (52.8%) used MRI; 49 of 106 (46.2%), ultrasound; and one of 106 (1.0%), stereotaxis. MRI-guided sampling was with needle biopsy rather than wire-localized surgical biopsy in 33 of 56 (58.9%) women, whereas ultrasound used needle biopsy in 47 of 49 (95.9%). Positive biopsy rates of sampling methods were 20.5% for needle biopsy, 46.2% for excisional biopsy, and 0% for mastectomy. The majority of initial biopsies for MRI-detected contralateral breast lesions used needle biopsy rather than surgical biopsy. Contralateral surgery could have been avoided in most cases had needle biopsy been performed because most excisional biopsy and all mastectomy results were benign. MRI-guided biopsy was significantly more likely than ultrasound-guided sampling to use wire-localized surgical biopsy rather than needle biopsy.

  4. 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. Copyright 2002 Wiley-Liss, Inc.

  5. The Efficiency Limits of Spin Exchange Optical Pumping Methods of 129Xe Hyperpolarization: Implications for in vivo MRI Applications

    NASA Astrophysics Data System (ADS)

    Freeman, Matthew S.

    Since the inception of hyperpolarized 129Xe MRI, the field has yearned for more efficient production of more highly polarized 129Xe. For nearly all polarizers built to date, both peak 129Xe polarization and production rate fall far below theoretical predictions. This thesis sought to develop a fundamental understanding of why the observed performance of large-scale 129Xe hyperpolarization lagged so badly behind theoretical predictions. This is done by thoroughly characterizing a high-volume, continuous-flow polarizer using optical cells having three different internal volumes, and employing two different laser sources. For each of these 6 combinations, 129Xe polarization was carefully measured as a function of production rate across a range of laser absorption levels. The resultant peak polarizations were consistently a factor of 2-3 lower than predicted across a range of absorption levels, and scaling of production rates deviated badly from predictions based on spin exchange efficiency. To bridge this gap, we propose that paramagnetic, activated Rb clusters form during spin exchange optical pumping (SEOP), and depolarize Rb and 129Xe, while unproductively scattering optical pumping light. When a model was built that incorporated the effects of clusters, its predictions matched observations for both polarization and production rate for all 6 systems studied. This permits us to place a limit on cluster number density of <2 x 109 cm-3. The work culminates with deploying this framework to identify methods to improve polarization to above 50%, leaving the SEOP cell. Combined with additional methods of preserving polarization, the polarization of a 300-mL batch of 129Xe increased from an average of 9%, before this work began, to a recent value of 34%. We anticipate that these developments will lay the groundwork for continued advancement and scaling up of SEOP-based hyperpolarization methods that may one day permit real-time, on-demand 129Xe MRI to become a reality.

  6. Methods to detect, characterize, and remove motion artifact in resting state fMRI

    PubMed Central

    Power, Jonathan D; Mitra, Anish; Laumann, Timothy O; Snyder, Abraham Z; Schlaggar, Bradley L; Petersen, Steven E

    2013-01-01

    Head motion systematically alters correlations in resting state functional connectivity fMRI (RSFC). In this report we examine impact of motion on signal intensity and RSFC correlations. We find that motion-induced signal changes (1) are often complex and variable waveforms, (2) are often shared across nearly all brain voxels, and (3) often persist more than 10 seconds after motion ceases. These signal changes, both during and after motion, increase observed RSFC correlations in a distance-dependent manner. Motion-related signal changes are not removed by a variety of motion-based regressors, but are effectively reduced by global signal regression. We link several measures of data quality to motion, changes in signal intensity, and changes in RSFC correlations. We demonstrate that improvements in data quality measures during processing may represent cosmetic improvements rather than true correction of the data. We demonstrate a within-subject, censoring-based artifact removal strategy based on volume censoring that reduces group differences due to motion to chance levels. We note conditions under which group-level regressions do and do not correct motion-related effects. PMID:23994314

  7. Methods to detect, characterize, and remove motion artifact in resting state fMRI.

    PubMed

    Power, Jonathan D; Mitra, Anish; Laumann, Timothy O; Snyder, Abraham Z; Schlaggar, Bradley L; Petersen, Steven E

    2014-01-01

    Head motion systematically alters correlations in resting state functional connectivity fMRI (RSFC). In this report we examine impact of motion on signal intensity and RSFC correlations. We find that motion-induced signal changes (1) are often complex and variable waveforms, (2) are often shared across nearly all brain voxels, and (3) often persist more than 10s after motion ceases. These signal changes, both during and after motion, increase observed RSFC correlations in a distance-dependent manner. Motion-related signal changes are not removed by a variety of motion-based regressors, but are effectively reduced by global signal regression. We link several measures of data quality to motion, changes in signal intensity, and changes in RSFC correlations. We demonstrate that improvements in data quality measures during processing may represent cosmetic improvements rather than true correction of the data. We demonstrate a within-subject, censoring-based artifact removal strategy based on volume censoring that reduces group differences due to motion to chance levels. We note conditions under which group-level regressions do and do not correct motion-related effects. © 2013 Elsevier Inc. All rights reserved.

  8. Comparison between modified Dixon MRI techniques, MR spectroscopic relaxometry, and different histologic quantification methods in the assessment of hepatic steatosis.

    PubMed

    Kukuk, Guido M; Hittatiya, Kanishka; Sprinkart, Alois M; Eggers, Holger; Gieseke, Jürgen; Block, Wolfgang; Moeller, Philipp; Willinek, Winfried A; Spengler, Ulrich; Trebicka, Jonel; Fischer, Hans-Peter; Schild, Hans H; Träber, Frank

    2015-10-01

    To compare systematically quantitative MRI, MR spectroscopy (MRS), and different histological methods for liver fat quantification in order to identify possible incongruities. Fifty-nine consecutive patients with liver disorders were examined on a 3 T MRI system. Quantitative MRI was performed using a dual- and a six-echo variant of the modified Dixon (mDixon) sequence, calculating proton density fat fraction (PDFF) maps, in addition to single-voxel MRS. Histological fat quantification included estimation of the percentage of hepatocytes containing fat vesicles as well as semi-automatic quantification (qHisto) using tissue quantification software. In 33 of 59 patients, the hepatic fat fraction was >5% as determined by MRS (maximum 45%, mean 17%). Dual-echo mDixon yielded systematically lower PDFF values than six-echo mDixon (mean difference 1.0%; P < 0.001). Six-echo mDixon correlated excellently with MRS, qHisto, and the estimated percentage of hepatocytes containing fat vesicles (R = 0.984, 0.967, 0.941, respectively, all P < 0.001). Mean values obtained by the estimated percentage of hepatocytes containing fat were higher by a factor of 2.5 in comparison to qHisto. Six-echo mDixon and MRS showed the best agreement with values obtained by qHisto. Six-echo mDixon, MRS, and qHisto provide the most robust and congruent results and are therefore most appropriate for reliable quantification of liver fat. • Six-echo mDixon correlates excellently with MRS, qHisto, and the estimated percentage of fat-containing hepatocytes. • Six-echo mDixon, MRS, and qHisto provide the most robust and congruent results. • Dual-echo mDixon yields systematically lower PDFF values than six-echo mDixon. • The percentage of fat-containing hepatocytes is 2.5-fold higher than fat fraction determined by qHisto. • Performance characteristics and systematic differences of the various methods should be considered.

  9. A new production method of elastic silicone carotid phantom based on MRI acquisition using rapid prototyping technique.

    PubMed

    Cao, Peng; Duhamel, Yvan; Olympe, Guillaume; Ramond, Bruno; Langevin, Francois

    2013-01-01

    In vitro experimental simulations of blood fluid in carotid artery require ideal phantoms that are as precise as possible. The purpose of this work is to demonstrate a method for carotid phantom fabrication by rapid prototyping technique (RP). By using 3D reconstructed projection of the 3D time-of-flight (TOF) Magnetic Resonance Imaging (MRI) sequence, a 12.5 cm multi-dimensional spatial structure of a carotid artery has been set up. Y-shaped and patient specific models have been generated respectively using silicone elastomer, which has a high resilience and a good tensile strength. The final patient specific model has internal carotid artery (ICA) with a highly spiraling siphon and an external carotid artery (ECA). Elastic properties of carotid walls have also been evaluated by Young's elastic modulus test and dynamic behaviors in optical and echography simulation experiments.

  10. Comparison between PET template-based method and MRI-based method for cortical quantification of florbetapir (AV-45) uptake in vivo.

    PubMed

    Saint-Aubert, L; Nemmi, F; Péran, P; Barbeau, E J; Payoux, P; Chollet, F; Pariente, J

    2014-05-01

    Florbetapir (AV-45) has been shown to be a reliable tool for assessing in vivo amyloid load in patients with Alzheimer's disease from the early stages. However, nonspecific white matter binding has been reported in healthy subjects as well as in patients with Alzheimer's disease. To avoid this issue, cortical quantification might increase the reliability of AV-45 PET analyses. In this study, we compared two quantification methods for AV-45 binding, a classical method relying on PET template registration (route 1), and a MRI-based method (route 2) for cortical quantification. We recruited 22 patients at the prodromal stage of Alzheimer's disease and 17 matched controls. AV-45 binding was assessed using both methods, and target-to-cerebellum mean global standard uptake values (SUVr) were obtained for each of them, together with SUVr in specific regions of interest. Quantification using the two routes was compared between the clinical groups (intragroup comparison), and between groups for each route (intergroup comparison). Discriminant analysis was performed. In the intragroup comparison, differences in uptake values were observed between route 1 and route 2 in both groups. In the intergroup comparison, AV-45 uptake was higher in patients than controls in all regions of interest using both methods, but the effect size of this difference was larger using route 2. In the discriminant analysis, route 2 showed a higher specificity (94.1 % versus 70.6 %), despite a lower sensitivity (77.3 % versus 86.4 %), and D-prime values were higher for route 2. These findings suggest that, although both quantification methods enabled patients at early stages of Alzheimer's disease to be well discriminated from controls, PET template-based quantification seems adequate for clinical use, while the MRI-based cortical quantification method led to greater intergroup differences and may be more suitable for use in current clinical research.

  11. 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.

  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. Regularization parameter selection for nonlinear iterative image restoration and MRI reconstruction using GCV and SURE-based methods.

    PubMed

    Ramani, Sathish; Liu, Zhihao; Rosen, Jeffrey; Nielsen, Jon-Fredrik; Fessler, Jeffrey A

    2012-08-01

    Regularized iterative reconstruction algorithms for imaging inverse problems require selection of appropriate regularization parameter values. We focus on the challenging problem of tuning regularization parameters for nonlinear algorithms for the case of additive (possibly complex) Gaussian noise. Generalized cross-validation (GCV) and (weighted) mean-squared error (MSE) approaches (based on Steinfs Unbiased Risk Estimate. SURE) need the Jacobian matrix of the nonlinear reconstruction operator (representative of the iterative algorithm) with respect to the data. We derive the desired Jacobian matrix for two types of nonlinear iterative algorithms: a fast variant of the standard iterative reweighted least-squares method and the contemporary split-Bregman algorithm, both of which can accommodate a wide variety of analysis- and synthesis-type regularizers. The proposed approach iteratively computes two weighted SURE-type measures: Predicted-SURE and Projected-SURE (that require knowledge of noise variance Ð2), and GCV (that does not need Ð2) for these algorithms. We apply the methods to image restoration and to magnetic resonance image (MRI) reconstruction using total variation (TV) and an analysis-type .1-regularization. We demonstrate through simulations and experiments with real data that minimizing Predicted-SURE and Projected-SURE consistently lead to near-MSE-optimal reconstructions. We also observed that minimizing GCV yields reconstruction results that are near-MSE-optimal for image restoration and slightly suboptimal for MRI. Theoretical derivations in this work related to Jacobian matrix evaluations can be extended, in principle, to other types of regularizers and reconstruction algorithms.

  14. MRI-based computational hemodynamics in patients with aortic coarctation using the lattice Boltzmann methods: Clinical validation study.

    PubMed

    Mirzaee, Hanieh; Henn, Thomas; Krause, Mathias J; Goubergrits, Leonid; Schumann, Christian; Neugebauer, Mathias; Kuehne, Titus; Preusser, Tobias; Hennemuth, Anja

    2017-01-01

    To introduce a scheme based on a recent technique in computational hemodynamics, known as the lattice Boltzmann methods (LBM), to noninvasively measure pressure gradients in patients with a coarctation of the aorta (CoA). To provide evidence on the accuracy of the proposed scheme, the computed pressure drop values are compared against those obtained using the reference standard method of catheterization. Pre- and posttreatment LBM-based pressure gradients for 12 patients with CoA were simulated for the time point of peak systole using the open source library OpenLB. Four-dimensional (4D) flow-sensitive phase-contrast MRI at 1.5 Tesla was used to acquire flow and to setup the simulation. The vascular geometry was reconstructed using 3D whole-heart MRI. Patients underwent pre- and postinterventional pressure catheterization as a reference standard. There is a significant linear correlation between the pretreatment catheter pressure drops and those computed based on the LBM simulation, r=.85, P<.001. The bias was -0.58 ± 4.1 mmHg and was not significant ( P=0.64) with a 95% confidence interval (CI) of -3.22 to 2.06. For the posttreatment results, the bias was larger and at -2.54 ± 3.53 mmHg with a 95% CI of -0.17 to -4.91 mmHg. The results indicate a reasonable agreement between the simulation results and the catheter measurements. LBM-based computational hemodynamics can be considered as an alternative to more traditional computational fluid dynamics schemes for noninvasive pressure calculations and can assist in diagnosis and therapy planning. 3 J. Magn. Reson. Imaging 2017;45:139-146. © 2016 The Authors Journal of Magnetic Resonance Imaging published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

  15. Regularization Parameter Selection for Nonlinear Iterative Image Restoration and MRI Reconstruction Using GCV and SURE-Based Methods

    PubMed Central

    Ramani, Sathish; Liu, Zhihao; Rosen, Jeffrey; Nielsen, Jon-Fredrik; Fessler, Jeffrey A.

    2012-01-01

    Regularized iterative reconstruction algorithms for imaging inverse problems require selection of appropriate regularization parameter values. We focus on the challenging problem of tuning regularization parameters for nonlinear algorithms for the case of additive (possibly complex) Gaussian noise. Generalized cross-validation (GCV) and (weighted) mean-squared error (MSE) approaches (based on Stein's Unbiased Risk Estimate— SURE) need the Jacobian matrix of the nonlinear reconstruction operator (representative of the iterative algorithm) with respect to the data. We derive the desired Jacobian matrix for two types of nonlinear iterative algorithms: a fast variant of the standard iterative reweighted least-squares method and the contemporary split-Bregman algorithm, both of which can accommodate a wide variety of analysis- and synthesis-type regularizers. The proposed approach iteratively computes two weighted SURE-type measures: Predicted-SURE and Projected-SURE (that require knowledge of noise variance σ2), and GCV (that does not need σ2) for these algorithms. We apply the methods to image restoration and to magnetic resonance image (MRI) reconstruction using total variation (TV) and an analysis-type ℓ1-regularization. We demonstrate through simulations and experiments with real data that minimizing Predicted-SURE and Projected-SURE consistently lead to near-MSE-optimal reconstructions. We also observed that minimizing GCV yields reconstruction results that are near-MSE-optimal for image restoration and slightly sub-optimal for MRI. Theoretical derivations in this work related to Jacobian matrix evaluations can be extended, in principle, to other types of regularizers and reconstruction algorithms. PMID:22531764

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

    PubMed

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

    2016-07-01

    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.

  17. 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.

  18. 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

    2016-03-24

    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.

  19. 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.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

  2. 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.

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

    PubMed

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

    2013-05-01

    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. 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. 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. 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. ADIMA enabled the simple classification of WML into two groups having different quantitative magnetic resonance properties, which can be reproducibly distinguished.

  4. A methodology for generating normal and pathological brain perfusion SPECT images for evaluation of MRI/SPECT fusion methods: application in epilepsy

    NASA Astrophysics Data System (ADS)

    Grova, C.; Jannin, P.; Biraben, A.; Buvat, I.; Benali, H.; Bernard, A. M.; Scarabin, J. M.; Gibaud, B.

    2003-12-01

    Quantitative evaluation of brain MRI/SPECT fusion methods for normal and in particular pathological datasets is difficult, due to the frequent lack of relevant ground truth. We propose a methodology to generate MRI and SPECT datasets dedicated to the evaluation of MRI/SPECT fusion methods and illustrate the method when dealing with ictal SPECT. The method consists in generating normal or pathological SPECT data perfectly aligned with a high-resolution 3D T1-weighted MRI using realistic Monte Carlo simulations that closely reproduce the response of a SPECT imaging system. Anatomical input data for the SPECT simulations are obtained from this 3D T1-weighted MRI, while functional input data result from an inter-individual analysis of anatomically standardized SPECT data. The method makes it possible to control the 'brain perfusion' function by proposing a theoretical model of brain perfusion from measurements performed on real SPECT images. Our method provides an absolute gold standard for assessing MRI/SPECT registration method accuracy since, by construction, the SPECT data are perfectly registered with the MRI data. The proposed methodology has been applied to create a theoretical model of normal brain perfusion and ictal brain perfusion characteristic of mesial temporal lobe epilepsy. To approach realistic and unbiased perfusion models, real SPECT data were corrected for uniform attenuation, scatter and partial volume effect. An anatomic standardization was used to account for anatomic variability between subjects. Realistic simulations of normal and ictal SPECT deduced from these perfusion models are presented. The comparison of real and simulated SPECT images showed relative differences in regional activity concentration of less than 20% in most anatomical structures, for both normal and ictal data, suggesting realistic models of perfusion distributions for evaluation purposes. Inter-hemispheric asymmetry coefficients measured on simulated data were found within

  5. A methodology for generating normal and pathological brain perfusion SPECT images for evaluation of MRI/SPECT fusion methods: application in epilepsy.

    PubMed

    Grova, C; Jannin, P; Biraben, A; Buvat, I; Benali, H; Bernard, A M; Scarabin, J M; Gibaud, B

    2003-12-21

    Quantitative evaluation of brain MRI/SPECT fusion methods for normal and in particular pathological datasets is difficult, due to the frequent lack of relevant ground truth. We propose a methodology to generate MRI and SPECT datasets dedicated to the evaluation of MRI/SPECT fusion methods and illustrate the method when dealing with ictal SPECT. The method consists in generating normal or pathological SPECT data perfectly aligned with a high-resolution 3D T1-weighted MRI using realistic Monte Carlo simulations that closely reproduce the response of a SPECT imaging system. Anatomical input data for the SPECT simulations are obtained from this 3D T1-weighted MRI, while functional input data result from an inter-individual analysis of anatomically standardized SPECT data. The method makes it possible to control the 'brain perfusion' function by proposing a theoretical model of brain perfusion from measurements performed on real SPECT images. Our method provides an absolute gold standard for assessing MRI/SPECT registration method accuracy since, by construction, the SPECT data are perfectly registered with the MRI data. The proposed methodology has been applied to create a theoretical model of normal brain perfusion and ictal brain perfusion characteristic of mesial temporal lobe epilepsy. To approach realistic and unbiased perfusion models, real SPECT data were corrected for uniform attenuation, scatter and partial volume effect. An anatomic standardization was used to account for anatomic variability between subjects. Realistic simulations of normal and ictal SPECT deduced from these perfusion models are presented. The comparison of real and simulated SPECT images showed relative differences in regional activity concentration of less than 20% in most anatomical structures, for both normal and ictal data, suggesting realistic models of perfusion distributions for evaluation purposes. Inter-hemispheric asymmetry coefficients measured on simulated data were found within

  6. 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

  7. 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.

  8. A time-harmonic target-field method for designing unshielded RF coils in MRI

    NASA Astrophysics Data System (ADS)

    While, Peter T.; Forbes, Larry K.; Crozier, Stuart

    2005-04-01

    Time-harmonic methods are required in the accurate design of RF coils as operating frequency increases. This paper presents such a method to find a current density solution on the coil that will induce some desired magnetic field upon an asymmetrically located target region within. This inverse method appropriately considers the geometry of the coil via a Fourier series expansion, and incorporates some new regularization penalty functions in the solution process. A new technique is introduced by which the complex, time-dependent current density solution is approximated by a static coil winding pattern. Several winding pattern solutions are given, with more complex winding patterns corresponding to more desirable induced magnetic fields.

  9. Generalized least-squares method applied to fMRI time series with empirically determined correlation matrix.

    PubMed

    Wicker, B; Fonlupt, P

    2003-03-01

    Functional magnetic resonance imaging (fMRI) time series analysis and statistical inferences about the effect of a cognitive task on the regional cerebral blood flow (rCBF) are largely based on the linear model. However, this method requires that the error vector is a gaussian variable with an identity correlation matrix. When this assumption cannot be accepted, statistical inferences can be made using generalized least squares. In this case, knowledge of the covariance matrix of the error vector is needed. In the present report, we propose a method that needs stationarity of the autocorrelation function but is more flexible than autoregressive model of order p (AR(p)) models because it is not necessary to predefine a relation between coefficients of the correlation matrix. We tested this method on sets of simulated data (with presence of an effect of interest or not) representing a time series with a monotonically decreasing autocorrelation function. This time series mimicked an experiment using a random event-related design that does not create correlation between scans. The autocorrelation function is empirically determined and used to reconstitute the correlation matrix as the toeplitz matrix built from the autocorrelation function. When applied to simulated time series with no effect of interest, this method allows the determination of F values corresponding to the accurate false positive level. Moreover, when applied to time series with an effect of interest, this method gives a density function of F values which allows the rejection of the null hypothesis. This method provides a flexible but interpretable time domain noise model.

  10. 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

  11. New method for fMRI investigations of language: defining ROIs functionally in individual subjects.

    PubMed

    Fedorenko, Evelina; Hsieh, Po-Jang; Nieto-Castañón, Alfonso; Whitfield-Gabrieli, Susan; Kanwisher, Nancy

    2010-08-01

    Previous neuroimaging research has identified a number of brain regions sensitive to different aspects of linguistic processing, but precise functional characterization of these regions has proven challenging. We hypothesize that clearer functional specificity may emerge if candidate language-sensitive regions are identified functionally within each subject individually, a method that has revealed striking functional specificity in visual cortex but that has rarely been applied to neuroimaging studies of language. This method enables pooling of data from corresponding functional regions across subjects rather than from corresponding locations in stereotaxic space (which may differ functionally because of the anatomical variability across subjects). However, it is far from obvious a priori that this method will work as it requires that multiple stringent conditions be met. Specifically, candidate language-sensitive brain regions must be identifiable functionally within individual subjects in a short scan, must be replicable within subjects and have clear correspondence across subjects, and must manifest key signatures of language processing (e.g., a higher response to sentences than nonword strings, whether visual or auditory). We show here that this method does indeed work: we identify 13 candidate language-sensitive regions that meet these criteria, each present in >or=80% of subjects individually. The selectivity of these regions is stronger using our method than when standard group analyses are conducted on the same data, suggesting that the future application of this method may reveal clearer functional specificity than has been evident in prior neuroimaging research on language.

  12. 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.

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

    PubMed

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

    2005-11-21

    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 B(1)-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.

  14. 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.

  15. 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

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

    PubMed

    Martin-Fernandez, Marcos; Villullas, Sergio

    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.

  17. 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.

  18. 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

  19. Toward implementing an MRI-based PET attenuation-correction method for neurologic studies on the MR-PET brain prototype.

    PubMed

    Catana, Ciprian; van der Kouwe, Andre; Benner, Thomas; Michel, Christian J; Hamm, Michael; Fenchel, Matthias; Fischl, Bruce; Rosen, Bruce; Schmand, Matthias; Sorensen, A Gregory

    2010-09-01

    Several factors have to be considered for implementing an accurate attenuation-correction (AC) method in a combined MR-PET scanner. In this work, some of these challenges were investigated, and an AC method based entirely on the MRI data obtained with a single dedicated sequence was developed and used for neurologic studies performed with the MR-PET human brain scanner prototype. The focus was on the problem of bone-air segmentation, selection of the linear attenuation coefficient for bone, and positioning of the radiofrequency coil. The impact of these factors on PET data quantification was studied in simulations and experimental measurements performed on the combined MR-PET scanner. A novel dual-echo ultrashort echo time (DUTE) MRI sequence was proposed for head imaging. Simultaneous MR-PET data were acquired, and the PET images reconstructed using the proposed DUTE MRI-based AC method were compared with the PET images that had been reconstructed using a CT-based AC method. Our data suggest that incorrectly accounting for the bone tissue attenuation can lead to large underestimations (>20%) of the radiotracer concentration in the cortex. Assigning a linear attenuation coefficient of 0.143 or 0.151 cm(-1) to bone tissue appears to give the best trade-off between bias and variability in the resulting images. Not identifying the internal air cavities introduces large overestimations (>20%) in adjacent structures. On the basis of these results, the segmented CT AC method was established as the silver standard for the segmented MRI-based AC method. For an integrated MR-PET scanner, in particular, ignoring the radiofrequency coil attenuation can cause large underestimations (i.e., MRI- and CT-based AC methods compare favorably in most of

  20. Better living through transparency: improving the reproducibility of fMRI results through comprehensive methods reporting.

    PubMed

    Carp, Joshua

    2013-09-01

    Recent studies suggest that a greater proportion of published scientific findings than expected cannot be replicated. The field of functional neuroimaging research is no exception to this trend, with estimates of false positive results ranging from 10 % to 40 %. While false positive results in neuroimaging studies stem from a variety of causes, incomplete methodological reporting is perhaps the most obvious: Most published reports of neuroimaging studies provide ambiguous or incomplete descriptions of their methods and results. If neuroimaging researchers do not report methods and results in adequate detail, independent scientists can neither check their work for errors nor accurately replicate their efforts. Thus, I argue that comprehensive methods reporting is essential for reproducible research. I recommend three strategies for improving transparency and reproducibility in neuroimaging research: improving natural language descriptions of research protocols; sharing source code for data collection and analysis; and sharing formal, machine-readable representations of methods and results. Last, I discuss the technological and cultural barriers to implementing these recommendations and suggest steps toward overcoming those barriers.

  1. UNFOLD-SENSE: a parallel MRI method with self-calibration and artifact suppression.

    PubMed

    Madore, Bruno

    2004-08-01

    This work aims at improving the performance of parallel imaging by using it with our "unaliasing by Fourier-encoding the overlaps in the temporal dimension" (UNFOLD) temporal strategy. A self-calibration method called "self, hybrid referencing with UNFOLD and GRAPPA" (SHRUG) is presented. SHRUG combines the UNFOLD-based sensitivity mapping strategy introduced in the TSENSE method by Kellman et al. (5), with the strategy introduced in the GRAPPA method by Griswold et al. (10). SHRUG merges the two approaches to alleviate their respective limitations, and provides fast self-calibration at any given acceleration factor. UNFOLD-SENSE further includes an UNFOLD artifact suppression scheme to significantly suppress artifacts and amplified noise produced by parallel imaging. This suppression scheme, which was published previously (4), is related to another method that was presented independently as part of TSENSE. While the two are equivalent at accelerations < or = 2.0, the present approach is shown here to be significantly superior at accelerations > 2.0, with up to double the artifact suppression at high accelerations. Furthermore, a slight modification of Cartesian SENSE is introduced, which allows departures from purely Cartesian sampling grids. This technique, termed variable-density SENSE (vdSENSE), allows the variable-density data required by SHRUG to be reconstructed with the simplicity and fast processing of Cartesian SENSE. UNFOLD-SENSE is given by the combination of SHRUG for sensitivity mapping, vdSENSE for reconstruction, and UNFOLD for artifact/amplified noise suppression. The method was implemented, with online reconstruction, on both an SSFP and a myocardium-perfusion sequence. The results from six patients scanned with UNFOLD-SENSE are presented.

  2. Segmentation of Brain MRI Using SOM-FCM-Based Method and 3D Statistical Descriptors

    PubMed Central

    Ortiz, Andrés; Palacio, Antonio A.; Górriz, Juan M.; Ramírez, Javier; Salas-González, Diego

    2013-01-01

    Current medical imaging systems provide excellent spatial resolution, high tissue contrast, and up to 65535 intensity levels. Thus, image processing techniques which aim to exploit the information contained in the images are necessary for using these images in computer-aided diagnosis (CAD) systems. Image segmentation may be defined as the process of parcelling the image to delimit different neuroanatomical tissues present on the brain. In this paper we propose a segmentation technique using 3D statistical features extracted from the volume image. In addition, the presented method is based on unsupervised vector quantization and fuzzy clustering techniques and does not use any a priori information. The resulting fuzzy segmentation method addresses the problem of partial volume effect (PVE) and has been assessed using real brain images from the Internet Brain Image Repository (IBSR). PMID:23762192

  3. A new method to record and control for 2D-movement kinematics during functional magnetic resonance imaging (fMRI).

    PubMed

    Hauptmann, Bjoern; Sosnik, Ronen; Smikt, Oded; Okon, Eli; Manor, David; Kushnir, Tammar; Flash, Tamar; Karni, Avi

    2009-03-01

    The recording of movement kinematics during functional magnetic resonance imaging (fMRI) experiments is complicated due to technical constraints of the imaging environment. Nevertheless, to study the functions of brain areas related to motor control, reliable and accurate records of movement trajectories and speed profiles are needed. We present a method designed to record and characterize the kinematic properties of drawing- and handwriting-like forearm movements during fMRI studies by recording pen stroke trajectories. The recording system consists of a translucent plastic board, a plastic pen containing fiber optics and a halogen light power source, a CCD camera, a video monitor and a PC with a video grabber card. Control experiments using a commercially available digitizer tablet have demonstrated the reliability of the data recorded during fMRI. Since the movement tracking signal is purely optical, there is no interaction with the MR (echoplanar) images. Thus, the method allows to obtain movement records with high spatial and temporal resolution which are suitable for the kinematic analysis of hand movements in fMRI studies.

  4. A method for u-fiber quantification from 7 T diffusion-weighted MRI data tested in patients with nonlesional focal epilepsy.

    PubMed

    O'Halloran, Rafael; Feldman, Rebecca; Marcuse, Lara; Fields, Madeline; Delman, Bradley; Frangou, Sophia; Balchandani, Priti

    2017-05-24

    In this methods development, we present an ultra-high-field, diffusion-weighted MRI method to quantitatively assess u-fibers and use it to compare u-fiber counts in nonlesional epilepsy patients with controls. Emerging evidence implicates white matter abnormalities in nonlesional epilepsy, including the short-range, cortical-cortical connections, or u-fibers. Eight patients with nonlesional epilepsy and eight demographically matched controls underwent 7 T MRI consisting of a T1-weighted sequence (0.7 mm isotropic resolution) and high-angular-resolved diffusion-weighted MRI (1.05 mm isotropic resolution, 68 directions). MRI data were used to quantify u-fiber counts in known u-fiber populations on the basis of an atlas and fiber tractography. From tractography, connectivity matrices summarizing the u-fiber counts were computed. Quantitative group comparisons were performed on the connectivity matrices. U-fiber counts were found to be lower on average in patients with epilepsy than in healthy controls. The results indicate that the density or the number of u-fibers is reduced in patients with nonlesional epilepsy. Future work will focus on histological validation and determining whether differences in u-fiber counts can be used clinically to noninvasively identify seizure-onset zones.

  5. 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.

  6. Algorithm-based method for detection of blood vessels in breast MRI for development of computer-aided diagnosis.

    PubMed

    Lin, Muqing; Chen, Jeon-Hor; Nie, Ke; Chang, Daniel; Nalcioglu, Orhan; Su, Min-Ying

    2009-10-01

    To develop a computer-based algorithm for detecting blood vessels that appear in breast dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI), and to evaluate the improvement in reducing the number of vascular pixels that are labeled by computer-aided diagnosis (CAD) systems as being suspicious of malignancy. The analysis was performed in 34 cases. The algorithm applied a filter bank based on wavelet transform and the Hessian matrix to detect linear structures as blood vessels on a two-dimensional maximum intensity projection (MIP). The vessels running perpendicular to the MIP plane were then detected based on the connectivity of enhanced pixels above a threshold. The nonvessel enhancements were determined and excluded based on their morphological properties, including those showing scattered small segment enhancements or nodular or planar clusters. The detected vessels were first converted to a vasculature skeleton by thinning and subsequently compared to the vascular track manually drawn by a radiologist. When evaluating the performance of the algorithm in identifying vascular tissue, the correct-detection rate refers to pixels identified by both the algorithm and radiologist, while the incorrect-detection rate refers to pixels identified by only the algorithm, and the missed-detection rate refers to pixels identified only by the radiologist. From 34 analyzed cases the median correct-detection rate was 85.6% (mean 84.9% +/- 7.8%), the incorrect-detection rate was 13.1% (mean 15.1% +/- 7.8%), and the missed-detection rate was 19.2% (mean 21.3% +/- 12.8%). When detected vessels were excluded in the hot-spot color-coding of the CAD system, they could reduce the labeling of vascular vessels in 2.6%-68.6% of hot-spot pixels (mean 16.6% +/- 15.9%). The computer algorithm-based method can detect most large vessels and provide an effective means in reducing the labeling of vascular pixels as suspicious on a DCE-MRI CAD system. This algorithm may improve the

  7. 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.

  8. 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

    2006-12-07

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  10. An MRI denoising method using image data redundancy and local SNR estimation.

    PubMed

    Golshan, Hosein M; Hasanzadeh, Reza P R; Yousefzadeh, Shahrokh C

    2013-09-01

    This paper presents an LMMSE-based method for the three-dimensional (3D) denoising of MR images assuming a Rician noise model. Conventionally, the LMMSE method estimates the noise-less signal values using the observed MR data samples within local neighborhoods. This is not an efficient procedure to deal with this issue while the 3D MR data intrinsically includes many similar samples that can be used to improve the estimation results. To overcome this problem, we model MR data as random fields and establish a principled way which is capable of choosing the samples not only from a local neighborhood but also from a large portion of the given data. To follow the similar samples within the MR data, an effective similarity measure based on the local statistical moments of images is presented. The parameters of the proposed filter are automatically chosen from the estimated local signal-to-noise ratio. To further enhance the denoising performance, a recursive version of the introduced approach is also addressed. The proposed filter is compared with related state-of-the-art filters using both synthetic and real MR datasets. The experimental results demonstrate the superior performance of our proposal in removing the noise and preserving the anatomical structures of MR images.

  11. 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

  12. Cortical activation by tactile stimulation to face and anterior neck areas: an fMRI study with three analytic methods.

    PubMed

    Lin, Chou-Ching K; Sun, Yung-Nien; Huang, Chung-I; Yu, Chin-Yin; Ju, Ming-Shaung

    2010-12-01

    The main purpose of this study was to investigate the sensory cortical activation of the anterior neck region and the relationship between the neck and face representation areas. Functional MRI by blood oxygenation level dependent measurements was performed while tactile stimulation was applied to the face or neck area. Nonpainful tactile stimuli were manually delivered by an experimenter at a frequency of ∼1 Hz. Block (epoch) design was adopted with a block duration of 30 s and a whole run duration of 6 min. For each location, two runs were performed. After the image data were preprocessed, both parameteric and nonparametric methods were performed to test the group results. The results showed that (1) unilateral face or neck stimulation could elicit bilateral cortical activation, (2) mainly the face representation and face-hand junction areas, but not the conventional neck representation area, were activated by face or neck stimulation, and (3) the activation areas were larger when right face or neck was stimulated. In conclusion, the sensory cortical representation area of the anterior neck region was mainly at the junction of hand and face representation area and the activated area was larger when the right face or neck was stimulated.

  13. A Supervoxel-Based Method for Groupwise Whole Brain Parcellation with Resting-State fMRI Data

    PubMed Central

    Wang, Jing; Wang, Haixian

    2016-01-01

    Node definition is a very important issue in human brain network analysis and functional connectivity studies. Typically, the atlases generated from meta-analysis, random criteria, and structural criteria are utilized as nodes in related applications. However, these atlases are not originally designed for such purposes and may not be suitable. In this study, we combined normalized cut (Ncut) and a supervoxel method called simple linear iterative clustering (SLIC) to parcellate whole brain resting-state fMRI data in order to generate appropriate brain atlases. Specifically, Ncut was employed to extract features from connectivity matrices, and then SLIC was applied on the extracted features to generate parcellations. To obtain group level parcellations, two approaches named mean SLIC and two-level SLIC were proposed. The cluster number varied in a wide range in order to generate parcellations with multiple granularities. The two SLIC approaches were compared with three state-of-the-art approaches under different evaluation metrics, which include spatial contiguity, functional homogeneity, and reproducibility. Both the group-to-group reproducibility and the group-to-subject reproducibility were evaluated in our study. The experimental results showed that the proposed approaches obtained relatively good overall clustering performances in different conditions that included different weighting functions, different sparsifying schemes, and several confounding factors. Therefore, the generated atlases are appropriate to be utilized as nodes for network analysis. The generated atlases and major source codes of this study have been made publicly available at http://www.nitrc.org/projects/slic/. PMID:28082885

  14. MRI brain tumor segmentation based on improved fuzzy c-means method

    NASA Astrophysics Data System (ADS)

    Deng, Wankai; Xiao, Wei; Pan, Chao; Liu, Jianguo

    2009-10-01

    This paper focuses on the image segmentation, which is one of the key problems in medical image processing. A new medical image segmentation method is proposed based on fuzzy c- means algorithm and spatial information. Firstly, we classify the image into the region of interest and background using fuzzy c means algorithm. Then we use the information of the tissues' gradient and the intensity inhomogeneities of regions to improve the quality of segmentation. The sum of the mean variance in the region and the reciprocal of the mean gradient along the edge of the region are chosen as an objective function. The minimum of the sum is optimum result. The result shows that the clustering segmentation algorithm is effective.

  15. A new method for improving functional-to-structural MRI alignment using local Pearson correlation.

    PubMed

    Saad, Ziad S; Glen, Daniel R; Chen, Gang; Beauchamp, Michael S; Desai, Rutvik; Cox, Robert W

    2009-02-01

    Accurate registration of Functional Magnetic Resonance Imaging (FMRI) T2-weighted volumes to same-subject high-resolution T1-weighted structural volumes is important for Blood Oxygenation Level Dependent (BOLD) FMRI and crucial for applications such as cortical surface-based analyses and pre-surgical planning. Such registration is generally implemented by minimizing a cost functional, which measures the mismatch between two image volumes over the group of proper affine transformations. Widely used cost functionals, such as mutual information (MI) and correlation ratio (CR), appear to yield decent alignments when visually judged by matching outer brain contours. However, close inspection reveals that internal brain structures are often significantly misaligned. Poor registration is most evident in the ventricles and sulcal folds, where CSF is concentrated. This observation motivated our development of an improved modality-specific cost functional which uses a weighted local Pearson coefficient (LPC) to align T2- and T1-weighted images. In the absence of an alignment gold standard, we used three human observers blinded to registration method to provide an independent assessment of the quality of the registration for each cost functional. We found that LPC performed significantly better (p<0.001) than generic cost functionals including MI and CR. Generic cost functionals were very often not minimal near the best alignment, thereby suggesting that optimization is not the cause of their failure. Lastly, we emphasize the importance of precise visual inspection of alignment quality and present an automated method for generating composite images that help capture errors of misalignment.

  16. Sensitivity of quantitative myocardial dynamic contrast-enhanced MRI to saturation pulse efficiency, noise and t1 measurement error: Comparison of nonlinearity correction methods.

    PubMed

    Broadbent, David A; Biglands, John D; Ripley, David P; Higgins, David M; Greenwood, John P; Plein, Sven; Buckley, David L

    2016-03-01

    To compare methods designed to minimize or correct signal nonlinearity in quantitative myocardial dynamic contrast-enhanced (DCE) MRI. DCE-MRI studies were simulated and data acquired in eight volunteers. Signal nonlinearity was corrected using either a dual-bolus approach or model-based correction using proton-density weighted imaging (conventional or dual-sequence acquisition) or T1 data (native or bookend). Scanning of healthy and infarcted myocardium at 3 T was simulated, including noise, saturation imperfection and T1 measurement error. Data were analyzed using model-based deconvolution with a one-compartment (mono-exponential) model. Substantial variation between methods was demonstrated in volunteers. In simulations the dual-bolus method proved stable for realistic levels of saturation efficiency but demonstrated bias due to residual nonlinearity. Model-based methods performed ideally in the absence of confounding error sources and were generally robust to noise or saturation imperfection, except for native T1 based correction which was highly sensitive to the latter. All methods demonstrated large variation in accuracy above an over-saturation level where baseline signal was nulled. For the dual-sequence approach this caused substantial bias at the saturation efficiencies observed in volunteers. The choice of nonlinearity correction method in myocardial DCE-MRI impacts on accuracy and precision of estimated parameters, particularly in the presence of nonideal saturation. © 2015 Wiley Periodicals, Inc.

  17. 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

  18. Multiplexed MRI methods for rapid estimation of global cerebral metabolic rate of oxygen consumption.

    PubMed

    Lee, Hyunyeol; Langham, Michael C; Rodriguez-Soto, Ana E; Wehrli, Felix W

    2017-04-01

    The global cerebral metabolic rate of oxygen (CMRO2), which reflects metabolic activity of the brain under various physiologic conditions, can be quantified using a method, referred to as 'OxFlow', which simultaneously measures hemoglobin oxygen saturation in a draining vein (Yv) and total cerebral blood flow (tCBF). Conventional OxFlow (Conv-OxFlow) entails four interleaves incorporated in a single pulse sequence - two for phase-contrast based measurement of tCBF in the supplying arteries of the neck, and two to measure the intra- to extravascular phase difference in the superior sagittal sinus to derive Yv [Jain et al., JCBFM 2010]. However, this approach limits achievable temporal resolution thus precluding capture of rapid changes of brain metabolic states such as the response to apneic stimuli. Here, we developed a time-efficient, multiplexed OxFlow method and evaluated its potential for measuring dynamic alterations in global CMRO2 during a breath-hold challenge. Two different implementations of multiplexed OxFlow were investigated: 1) simultaneous-echo-refocusing based OxFlow (SER-OxFlow) and 2) simultaneous-multi-slice imaging-based dual-band OxFlow (DB-OxFlow). The two sequences were implemented on 3T scanners (Siemens TIM Trio and Prisma) and their performance was evaluated in comparison to Conv-OxFlow in ten healthy subjects for baseline CMRO2 quantification. Comparison of measured parameters (Yv, tCBF, CMRO2) revealed no significant bias of SER-OxFlow and DB-OxFlow, with respect to the reference Conv-OxFlow while improving temporal resolution two-fold (12.5 versus 25s). Further acceleration shortened scan time to 8 and 6s for SER and DB-OxFlow, respectively, for time-resolved CMRO2 measurement. The two sequences were able of capturing smooth transitions of Yv, tCBF, and CMRO2 over the time course consisting of 30s of normal breathing, 30s of volitional apnea, and 90s of recovery. While both SER- and DB-OxFlow techniques provide significantly improved

  19. An accurate and efficient bayesian method for automatic segmentation of brain MRI.

    PubMed

    Marroquin, J L; Vemuri, B C; Botello, S; Calderon, F; Fernandez-Bouzas, A

    2002-08-01

    Automatic three-dimensional (3-D) segmentation of the brain from magnetic resonance (MR) scans is a challenging problem that has received an enormous amount of attention lately. Of the techniques reported in the literature, very few are fully automatic. In this paper, we present an efficient and accurate, fully automatic 3-D segmentation procedure for brain MR scans. It has several salient features; namely, the following. 1) Instead of a single multiplicative bias field that affects all tissue intensities, separate parametric smooth models are used for the intensity of each class. 2) A brain atlas is used in conjunction with a robust registration procedure to find a nonrigid transformation that maps the standard brain to the specimen to be segmented. This transformation is then used to: segment the brain from nonbrain tissue; compute prior probabilities for each class at each voxel location and find an appropriate automatic initialization. 3) Finally, a novel algorithm is presented which is a variant of the expectation-maximization procedure, that incorporates a fast and accurate way to find optimal segmentations, given the intensity models along with the spatial coherence assumption. Experimental results with both synthetic and real data are included, as well as comparisons of the performance of our algorithm with that of other published methods.

  20. A novel background field removal method for MRI using projection onto dipole fields (PDF).

    PubMed

    Liu, Tian; Khalidov, Ildar; de Rochefort, Ludovic; Spincemaille, Pascal; Liu, Jing; Tsiouris, A John; Wang, Yi

    2011-11-01

    For optimal image quality in susceptibility-weighted imaging and accurate quantification of susceptibility, it is necessary to isolate the local field generated by local magnetic sources (such as iron) from the background field that arises from imperfect shimming and variations in magnetic susceptibility of surrounding tissues (including air). Previous background removal techniques have limited effectiveness depending on the accuracy of model assumptions or information input. In this article, we report an observation that the magnetic field for a dipole outside a given region of interest (ROI) is approximately orthogonal to the magnetic field of a dipole inside the ROI. Accordingly, we propose a nonparametric background field removal technique based on projection onto dipole fields (PDF). In this PDF technique, the background field inside an ROI is decomposed into a field originating from dipoles outside the ROI using the projection theorem in Hilbert space. This novel PDF background removal technique was validated on a numerical simulation and a phantom experiment and was applied in human brain imaging, demonstrating substantial improvement in background field removal compared with the commonly used high-pass filtering method. Copyright © 2011 John Wiley & Sons, Ltd.

  1. [A case of atypical type of Sturge-Weber syndrome demonstrated reversible change by MRI FLAIR method in ictus and in postictal state].

    PubMed

    Sasaki, M; Igarashi, K; Suzuki, S; Saito, K

    1999-07-01

    We report a patient of atypical type of Sturge-Weber syndrome who demonstrated a reversible change by MRI FLAIR method in ictus and postictal state. A 5-year-old boy was admitted to our hospital because of severe headache, vomiting and loss of consciousness with his eyes conjugated to left for a few minutes. He had no facial nevus and other abnormal findings in physical examination. CT scan showed two small calcifications in the right occipital lobe. Postcontrast T 1-weighted image of MRI demonstrated a right parieto-occipital leptomeningeal enhancement. We diagnosed this case as an atypical type of Sturge-Weber syndrome. Although, on admission, FLAIR method showed the area of high signal intensity, after anticonvulsant therapy, those abnormal area disappeared. It is presumably detected by FLAIR method slight extravasation of plasma element in the surface of the brain due to regional hyperperfusion in ictus.

  2. Gradient refractive index of the crystalline lens of the Black Oreo Dory (Allocyttus Niger): comparison of magnetic resonance imaging (MRI) and laser ray-trace methods.

    PubMed

    Garner, L F; Smith, G; Yao, S; Augusteyn, R C

    2001-04-01

    The gradient refractive index of the crystalline lens in the Black Oreo Dory (Allocyttus Niger) was determined using two methods; an optimisation program based on finite ray-tracing and the path of laser beams through the lens, and magnetic resonance imaging (MRI) and the linear relationship between refractive index and nuclear transverse relaxation rates. The methods showed good agreement in the cortical zone of the lens, but the lack of free water in the core of the lens made MRI measurement impossible in this region. The laser-optimisation method gave mean values of 1.368 and 1.543 for the surface and core refractive indices respectively, with a radial distribution for the gradient refractive index given by n(r)=1.543-0.121r2-0.033r4-0.021r6.

  3. “Black Bone” MRI: a potential non-ionizing method for three-dimensional cephalometric analysis—a preliminary feasibility study

    PubMed Central

    Watt-Smith, S R; Golding, S J

    2013-01-01

    Objectives: CT offers a three-dimensional solution to the inaccuracies associated with lateral cephalogram-based cephalometric analysis. However, it is associated with significant concerns regarding ionizing radiation exposure. MRI offers a non-ionizing alternative, but this has been less well investigated. We present a novel gradient echo MRI sequence (“Black Bone”) and highlight the potential of this sequence in cephalometric analysis. Methods: After regional ethics approval, “Black Bone” imaging was obtained in eight patients in whom lateral cephalograms were available. “Black Bone”, T1 and T2 weighted spin echo imaging were obtained in the mid-sagittal plane, and measurements were compared with those obtained on the lateral cephalogram using both the Advantage Windows Workstation (GE Medical Systems, Buckinghamshire, UK) and the Dolphin® cephalometric software (v. 11.5.04.23, Premium; Dolphin Imaging, Chatsworth, CA) by one assessor. Further assessment was made by scoring the ease of landmark identification on a ten-point scale. Results: “Black Bone” imaging surpassed T1 and T2 weighted imaging in terms of cephalometric landmark identification. A number of mid-sagittal cephalometric landmarks could not be clearly identified on T2 weighted imaging, making analysis impossible. Measurements on “Black Bone” demonstrated the smallest discrepancy when compared with those obtained on the lateral cephalogram. The discrepancy seen between measurements completed on mid-sagittal MRI and the lateral cephalogram was compounded by inherent inaccuracies of the lateral cephalogram. The overall mean discrepancy between distance measurements on “Black Bone” imaging and those on the lateral cephalogram was 1–2 mm. Conclusions: Overall, “Black Bone” MRI offered an improved method of cephalometric landmark identification over routine MRI sequences, and provides a potential non-ionizing alternative to CT for three-dimensional cephalometrics. PMID

  4. Active shimming method for a 21.3 MHz small-animal MRI magnet

    NASA Astrophysics Data System (ADS)

    Chen, Shanshan; Xia, Tian; Miao, Zhiying; Xu, Luoyuan; Wang, Hongzhi; Dai, Shuguang

    2017-04-01

    In a 21.3 MHz animal nuclear magnetic resonance (NMR) analyzer and imaging system, high uniformity of the static field B 0 is a crucial prerequisite for obtaining high-quality images and detecting weak signals with short relaxation time. Using only passive shimming and gradient shimming, it is impossible to achieve perfect B 0 uniformity. This paper presents an approach involving high-order active shimming for an NMR analyzer and an imaging magnet. The diameter spherical volume (DSV) of the magnet is only 60 mm. The spherical harmonic function is introduced to analyze the magnetic field and provide a foundation for active shimming. Eleven pairs of bi-planar active shim coils (X, Y, Z, XZ, YZ, Z 2, X 2  +  Y 2, X 2  -  Y 2, Z 3, Z 4, Z 5) were designed using the target field-and stream-function methods, and coils were manufactured with printed circuit board technology in this research. The magnetic field created by these electrified shim coils compensates effectively and accurately for the static magnetic field B 0. The full width at half maximum of the resonance spectrum was used to measure the shimming effect. The results of practical shimming experiments in a 21.3 MHz animal NMR analyzer and imaging device showed that this new approach helps to reduce inhomogeneity from 24 ppm (24  ×  10-6) to 0.39 ppm (0.39  ×  10-6) over a 60 mm DSV, which meets the requirements of imaging and analytical practice.

  5. 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

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

    PubMed Central

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

    2017-01-01

    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 R2 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: R2 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: R2 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: (R2 0·70 – 0·82). Estimated TATFM correlated well with published prediction equations for total body fat based on underwater weighing (R2 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

  7. MRI-determined liver proton density fat fraction, with MRS validation: Comparison of regions of interest sampling methods in patients with type 2 diabetes.

    PubMed

    Vu, Kim-Nhien; Gilbert, Guillaume; Chalut, Marianne; Chagnon, Miguel; Chartrand, Gabriel; Tang, An

    2016-05-01

    To assess the agreement between published magnetic resonance imaging (MRI)-based regions of interest (ROI) sampling methods using liver mean proton density fat fraction (PDFF) as the reference standard. This retrospective, internal review board-approved study was conducted in 35 patients with type 2 diabetes. Liver PDFF was measured by magnetic resonance spectroscopy (MRS) using a stimulated-echo acquisition mode sequence and MRI using a multiecho spoiled gradient-recalled echo sequence at 3.0T. ROI sampling methods reported in the literature were reproduced and liver mean PDFF obtained by whole-liver segmentation was used as the reference standard. Intraclass correlation coefficients (ICCs), Bland-Altman analysis, repeated-measures analysis of variance (ANOVA), and paired t-tests were performed. ICC between MRS and MRI-PDFF was 0.916. Bland-Altman analysis showed excellent intermethod agreement with a bias of -1.5 ± 2.8%. The repeated-measures ANOVA found no systematic variation of PDFF among the nine liver segments. The correlation between liver mean PDFF and ROI sampling methods was very good to excellent (0.873 to 0.975). Paired t-tests revealed significant differences (P < 0.05) with ROI sampling methods that exclusively or predominantly sampled the right lobe. Significant correlations with mean PDFF were found with sampling methods that included higher number of segments, total area equal or larger than 5 cm(2) , or sampled both lobes (P = 0.001, 0.023, and 0.002, respectively). MRI-PDFF quantification methods should sample each liver segment in both lobes and include a total surface area equal or larger than 5 cm(2) to provide a close estimate of the liver mean PDFF. © 2015 Wiley Periodicals, Inc.

  8. A probability-based multi-cycle sorting method for 4D-MRI: A simulation study.

    PubMed

    Liang, Xiao; Yin, Fang-Fang; Liu, Yilin; Cai, Jing

    2016-12-01

    To develop a novel probability-based sorting method capable of generating multiple breathing cycles of 4D-MRI images and to evaluate performance of this new method by comparing with conventional phase-based methods in terms of image quality and tumor motion measurement. Based on previous findings that breathing motion probability density function (PDF) of a single breathing cycle is dramatically different from true stabilized PDF that resulted from many breathing cycles, it is expected that a probability-based sorting method capable of generating multiple breathing cycles of 4D images may capture breathing variation information missing from conventional single-cycle sorting methods. The overall idea is to identify a few main breathing cycles (and their corresponding weightings) that can best represent the main breathing patterns of the patient and then reconstruct a set of 4D images for each of the identified main breathing cycles. This method is implemented in three steps: (1) The breathing signal is decomposed into individual breathing cycles, characterized by amplitude, and period; (2) individual breathing cycles are grouped based on amplitude and period to determine the main breathing cycles. If a group contains more than 10% of all breathing cycles in a breathing signal, it is determined as a main breathing pattern group and is represented by the average of individual breathing cycles in the group; (3) for each main breathing cycle, a set of 4D images is reconstructed using a result-driven sorting method adapted from our previous study. The probability-based sorting method was first tested on 26 patients' breathing signals to evaluate its feasibility of improving target motion PDF. The new method was subsequently tested for a sequential image acquisition scheme on the 4D digital extended cardiac torso (XCAT) phantom. Performance of the probability-based and conventional sorting methods was evaluated in terms of target volume precision and accuracy as measured

  9. 139 Clinically Applicable and Biologically Validated MRI Radiomic Test Method Predicts Glioblastoma Genomic Landscape and Survival.

    PubMed

    Zinn, Pascal O; Singh, Sanjay K; Kotrotsou, Aikaterini; Zandi, Faramak; Thomas, Ginu; Hatami, Masumeh; Luedi, Markus M; Elakkad, Ahmed; Hassan, Islam; Gumin, Joy; Sulman, Erik P; Lang, Frederick F; Colen, Rivka R

    2016-08-01

    Imaging is the modality of choice for noninvasive characterization of biological tissue and organ systems; imaging serves as early diagnostic tool for most disease processes and is rapidly evolving, thus transforming the way we diagnose and follow patients over time. A vast number of cancer imaging characteristics have been correlated to underlying genomics; however, none have established causality. Therefore, our objectives were to test if there is a causal relationship between imaging and genomic information; and to develop a clinically relevant radiomic pipeline for glioblastoma molecular characterization. Functional validation was performed using a prototypic in vivo RNA-interference-based orthotopic xenograft mouse model. The automated pipeline collects 4800 MRI-derived texture features per tumor. Using univariate feature selection and boosted tree predictive modeling, a patient-specific genomic probability map was derived and patient survival predicted (The Cancer Genome Atlas/MD Anderson data sets). Data demonstrated a significant xenograft to human association (area under the curve [AUC] 84%, P < .001). Further, epidermal growth factor receptor amplification (AUC 86%, P < .0001), O-methylguanine-DNA-methyltransferase methylation/expression (AUC 92%, P = .001), glioblastoma molecular subgroups (AUC 88%, P = .001), and survival in 2 independent data sets (AUC 90%, P < .001) was predicted. Our results for the first time illustrate a causal relationship between imaging features and genomic tumor composition. We present a directly clinically applicable analytical imaging method termed Radiome Sequencing to allow for automated image analysis, prediction of key genomic events, and survival. This method is scalable and applicable to any type of medical imaging. Further, it allows for human-mouse matched coclinical trials, in-depth end point analysis, and upfront noninvasive high-resolution radiomics-based diagnostic, prognostic, and predictive biomarker development.

  10. Structural MRI volumetric analysis in patients with organic amnesia, 1: methods and comparative findings across diagnostic groups

    PubMed Central

    Colchester, A; Kingsley, D; Lasserson, D; Kendall, B; Bello, F; Rush, C; Stevens, T; Goodman, G; Heilpern, G; Stanhope, N; Kopelman, M

    2001-01-01

    BACKGROUND—If they are to be replicable, MRI volume measurements require explicit definitions of structures and of criteria for delineating these structures on MRI. Previously published volumes in healthy subjects show considerable differences in measurements across different studies, including a fourfold variation in estimates of hippocampal volume. Previous neuroimaging reports in patients with Korsakoff syndrome have generally found widespread or non-specific change, whereas in patients with herpes encephalitis the extent of pathological involvement reported beyond the temporal lobes has varied.
METHOD—In the present study, a clear set of anatomical criteria and detailed MRI segmentation procedures were applied to measure whole brain, frontal and temporal lobe, and anterolateral and medial temporal volumes, as well as thalamic areas in patients with organic amnesia (from Korsakoff's syndrome, herpes encephalitis, and focal frontal lesions) as well as healthy controls.
RESULTS—Patients with Korsakoff's syndrome showed decreased thalamic measurements but no significant changes in the medial temporal lobes, whereas patients with herpes encephalitis showed severe medial temporal but not thalamic atrophy. In the patients with known frontal lobe lesions, quantitative analysis on MRI showed reduced frontal lobe volume but no significant temporal lobe or thalamic atrophy.
CONCLUSION—Quantified MRI can be a useful technique with which to examine brain-cognitive relations, provided that detailed techniques are explicitly described. In particular, specific patterns of volume change can be found in vivo in patients with Korsakoff's syndrome and those with herpes encephalitis.

 PMID:11413256

  11. 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

  12. 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

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

    PubMed Central

    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

    2015-01-01

    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

  14. Scoring with the Berlin MRI method for assessment of spinal inflammatory activity in patients with ankylosing spondylitis: a calibration exercise among rheumatologists.

    PubMed

    Carmona, Loreto; Sellas, Agusti; Rodríguez-Lozano, Carlos; Juanola, Xavier; García Llorente, José Francisco; Fernández Sueiro, José Luis; Linares, Luis Francisco; de Castro, M Carmen; Moreno, Mireia; Zarco, Pedro; Ariza, Rafael; Baraliakos, Xenofon; de Miguel, Eugenio

    2013-01-01

    To test the reliability of the Berlin MRI scoring method and the effect of a calibration exercise on the score's reliability among untrained readers in MRI examinations of patients with established ankylosing spondylitis (AS). Eleven rheumatologists read blinded images of 20 AS patients before and after a two-day workshop on the Berlin MRI scoring method. Reliability (intra- and inter-reader) and concordance with the expert (all measured by intraclass correlation coefficient (ICC)) were compared before and after 2 weeks of the training. Feasibility in terms of time and difficulty was also measured. The mean Berlin score increased from (mean ± standard deviation) 5.04 ± 6.41 before to 6.40±7.08 after the calibration exercise (p<0.01). Inter-reader ICC decreased from 0.83 (95% CI: 0.75-0.93) to 0.78 (95% CI: 0.66-0.90), and intra-reader ICC from 0.89 (95% CI: 0.84-0.94) to 0.87 (95% CI: 0.82-0.92). Agreement with an experienced reader improved after the calibration exercise, with ICC = 0.59 (95% CI 0.45-0.76) before vs. ICC = 0.65 (95% CI 0.50-0.80) after training. The Berlin method is a reliable scoring method for assessment of spinal inflammatory activity by using MRI in patients with AS, even in the hands of inexperienced readers. A calibration exercise can improve feasibility and sensitivity of the scoring method.

  15. [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.

  16. Brief Report: Methods for Acquiring Structural MRI Data in Very Young Children with Autism Without the Use of Sedation

    PubMed Central

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

    2016-01-01

    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. Alternatively, with some older and higher functioning children, the MRI was conducted while the child was awake and watching a video. Both strategies relied heavily on the creation of a child and family friendly MRI environment and the involvement of parents as collaborators in the project. Scanning very young children with autism, typical development, and developmental delays without the use of sedation or anesthesia was possible in the majority of cases. PMID:18157624

  17. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. [MRI-based radiotherapy planning].

    PubMed

    Largent, A; Nunes, J-C; Lafond, C; Périchon, N; Castelli, J; Rolland, Y; Acosta, O; de Crevoisier, R

    2017-07-06

    MRI-based radiotherapy planning is a topical subject due to the introduction of a new generation of treatment machines combining a linear accelerator and a MRI. One of the issues for introducing MRI in this task is the lack of information to provide tissue density information required for dose calculation. To cope with this issue, two strategies may be distinguished from the literature. Either a synthetic CT scan is generated from the MRI to plan the dose, or a dose is generated from the MRI based on physical underpinnings. Within the first group, three approaches appear: bulk density mapping assign a homogeneous density to different volumes of interest manually defined on a patient MRI; machine learning-based approaches model local relationship between CT and MRI image intensities from multiple data, then applying the model to a new MRI; atlas-based approaches use a co-registered training data set (CT-MRI) which are registered to a new MRI to create a pseudo CT from spatial correspondences in a final fusion step. Within the second group, physics-based approaches aim at computing the dose directly from the hydrogen contained within the tissues, quantified by MRI. Excepting the physics approach, all these methods generate a synthetic CT called "pseudo CT", on which radiotherapy planning will be finally realized. This literature review shows that atlas- and machine learning-based approaches appear more accurate dosimetrically. Bulk density approaches are not appropriate for bone localization. The fastest methods are machine learning and the slowest are atlas-based approaches. The less automatized are bulk density assignation methods. The physical approaches appear very promising methods. Finally, the validation of these methods is crucial for a clinical practice, in particular in the perspective of adaptive radiotherapy delivered by a linear accelerator combined with an MRI scanner. Copyright © 2017. Published by Elsevier SAS.

  19. Presentation of variations in the anterior part of the circle of Willis as a result of MRI-angiography method.

    PubMed

    Voljevica, Alma; Kulenovic, Amela; Kapur, Eldan; Talovic, Elvira; Vuckovic, Ilvana; Luinovic, Almira

    2004-01-01

    As it is well known the beginning, the course and the result of the cerebral-vasculare disease depends on, among other stuff, the possibility of establishment of the brain collateral circulation. The Willis's artery circle based on brain is the most important anastomoses between the blood circulation of the both, carotid and basilar artery. However, in almost half of the cases of the examined circle of Willis, certain deviations from the normal anatomy configuration have been identified that immensely facilitate occurance of vascular diseases, because it makes difficult establishment of collateral blood circulation. In this particular study, 150 MRI patient's angiographics had been analyzed that were processed at the Radiology Institute of the Clinic Center of the University of Sarajevo. The morphologic variations of the circle of Willis were analyzed on these angiographics and those were patients who did not have any signs of cerebral-vasculare diseases. We have tried to determine which variations are the most commonly occuring in the front segment of the circle of Willis with two target groups (older -- above 60 years old and younger- up to 34 years old) and including both genders. The method of the MR angiography in two projections enabled good visualisation of all components of the circle of Willis and based on their analysis we have achieved the following results. The complete front configuration of the circle of Willis had been found with all patients in 76,7% of the cases. We noted slightly higher percentage of the anterior configuration with younger category of patients compared to older patients, and with males compared to females. Out of the variations that damage the anterior segment of the circle of Willis, the first one, according to the frequency of occuring, is the variation of the type of hypoplasia or aplasia of Al segment of the anterior cerebral artery, and then the variation marked as duplication or multiplication of the anterior communicating

  20. Multidimensional diffusion MRI

    NASA Astrophysics Data System (ADS)

    Topgaard, Daniel

    2017-02-01

    Principles from multidimensional NMR spectroscopy, and in particular solid-state NMR, have recently been transferred to the field of diffusion MRI, offering non-invasive characterization of heterogeneous anisotropic materials, such as the human brain, at an unprecedented level of detail. Here we revisit the basic physics of solid-state NMR and diffusion MRI to pinpoint the origin of the somewhat unexpected analogy between the two fields, and provide an overview of current diffusion MRI acquisition protocols and data analysis methods to quantify the composition of heterogeneous materials in terms of diffusion tensor distributions with size, shape, and orientation dimensions. While the most advanced methods allow estimation of the complete multidimensional distributions, simpler methods focus on various projections onto lower-dimensional spaces as well as determination of means and variances rather than actual distributions. Even the less advanced methods provide simple and intuitive scalar parameters that are directly related to microstructural features that can be observed in optical microscopy images, e.g. average cell eccentricity, variance of cell density, and orientational order - properties that are inextricably entangled in conventional diffusion MRI. Key to disentangling all these microstructural features is MRI signal acquisition combining isotropic and directional dimensions, just as in the field of multidimensional solid-state NMR from which most of the ideas for the new methods are derived.

  1. Attenuation correction methods suitable for brain imaging with a PET/MRI scanner: a comparison of tissue atlas and template attenuation map approaches.

    PubMed

    Malone, Ian B; Ansorge, Richard E; Williams, Guy B; Nestor, Peter J; Carpenter, T Adrian; Fryer, Tim D

    2011-07-01

    Modeled attenuation correction (AC) will be necessary for combined PET/MRI scanners not equipped with transmission scanning hardware. We compared 2 modeled AC approaches that use nonrigid registration with rotating (68)Ge rod-based measured AC for 10 subjects scanned with (18)F-FDG. Two MRI and attenuation map pairs were evaluated: tissue atlas-based and measured templates. The tissue atlas approach used a composite of the BrainWeb and Zubal digital phantoms, whereas the measured templates were produced by averaging spatially normalized measured MR image and coregistered attenuation maps. The composite digital phantom was manually edited to include 2 additional tissue classes (paranasal sinuses, and ethmoidal air cells or nasal cavity). In addition, 3 attenuation values for bone were compared. The MRI and attenuation map pairs were used to generate subject-specific attenuation maps via nonrigid registration of the MRI to the MR image of the subject. SPM2 and a B-spline free-form deformation algorithm were used for the nonrigid registration. To determine the accuracy of the modeled AC approaches, radioactivity concentration was assessed on a voxelwise and regional basis. The template approach produced better spatial consistency than the phantom-based atlas, with an average percentage error in radioactivity concentration across the regions, compared with measured AC, of -1.2% ± 1.2% and -1.5% ± 1.9% for B-spline and SPM2 registration, respectively. In comparison, the tissue atlas method with B-spline registration produced average percentage errors of 0.0% ± 3.0%, 0.9% ± 2.9%, and 2.9% ± 2.8% for bone attenuation values of 0.143 cm(-1), 0.152 cm(-1), and 0.172 cm(-1), respectively. The largest errors for the template AC method were found in parts of the frontal cortex (-3%) and the cerebellar vermis (-5%). Intersubject variability was higher with SPM2 than with B-spline. Compared with measured AC, template AC with B-spline and SPM2 achieved a correlation

  2. Knee MRI

    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 ...

  3. Shoulder MRI

    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 ...

  4. Shoulder MRI

    MedlinePlus

    ... of the shoulder uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  5. Knee MRI

    MedlinePlus

    ... of the knee uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  6. MRI renaissance.

    PubMed

    Hensley, S

    1997-12-01

    A few years ago, magnetic resonance imaging was healthcare's version of a foreign sports car-flashy, expensive and impractical. Now, after years in the doldrums, sales of MRI systems are roaring back. An aging fleet of MRI scanners due for replacement and a hearty increase in doctors' use of the versatile imaging tools are combining to fuel the surge in demand, vendors and customers say.

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.…

  12. 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.…

  13. 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.

  14. 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.

  15. A novel AIF tracking method and comparison of DCE-MRI parameters using individual and population-based AIFs in human breast cancer

    NASA Astrophysics Data System (ADS)

    Li, Xia; Welch, E. Brian; Arlinghaus, Lori R.; Bapsi Chakravarthy, A.; Xu, Lei; Farley, Jaime; Loveless, Mary E.; Mayer, Ingrid A.; Kelley, Mark C.; Meszoely, Ingrid M.; Means-Powell, Julie A.; Abramson, Vandana G.; Grau, Ana M.; Gore, John C.; Yankeelov, Thomas E.

    2011-09-01

    Quantitative analysis of dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data requires the accurate determination of the arterial input function (AIF). A novel method for obtaining the AIF is presented here and pharmacokinetic parameters derived from individual and population-based AIFs are then compared. A Philips 3.0 T Achieva MR scanner was used to obtain 20 DCE-MRI data sets from ten breast cancer patients prior to and after one cycle of chemotherapy. Using a semi-automated method to estimate the AIF from the axillary artery, we obtain the AIF for each patient, AIFind, and compute a population-averaged AIF, AIFpop. The extended standard model is used to estimate the physiological parameters using the two types of AIFs. The mean concordance correlation coefficient (CCC) for the AIFs segmented manually and by the proposed AIF tracking approach is 0.96, indicating accurate and automatic tracking of an AIF in DCE-MRI data of the breast is possible. Regarding the kinetic parameters, the CCC values for Ktrans, vp and ve as estimated by AIFind and AIFpop are 0.65, 0.74 and 0.31, respectively, based on the region of interest analysis. The average CCC values for the voxel-by-voxel analysis are 0.76, 0.84 and 0.68 for Ktrans, vp and ve, respectively. This work indicates that Ktrans and vp show good agreement between AIFpop and AIFind while there is a weak agreement on ve.

  16. 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

  17. 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

  18. Concurrent fNIRS-fMRI measurement to validate a method for separating deep and shallow fNIRS signals by using multidistance optodes

    PubMed Central

    Funane, Tsukasa; Sato, Hiroki; Yahata, Noriaki; Takizawa, Ryu; Nishimura, Yukika; Kinoshita, Akihide; Katura, Takusige; Atsumori, Hirokazu; Fukuda, Masato; Kasai, Kiyoto; Koizumi, Hideaki; Kiguchi, Masashi

    2015-01-01

    Abstract. It has been reported that a functional near-infrared spectroscopy (fNIRS) signal can be contaminated by extracerebral contributions. Many algorithms using multidistance separations to address this issue have been proposed, but their spatial separation performance has rarely been validated with simultaneous measurements of fNIRS and functional magnetic resonance imaging (fMRI). We previously proposed a method for discriminating between deep and shallow contributions in fNIRS signals, referred to as the multidistance independent component analysis (MD-ICA) method. In this study, to validate the MD-ICA method from the spatial aspect, multidistance fNIRS, fMRI, and laser-Doppler-flowmetry signals were simultaneously obtained for 12 healthy adult males during three tasks. The fNIRS signal was separated into deep and shallow signals by using the MD-ICA method, and the correlation between the waveforms of the separated fNIRS signals and the gray matter blood oxygenation level–dependent signals was analyzed. A three-way analysis of variance (signal depth×Hb kind×task) indicated that the main effect of fNIRS signal depth on the correlation is significant [F(1,1286)=5.34, p<0.05]. This result indicates that the MD-ICA method successfully separates fNIRS signals into spatially deep and shallow signals, and the accuracy and reliability of the fNIRS signal will be improved with the method. PMID:26157983

  19. 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.

  20. 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

  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. The evaluation of non-ischemic dilated cardiomyopathy with T1 mapping and ECV methods using 3T cardiac MRI.

    PubMed

    Görmeli, Cemile Ayşe; Özdemir, Zeynep Maraş; Kahraman, Ayşegül Sağır; Yağmur, Jülide; Özdemir, Ramazan; Çolak, Cemil

    2017-02-01

    The aim of this study was to examine the correlation between ventricular function and the extracellular volume fraction (ECV) in patients with non-ischemic dilated cardiomyopathy (NIDCM) using 3.0 T magnetic resonance imaging (MRI). We also hypothesized that native T1 and ECV values would be increased in patients with NIDCM, independent of the left ventricular ejection fraction (LVEF). The findings of our study could lead to further studies of the follow-up protocols. In total, 53 consecutive dilated cardiomyopathy patients who had undergone cardiac MRI were functionally evaluated and underwent tissue characterization. The mean native T1 value was 1235 ± 10 ms, and the mean ECV value was 35.4 ± 2.7% in the myocardia. The LVEF values ranged from 29 to 44%. No significant correlations were observed between functional analysis measurements and native T1 or ECV values. Our results showed that myocardial fibrosis is unrelated to cardiac functional findings in NIDCM patients. Therefore, we propose that these patients should be evaluated using MRI and tissue characterization techniques, in addition to cardiac functional analysis.

  3. Integrating atlas and graph cut methods for right ventricle blood-pool segmentation from cardiac cine MRI

    NASA Astrophysics Data System (ADS)

    Dangi, Shusil; Linte, Cristian A.

    2017-03-01

    Segmentation of right ventricle from cardiac MRI images can be used to build pre-operative anatomical heart models to precisely identify regions of interest during minimally invasive therapy. Furthermore, many functional parameters of right heart such as right ventricular volume, ejection fraction, myocardial mass and thickness can also be assessed from the segmented images. To obtain an accurate and computationally efficient segmentation of right ventricle from cardiac cine MRI, we propose a segmentation algorithm formulated as an energy minimization problem in a graph. Shape prior obtained by propagating label from an average atlas using affine registration is incorporated into the graph framework to overcome problems in ill-defined image regions. The optimal segmentation corresponding to the labeling with minimum energy configuration of the graph is obtained via graph-cuts and is iteratively refined to produce the final right ventricle blood pool segmentation. We quantitatively compare the segmentation results obtained from our algorithm to the provided gold-standard expert manual segmentation for 16 cine-MRI datasets available through the MICCAI 2012 Cardiac MR Right Ventricle Segmentation Challenge according to several similarity metrics, including Dice coefficient, Jaccard coefficient, Hausdorff distance, and Mean absolute distance error.

  4. Functional MRI for radiotherapy of gliomas.

    PubMed

    Chang, Jenghwa; Narayana, Ashwatha

    2010-08-01

    In this paper, we review the applications of functional magnetic resonance imaging (MRI) for target delineation and critical organ avoidance for brain radiotherapy. In this article we distinguish functional MRI from brain functional MRI (fMRI). Functional MRI includes magnetic resonance spectroscopic imaging (MRSI), perfusion MRI, diffusion tensor imaging (DTI) and brain fMRI. These functional MRI modalities can provide unique metabolic, pathological and physiological information that are not available in anatomic MRI and can potentially improve the treatment outcomes of brain tumors. For example, both choline (Cho) to N-acetylaspartate (NAA) and Cho to creatine (Cr) ratios from MRSI increase with increasing tumor malignancy and can be used to grade gliomas. Relative cerebral blood volume (rCBV) measurements from dynamic susceptibility contrast perfusion magnetic resonance imaging (DSC MRI) are superior to conventional contrast-enhanced MRI in predicting tumor biology and may be even superior to pathologic assessment in predicting patient clinical outcomes. Brain fMRI can help identify and avoid functionally critical areas when constructing treatment plans for brain radiotherapy. In the past, functional MRI measurements have not been routinely used in a clinical arena due to the experimental nature of these imaging modalities. As these methods become more commonly used and effective image co-registration algorithms become available, integration of functional MRI into the treatment process of brain radiotherapy now appears to be clinically feasible, at least in major medical centers.

  5. Fast numerical design of spatial-selective rf pulses in MRI using Krotov and quasi-Newton based optimal control methods.

    PubMed

    Vinding, Mads S; Maximov, Ivan I; Tošner, Zdenĕk; Nielsen, Niels Chr

    2012-08-07

    The use of increasingly strong magnetic fields in magnetic resonance imaging (MRI) improves sensitivity, susceptibility contrast, and spatial or spectral resolution for functional and localized spectroscopic imaging applications. However, along with these benefits come the challenges of increasing static field (B(0)) and rf field (B(1)) inhomogeneities induced by radial field susceptibility differences and poorer dielectric properties of objects in the scanner. Increasing fields also impose the need for rf irradiation at higher frequencies which may lead to elevated patient energy absorption, eventually posing a safety risk. These reasons have motivated the use of multidimensional rf pulses and parallel rf transmission, and their combination with tailoring of rf pulses for fast and low-power rf performance. For the latter application, analytical and approximate solutions are well-established in linear regimes, however, with increasing nonlinearities and constraints on the rf pulses, numerical iterative methods become attractive. Among such procedures, optimal control methods have recently demonstrated great potential. Here, we present a Krotov-based optimal control approach which as compared to earlier approaches provides very fast, monotonic convergence even without educated initial guesses. This is essential for in vivo MRI applications. The method is compared to a second-order gradient ascent method relying on the Broyden-Fletcher-Goldfarb-Shanno (BFGS) quasi-Newton method, and a hybrid scheme Krotov-BFGS is also introduced in this study. These optimal control approaches are demonstrated by the design of a 2D spatial selective rf pulse exciting the letters "JCP" in a water phantom.

  6. 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.

  7. TU-CD-BRA-04: Evaluation of An Atlas-Based Segmentation Method for Prostate and Peripheral Zone Regions On MRI

    SciTech Connect

    Nelson, AS; Piper, J; Curry, K; Swallen, A; Padgett, K; Pollack, A; Stoyanova, RS

    2015-06-15

    Purpose: Prostate MRI plays an important role in diagnosis, biopsy guidance, and therapy planning for prostate cancer. Prostate MRI contours can be used to aid in image fusion for ultrasound biopsy guidance and delivery of radiation. Our goal in this study is to evaluate an automatic atlas-based segmentation method for generating prostate and peripheral zone (PZ) contours on MRI. Methods: T2-weighted MRIs were acquired on 3T-Discovery MR750 System (GE, Milwaukee). The Volumes of Interest (VOIs): prostate and PZ were outlined by an expert radiation oncologist and used to create an atlas library for atlas-based segmentation. The atlas-segmentation accuracy was evaluated using a leave-one-out analysis. The method involved automatically finding the atlas subject that best matched the test subject followed by a normalized intensity-based free-form deformable registration of the atlas subject to the test subject. The prostate and PZ contours were transformed to the test subject using the same deformation. For each test subject the three best matches were used and the final contour was combined using Majority Vote. The atlas-segmentation process was fully automatic. Dice similarity coefficients (DSC) and mean Hausdorff values were used for comparison. Results: VOIs contours were available for 28 subjects. For the prostate, the atlas-based segmentation method resulted in an average DSC of 0.88+/−0.08 and a mean Hausdorff distance of 1.1+/−0.9mm. The number of patients (#) in DSC ranges are as follows: 0.60–0.69(1), 0.70–0.79(2), 0.80–0.89(13), >0.89(11). For the PZ, the average DSC was 0.72+/−0.17 and average Hausdorff of 0.9+/−0.9mm. The number of patients (#) in DSC ranges are as follows: <0.60(4), 0.60–0.69(6), 0.70–0.79(7), 0.80–0.89(9), >0.89(1). Conclusion: The MRI atlas-based segmentation method achieved good results for both the whole prostate and PZ compared to expert defined VOIs. The technique is fast, fully automatic, and has the potential

  8. Chest MRI

    MedlinePlus

    ... as the contrast dye is injected. The MRI machine is a large, tunnel-like machine that has a table. You will lie still ... table, and the table will slide into the machine. You will hear loud humming, tapping, and buzzing ...

  9. Cardiac MRI

    MedlinePlus

    ... as the contrast dye is injected. The MRI machine is a large, tunnel-like machine that has a table. You will lie still ... table and the table will slide into the machine. You will hear loud humming, tapping, and buzzing ...

  10. A fuzzy integral method based on the ensemble of neural networks to analyze fMRI data for cognitive state classification across multiple subjects.

    PubMed

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

    2016-12-01

    The huge number of voxels in fMRI over time poses a major challenge to for effective analysis. Fast, accurate, and reliable classifiers are required for estimating the decoding accuracy of brain activities. Although machine-learning classifiers seem promising, individual classifiers have their own limitations. To address this limitation, the present paper proposes a method based on the ensemble of neural networks to analyze fMRI data for cognitive state classification for application across multiple subjects. Similarly, the fuzzy integral (FI) approach has been employed as an efficient tool for combining different classifiers. The FI approach led to the development of a classifiers ensemble technique that performs better than any of the single classifier by reducing the misclassification, the bias, and the variance. The proposed method successfully classified the different cognitive states for multiple subjects with high accuracy of classification. Comparison of the performance improvement, while applying ensemble neural networks method, vs. that of the individual neural network strongly points toward the usefulness of the proposed method.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Evaluating methods of correcting for multiple comparisons implemented in SPM12 in social neuroscience fMRI studies: an example from moral psychology.

    PubMed

    Han, Hyemin; Glenn, Andrea L

    2017-05-15

    In fMRI research, the goal of correcting for multiple comparisons is to identify areas of activity that reflect true effects, and thus would be expected to replicate in future studies. Finding an appropriate balance between trying to minimize false positives (Type I error) while not being too stringent and omitting true effects (Type II error) can be challenging. Furthermore, the advantages and disadvantages of these types of errors may differ for different areas of study. In many areas of social neuroscience that involve complex processes and considerable individual differences, such as the study of moral judgment, effects are typically smaller and statistical power weaker, leading to the suggestion that less stringent corrections that allow for more sensitivity may be beneficial and also result in more false positives. Using moral judgment fMRI data, we evaluated four commonly used methods for multiple comparison correction implemented in Statistical Parametric Mapping 12 by examining which method produced the most precise overlap with results from a meta-analysis of relevant studies and with results from nonparametric permutation analyses. We found that voxelwise thresholding with familywise error correction based on Random Field Theory provides a more precise overlap (i.e., without omitting too few regions or encompassing too many additional regions) than either clusterwise thresholding, Bonferroni correction, or false discovery rate correction methods.

  16. MRI of the placenta - a short review.

    PubMed

    Dekan, Sabine; Linduska, Nina; Kasprian, Gregor; Prayer, Daniela

    2012-05-01

    While ultrasound is still the gold standard method of placental investigation, magnetic resonance imaging (MRI) has certain benefits. In advanced gestational age, obese women, and posterior placental location, MRI is advantageous due to the larger field of view and its multiplanar capabilities. Some pathologies are seen more clearly in MRI, such as infarctions and placental invasive disorders. The future development is towards functional placental MRI. Placental MRI has become an important complementary method for evaluation of placental anatomy and pathologies contributing to fetal problems such as intrauterine growth restriction.

  17. 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.

  18. 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

  19. Improved operator agreement and efficiency using the minimum area contour change method for delineation of hyperintense multiple sclerosis lesions on FLAIR MRI

    PubMed Central

    2013-01-01

    Background Activity of disease in patients with multiple sclerosis (MS) is monitored by detecting and delineating hyper-intense lesions on MRI scans. The Minimum Area Contour Change (MACC) algorithm has been created with two main goals: a) to improve inter-operator agreement on outlining regions of interest (ROIs) and b) to automatically propagate longitudinal ROIs from the baseline scan to a follow-up scan. Methods The MACC algorithm first identifies an outer bound for the solution path, forms a high number of iso-contour curves based on equally spaced contour values, and then selects the best contour value to outline the lesion. The MACC software was tested on a set of 17 FLAIR MRI images evaluated by a pair of human experts and a longitudinal dataset of 12 pairs of T2-weighted Fluid Attenuated Inversion Recovery (FLAIR) images that had lesion analysis ROIs drawn by a single expert operator. Results In the tests where two human experts evaluated the same MRI images, the MACC program demonstrated that it could markedly reduce inter-operator outline error. In the longitudinal part of the study, the MACC program created ROIs on follow-up scans that were in close agreement to the original expert’s ROIs. Finally, in a post-hoc analysis of 424 follow-up scans 91% of propagated MACC were accepted by an expert and only 9% of the final accepted ROIS had to be created or edited by the expert. Conclusion When used with an expert operator's verification of automatically created ROIs, MACC can be used to improve inter- operator agreement and decrease analysis time, which should improve data collected and analyzed in multicenter clinical trials. PMID:24004511

  20. Performance comparison of deep learning and segmentation-based radiomic methods in the task of distinguishing benign and malignant breast lesions on DCE-MRI

    NASA Astrophysics Data System (ADS)

    Antropova, Natasha; Huynh, Benjamin; Giger, Maryellen

    2017-03-01

    Intuitive segmentation-based CADx/radiomic features, calculated from the lesion segmentations of dynamic contrast-enhanced magnetic resonance images (DCE-MRIs) have been utilized in the task of distinguishing between malignant and benign lesions. Additionally, transfer learning with pre-trained deep convolutional neural networks (CNNs) allows for an alternative method of radiomics extraction, where the features are derived directly from the image data. However, the comparison of computer-extracted segmentation-based and CNN features in MRI breast lesion characterization has not yet been conducted. In our study, we used a DCE-MRI database of 640 breast cases - 191 benign and 449 malignant. Thirty-eight segmentation-based features were extracted automatically using our quantitative radiomics workstation. Also, 2D ROIs were selected around each lesion on the DCE-MRIs and directly input into a pre-trained CNN AlexNet, yielding CNN features. Each method was investigated separately and in combination in terms of performance in the task of distinguishing between benign and malignant lesions. Area under the ROC curve (AUC) served as the figure of merit. Both methods yielded promising classification performance with round-robin cross-validated AUC values of 0.88 (se =0.01) and 0.76 (se=0.02) for segmentationbased and deep learning methods, respectively. Combination of the two methods enhanced the performance in malignancy assessment resulting in an AUC value of 0.91 (se=0.01), a statistically significant improvement over the performance of the CNN method alone.

  1. Magnetic resonance imaging (MRI) and relaxation spectrum analysis as methods to investigate swelling in whey protein gels.

    PubMed

    Oztop, Mecit H; Rosenberg, Moshe; Rosenberg, Yael; McCarthy, Kathryn L; McCarthy, Michael J

    2010-10-01

    Effective means for controlled delivery of nutrients and nutraceuticals are needed. Whey protein-based gels, as a model system and as a potential delivery system, exhibit pH-dependent swelling when placed in aqueous solutions. Understanding the physics that govern gel swelling is thus important when designing gel-based delivery platforms. The extent of swelling over time was monitored gravimetrically. In addition to gravimetric measurements, magnetic resonance imaging (MRI) a real-time noninvasive imaging technique that quantified changes in geometry and water content of these gels was utilized. Heat-set whey protein gels were prepared at pH 7 and swelling was monitored in aqueous solutions with pH values of 2.5, 7, and 10. Changes in dimension over time, as characterized by the number of voxels in an image, were correlated to gravimetric measurements. Excellent correlations between mass uptake and volume change (R(2)= 0.99) were obtained for the gels in aqueous solutions at pH 7 and 10, but not for gels in the aqueous solution at pH 2.5. To provide insight into the mechanisms for water uptake, nuclear magnetic resonance (NMR) relaxation times were measured in independent experiments. The relaxation spectrum for the spin-spin relaxation time (T(2)) showed the presence of 3 proton pools for pH 7 and 10 trials and 4 proton pools for pH 2.5 trials. Results demonstrate that MRI and NMR relaxation measurements provided information about swelling in whey protein gels that can constitute a new means for investigating and developing effective delivery systems for foods.

  2. 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

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

    PubMed Central

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

    2015-01-01

    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, and consequently tractography and the ability to recover complex white-matter pathways, as well as 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/mm2) common to clinical studies. We found the BSM and CSD methods consistently yielded the least fiber orientation error and simultaneously greatest detection rate of

  4. 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

  5. A Technique for Generating Volumetric Cine MRI (VC-MRI)

    PubMed Central

    Harris, Wendy; Ren, Lei; Cai, Jing; Zhang, You; Chang, Zheng; Yin, Fang-Fang

    2016-01-01

    Purpose To develop a technique to generate on-board volumetric-cine MRI (VC-MRI) using patient prior images, motion modeling and on-board 2D-cine MRI. Methods One phase of a 4D-MRI acquired during patient simulation is used as patient prior images. 3 major respiratory deformation patterns of the patient are extracted from 4D-MRI based on principal-component-analysis. The on-board VC-MRI at any instant is considered as a deformation of the prior MRI. The deformation field is represented as a linear combination of the 3 major deformation patterns. The coefficients of the deformation patterns are solved by the data fidelity constraint using the acquired on-board single 2D-cine MRI. The method was evaluated using both XCAT simulation of lung cancer patients and MRI data from four real liver cancer patients. The accuracy of the estimated VC-MRI was quantitatively evaluated using Volume-Percent-Difference(VPD), Center-of-Mass-Shift(COMS), and target tracking errors. Effects of acquisition orientation, region-of-interest(ROI) selection, patient breathing pattern change and noise on the estimation accuracy were also evaluated. Results Image subtraction of ground-truth with estimated on-board VC-MRI shows fewer differences than image subtraction of ground-truth with prior image. Agreement between profiles in the estimated and ground-truth VC-MRI was achieved with less than 6% error for both XCAT and patient data. Among all XCAT scenarios, the VPD between ground-truth and estimated lesion volumes was on average 8.43±1.52% and the COMS was on average 0.93±0.58mm across all time-steps for estimation based on the ROI region in the sagittal cine images. Matching to ROI in the sagittal view achieved better accuracy when there was substantial breathing pattern change. The technique was robust against noise levels up to SNR=20. For patient data, average tracking errors were less than 2 mm in all directions for all patients. Conclusions Preliminary studies demonstrated the

  6. Integrated speech enhancement for functional MRI environment.

    PubMed

    Pathak, Nishank; Milani, Ali A; Panahi, Issa; Briggs, Richard

    2009-01-01

    This paper presents an integrated speech enhancement (SE) method for the noisy MRI environment. We show that the performance of SE system improves considerably when the speech signal dominated by MRI acoustic noise at very low SNR is enhanced in two successive stages using two-channel SE methods followed by a single-channel post processing SE algorithm. Actual MRI noisy speech data are used in our experiments showing the improved performance of the proposed SE method.

  7. MRI in ocular drug delivery.

    PubMed

    Li, S Kevin; Lizak, Martin J; Jeong, Eun-Kee

    2008-11-01

    Conventional pharmacokinetic methods for studying ocular drug delivery are invasive and cannot be conveniently applied to humans. The advancement of MRI technology has provided new opportunities in ocular drug-delivery research. MRI provides a means to non-invasively and continuously monitor ocular drug-delivery systems with a contrast agent or compound labeled with a contrast agent. It is a useful technique in pharmacokinetic studies, evaluation of drug-delivery methods, and drug-delivery device testing. Although the current status of the technology presents some major challenges to pharmaceutical research using MRI, it has a lot of potential. In the past decade, MRI has been used to examine ocular drug delivery via the subconjunctival route, intravitreal injection, intrascleral injection to the suprachoroidal space, episcleral and intravitreal implants, periocular injections, and ocular iontophoresis. In this review, the advantages and limitations of MRI in the study of ocular drug delivery are discussed. Different MR contrast agents and MRI techniques for ocular drug-delivery research are compared. Ocular drug-delivery studies using MRI are reviewed.

  8. MRI in ocular drug delivery

    PubMed Central

    Li, S. Kevin; Lizak, Martin J.; Jeong, Eun-Kee

    2008-01-01

    Conventional pharmacokinetic methods for studying ocular drug delivery are invasive and cannot be conveniently applied to humans. The advancement of MRI technology has provided new opportunities in ocular drug-delivery research. MRI provides a means to non-invasively and continuously monitor ocular drug-delivery systems with a contrast agent or compound labeled with a contrast agent. It is a useful technique in pharmacokinetic studies, evaluation of drug-delivery methods, and drug-delivery device testing. Although the current status of the technology presents some major challenges to pharmaceutical research using MRI, it has a lot of potential. In the past decade, MRI has been used to examine ocular drug delivery via the subconjunctival route, intravitreal injection, intrascleral injection to the suprachoroidal space, episcleral and intravitreal implants, periocular injections, and ocular iontophoresis. In this review, the advantages and limitations of MRI in the study of ocular drug delivery are discussed. Different MR contrast agents and MRI techniques for ocular drug-delivery research are compared. Ocular drug-delivery studies using MRI are reviewed. PMID:18186077

  9. 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

  10. Combination of a model-deformation method and a positional MRI to quantify the effects of posture on the anatomical structures of the trunk.

    PubMed

    Lafon, Y; Smith, F W; Beillas, P

    2010-05-07

    Understanding the postural effects on organs and skeleton could be crucial for several applications. This paper reports on a methodology to quantify the three-dimensional effects of postures on deformable anatomical structures. A positional MRI scanner was used to image the full trunk in four postures: supine, standing, seated and forward-flexed. The MRI stacks were processed with a custom toolbox, implemented using open source software. The semi-automated segmentation was based on the deformation of generic models of the pelvis, sternum, femoral heads, spine, liver, kidneys, spleen, skin, thoracic and abdominal cavities. The toolbox was designed to be easily extended by additional image filters, deformation schemes, or new generic models. Results obtained on one subject demonstrate that the method can be used to quantify the effects of postures on skeleton and organs. The spinal curvature, the pelvic parameters and the volume of the thoracic cavity were affected by the four postures. The volumes of the kidneys, spleen, liver and abdominal object were mostly unaffected. The movement of organs was coherent with the effect of gravity. The deformation of organs between postures was expressed using geometrical transformations. Investigations should be pursued on a larger population to confirm the patterns observed on the first subject. Copyright 2010 Elsevier Ltd. All rights reserved.

  11. MRI of intact plants.

    PubMed

    Van As, Henk; Scheenen, Tom; Vergeldt, Frank J

    2009-01-01

    Nuclear magnetic resonance imaging (MRI) is a non-destructive and non-invasive technique that can be used to acquire two- or even three-dimensional images of intact plants. The information within the images can be manipulated and used to study the dynamics of plant water relations and water transport in the stem, e.g., as a function of environmental (stress) conditions. Non-spatially resolved portable NMR is becoming available to study leaf water content and distribution of water in different (sub-cellular) compartments. These parameters directly relate to stomatal water conductance, CO(2) uptake, and photosynthesis. MRI applied on plants is not a straight forward extension of the methods discussed for (bio)medical MRI. This educational review explains the basic physical principles of plant MRI, with a focus on the spatial resolution, factors that determine the spatial resolution, and its unique information for applications in plant water relations that directly relate to plant photosynthetic activity. © Springer Science+Business Media B.V. 2009

  12. An integrated model-driven method for in-treatment upper airway motion tracking using cine MRI in head and neck radiation therapy.

    PubMed

    Li, Hua; Chen, Hsin-Chen; Dolly, Steven; Li, Harold; Fischer-Valuck, Benjamin; Victoria, James; Dempsey, James; Ruan, Su; Anastasio, Mark; Mazur, Thomas; Gach, Michael; Kashani, Rojano; Green, Olga; Rodriguez, Vivian; Gay, Hiram; Thorstad, Wade; Mutic, Sasa

    2016-08-01

    For the first time, MRI-guided radiation therapy systems can acquire cine images to dynamically monitor in-treatment internal organ motion. However, the complex head and neck (H&N) structures and low-contrast/resolution of on-board cine MRI images make automatic motion tracking a very challenging task. In this study, the authors proposed an integrated model-driven method to automatically track the in-treatment motion of the H&N upper airway, a complex and highly deformable region wherein internal motion often occurs in an either voluntary or involuntary manner, from cine MRI images for the analysis of H&N motion patterns. Considering the complex H&N structures and ensuring automatic and robust upper airway motion tracking, the authors firstly built a set of linked statistical shapes (including face, face-jaw, and face-jaw-palate) using principal component analysis from clinically approved contours delineated on a set of training data. The linked statistical shapes integrate explicit landmarks and implicit shape representation. Then, a hierarchical model-fitting algorithm was developed to align the linked shapes on the first image frame of a to-be-tracked cine sequence and to localize the upper airway region. Finally, a multifeature level set contour propagation scheme was performed to identify the upper airway shape change, frame-by-frame, on the entire image sequence. The multifeature fitting energy, including the information of intensity variations, edge saliency, curve geometry, and temporal shape continuity, was minimized to capture the details of moving airway boundaries. Sagittal cine MR image sequences acquired from three H&N cancer patients were utilized to demonstrate the performance of the proposed motion tracking method. The tracking accuracy was validated by comparing the results to the average of two manual delineations in 50 randomly selected cine image frames from each patient. The resulting average dice similarity coefficient (93.28%  ±  1

  13. Discriminant analysis of MRI measures as a method to determine the presence of dementia of the Alzheimer type.

    PubMed

    DeCarli, C; Murphy, D G; McIntosh, A R; Teichberg, D; Schapiro, M B; Horwitz, B

    1995-07-28

    Multivariate discriminant analysis of brain volumes obtained from semiautomated magnetic resonance image (MRI) quantification was used in an attempt to identify demented patients very early in the course of the disease. Temporal and posterior frontal brain volumes were quantified from MRIs in a cross-sectional study of 31 male and female patients with dementia of the Alzheimer type (DAT) and 29 age- and sex-matched healthy comparison subjects. Mean scores on the Folstein Mini-Mental State Examination (MMS) were in the mild range for the DAT group (20 +/- 6.6), but patients with moderate and severe dementia were also included (MMS range of entire DAT group = 4-28). Significant mean differences in frontal and temporal lobe brain volumes were found between the DAT group and the age- and sex-matched healthy comparison group, but the sensitivity of any single measure was limited to 87% with a specificity of 83%. Initial multivariate discriminant analysis revealed significant gender differences among the healthy subjects, but not the DAT patients. The large group size allowed for subsequent discriminant analyses to be performed by gender. All healthy subjects and DAT patients were correctly classified by gender-specific discriminant functions. The male discriminant variables included brain volume, age, and temporal lobe measures. Inclusion of age in the male discriminant function accounted for age-related brain atrophy, a finding that may have emerged as a consequence of the broad age range of the male DAT population (50-81 years). The male discriminant function was also successfully applied to an independent group of mildly demented subjects that included patients for whom the diagnosis of dementia was uncertain but verified by follow-up clinical evaluations. Measures of temporal lobe brain matter and temporal lobe cerebrospinal fluid volumes were the significant discriminator variables for the women. Quantitative MRI and multivariate discriminant analysis showed

  14. 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 ...

  15. MRI (Magnetic Resonance Imaging)

    MedlinePlus

    ... Procedures Medical Imaging MRI (Magnetic Resonance Imaging) MRI (Magnetic Resonance Imaging) Share Tweet Linkedin Pin it More sharing options Linkedin Pin it Email Print Magnetic Resonance Imaging (MRI) is a medical imaging procedure for making ...

  16. Anti–citrullinated protein antibody positivity correlates with cartilage damage and proteoglycan levels in patients with rheumatoid arthritis in the hand joints.

    PubMed

    Renner, Nina; Krönke, Gerhard; Rech, Jürgen; Uder, Michael; Janka, Rolf; Lauer, Lars; Paul, Dominik; Herz, Barbara; Schlechtweg, Philipp; Hennig, Friedrich Frank; Schett, Georg; Welsch, Götz

    2014-12-01

    Objective: To investigate the factors associated with cartilage proteoglycan content in patients with rheumatoid arthritis (RA) Methods: 32 RA patients received high-field 3 Tesla Gadolinium-Enhanced MRI of Cartilage (dGEMRIC) for determining cartilage proteoglycan content. Measurements were performed in three individual cartilage regions (medial, central, lateral) of the metacarpophalangeal joints 2 and 3. dGEMRIC values were then related to disease duration, disease activity, anti-citrullinated protein antibody (ACPA) status, rheumatoid factor status and C-reactive protein level. Results: dGEMRIC values were not significantly different between the MCP2 and MCP3 joint. Inter-class correlations were high (>0.92) for all three (medial, central and lateral) cartilage compartments. dGEMRIC values were significantly lower in RA patients with longer disease duration (≥3 years) and those with ACPA positivity than those with a short disease duration (<3 years)(p=0.034) or negative ACPA (p=0.0002), respectively. In contrast, no association between cartilage proteoglycan content and disease activity, C-reactive protein level and rheumatoid factor status was found. Conclusion: Decreased cartilage proteoglycan content in RA patients is associated with disease duration and ACPA positivity but not with the actual disease activity, CRP level or rheumatoid factor status. These data suggest that the cumulative burden of inflammation as well as ACPA are the determinants for cartilage damage in RA.

  17. 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.

  18. Quantitative phase-contrast MRI study of cerebrospinal fluid flow: a method for identifying patients with normal-pressure hydrocephalus.

    PubMed

    Forner Giner, J; Sanz-Requena, R; Flórez, N; Alberich-Bayarri, A; García-Martí, G; Ponz, A; Martí-Bonmatí, L

    2014-03-01

    The aim of this study is to evaluate the use of phase-contrast MR imaging to diagnose normal pressure hydrocephalus (NPH) and differentiate it from other neurological disorders with similar clinical symptoms. The study included 108 subjects, of whom 61 were healthy controls and 47, patients; in the patient group, 19 had cerebrovascular disease (CVD) and 28 had NPH. All patients underwent a phase-contrast MRI study and several CSF flow and velocity parameters were measured at the aqueduct of Sylvius. Discriminant analyses were performed to evaluate the classification capacity of both individual parameters and the combination of different parameters. Maximum diastolic velocity, mean flow, and stroke volume showed statistically significant differences that could be used to distinguish between NPH and CVD patients (P<.001). Stroke volume and mean flow showed no false positive results and successful classification rates of 86% and 79%, respectively. No other parameters or combination produced better results. Phase-contrast MR imaging is a useful tool for the early diagnosis of patients with NPH. CSF flow quantitative parameters, along with morphological features in a conventional MR study, enable us to differentiate between NPH and CVD patients. Copyright © 2012 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

  19. MRI of plants and foods.

    PubMed

    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.

  20. Cardiac MRI in patients with complex CHD following primary or secondary implantation of MRI-conditional pacemaker system.

    PubMed

    Al-Wakeel, Nadya; O h-Ici, Darach; Schmitt, Katharina R; Messroghli, Daniel R; Riesenkampff, Eugénie; Berger, Felix; Kuehne, Titus; Peters, Bjoern

    2016-02-01

    In patients with CHD, cardiac MRI is often indicated for functional and anatomical assessment. With the recent introduction of MRI-conditional pacemaker systems, cardiac MRI has become accessible for patients with pacemakers. The present clinical study aims to evaluate safety, susceptibility artefacts, and image reading of cardiac MRI in patients with CHD and MRI-conditional pacemaker systems. Material and methods CHD patients with MRI-conditional pacemaker systems and a clinical need for cardiac MRI were examined with a 1.5-T MRI system. Lead function was tested before and after MRI. Artefacts and image readings were evaluated using a four-point grading scale. A total of nine patients with CHD (mean age 34.0 years, range 19.5-53.6 years) received a total of 11 cardiac MRI examinations. Owing to clinical indications, seven patients had previously been converted from conventional to MRI-conditional pacemaker systems. All MRI examinations were completed without adverse effects. Device testing immediately after MRI and at follow-up showed no alteration of pacemaker device and lead function. Clinical questions could be addressed and answered in all patients. Cardiac MRI can be performed safely with high certainty of diagnosis in CHD patients with MRI-conditional pacemaker systems. In case of clinically indicated lead and box changing, CHD patients with non-MRI-conditional pacemaker systems should be considered for complete conversion to MRI-conditional systems.

  1. A model-constrained Monte Carlo method for blind arterial input function estimation in dynamic contrast-enhanced MRI: I. Simulations.

    PubMed

    Schabel, Matthias C; Fluckiger, Jacob U; DiBella, Edward V R

    2010-08-21

    Widespread adoption of quantitative pharmacokinetic modeling methods in conjunction with dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has led to increased recognition of the importance of obtaining accurate patient-specific arterial input function (AIF) measurements. Ideally, DCE-MRI studies use an AIF directly measured in an artery local to the tissue of interest, along with measured tissue concentration curves, to quantitatively determine pharmacokinetic parameters. However, the numerous technical and practical difficulties associated with AIF measurement have made the use of population-averaged AIF data a popular, if sub-optimal, alternative to AIF measurement. In this work, we present and characterize a new algorithm for determining the AIF solely from the measured tissue concentration curves. This Monte Carlo blind estimation (MCBE) algorithm estimates the AIF from the subsets of D concentration-time curves drawn from a larger pool of M candidate curves via nonlinear optimization, doing so for multiple (Q) subsets and statistically averaging these repeated estimates. The MCBE algorithm can be viewed as a generalization of previously published methods that employ clustering of concentration-time curves and only estimate the AIF once. Extensive computer simulations were performed over physiologically and experimentally realistic ranges of imaging and tissue parameters, and the impact of choosing different values of D and Q was investigated. We found the algorithm to be robust, computationally efficient and capable of accurately estimating the AIF even for relatively high noise levels, long sampling intervals and low diversity of tissue curves. With the incorporation of bootstrapping initialization, we further demonstrated the ability to blindly estimate AIFs that deviate substantially in shape from the population-averaged initial guess. Pharmacokinetic parameter estimates for K(trans), k(ep), v(p) and v(e) all showed relative biases and

  2. 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

  3. Calculation of susceptibility through multiple orientation sampling (COSMOS): a method for conditioning the inverse problem from measured magnetic field map to susceptibility source image in MRI.

    PubMed

    Liu, Tian; Spincemaille, Pascal; de Rochefort, Ludovic; Kressler, Bryan; Wang, Yi

    2009-01-01

    Magnetic susceptibility differs among tissues based on their contents of iron, calcium, contrast agent, and other molecular compositions. Susceptibility modifies the magnetic field detected in the MR signal phase. The determination of an arbitrary susceptibility distribution from the induced field shifts is a challenging, ill-posed inverse problem. A method called "calculation of susceptibility through multiple orientation sampling" (COSMOS) is proposed to stabilize this inverse problem. The field created by the susceptibility distribution is sampled at multiple orientations with respect to the polarization field, B(0), and the susceptibility map is reconstructed by weighted linear least squares to account for field noise and the signal void region. Numerical simulations and phantom and in vitro imaging validations demonstrated that COSMOS is a stable and precise approach to quantify a susceptibility distribution using MRI.

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

    PubMed Central

    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

  5. Arthroscopic, histological and MRI analyses of cartilage repair after a minimally invasive method of transplantation of allogeneic synovial mesenchymal stromal cells into cartilage defects in pigs

    PubMed Central

    Nakamura, Tomomasa; Sekiya, Ichiro; Muneta, Takeshi; Hatsushika, Daisuke; Horie, Masafumi; Tsuji, Kunikazu; Kawarasaki, Tatsuo; Watanabe, Atsuya; Hishikawa, Shuji; Fujimoto, Yasuhiro; Tanaka, Hozumi; Kobayashi, Eiji

    2012-01-01

    Background aims Transplantation of synovial mesenchymal stromal cells (MSCs) may induce repair of cartilage defects. We transplanted synovial MSCs into cartilage defects using a simple method and investigated its usefulness and repair process in a pig model. Methods The chondrogenic potential of the porcine MSCs was compared in vitro. Cartilage defects were created in both knees of seven pigs, and divided into MSCs treated and non-treated control knees. Synovial MSCs were injected into the defect, and the knee was kept immobilized for 10 min before wound closure. To visualize the actual delivery and adhesion of the cells, fluorescence-labeled synovial MSCs from transgenic green fluorescent protein (GFP) pig were injected into the defect in a subgroup of two pigs. In these two animals, the wounds were closed before MSCs were injected and observed for 10 min under arthroscopic control. The defects were analyzed sequentially arthroscopically, histologically and by magnetic resonance imaging (MRI) for 3 months. Results Synovial MSCs had a higher chondrogenic potential in vitro than the other MSCs examined. Arthroscopic observations showed adhesion of synovial MSCs and membrane formation on the cartilage defects before cartilage repair. Quantification analyses for arthroscopy, histology and MRI revealed a better outcome in the MSC-treated knees than in the non-treated control knees. Conclusions Leaving a synovial MSC suspension in cartilage defects for 10 min made it possible for cells to adhere in the defect in a porcine cartilage defect model. The cartilage defect was first covered with membrane, then the cartilage matrix emerged after transplantation of synovial MSCs. PMID:22309371

  6. WE-G-217A-05: Automatic Method for RF Coil Assessment in Clinical MRI: A Three-Dimensional Approach.

    PubMed

    Peng, Q

    2012-06-01

    MRI RF coil assessment is usually evaluated with region-of-interest (ROI) analysis from a single 2D phantom image. This simple approach has worked well for large volume coils or phased-array coil with large receivers, but not the high density phased-array coils characterized by 3D array arrangement of their multiple receivers. This abstract proposes a novel approach for quantitative coil assessment based on 3D imaging and 3D ROI analysis. To characterize all receivers of the coil of interest, a large uniform phantom (preferably a corresponding anthropometric phantom) and a large 3D geometric coverage fully includes the coil sensitivity volume was applied during MR imaging. After imaging, data from all receivers were used to reconstruct a composite 3D image, and to reconstruct 3D images from each individual receiver, leading to a total of N+1 3D image datasets (where N is the number of coil channels). IDL programs were developed to automatically perform ROI analysis on the composite image and on the individual receiver images. Instead of choosing one single 2D slice out of each 3D dataset, the whole 3D dataset was treated as a 3D image, and 3D ROIs were automatically generated for coil assessment. This 3D coil evaluation approach could be applied to all clinical coils including quadrature body/head coils, and phased-array coils with 2 to 32 channels. 3D sensitivity map could be generated to check receiver function visually. 3D mean SNR, max SNR, and uniformity could be obtained from composite and individual channel 3D images fully automatically. Coil/receiver performance assessment was very fast and straightforward, regardless of the number of receivers of the coil. 3D imaging in combination with 3D automatic ROI analysis is a fast, convenient, and less subjective approach for quantitative coil assessment, particularly for high density phased-array coils. © 2012 American Association of Physicists in Medicine.

  7. MRI of human hair.

    PubMed

    Mattle, Eveline; Weiger, Markus; Schmidig, Daniel; Boesiger, Peter; Fey, Michael

    2009-06-01

    Hair care for humans is a major world industry with specialised tools, chemicals and techniques. Studying the effect of hair care products has become a considerable field of research, and besides mechanical and optical testing numerous advanced analytical techniques have been employed in this area. In the present work, another means of studying the properties of hair is added by demonstrating the feasibility of magnetic resonance imaging (MRI) of the human hair. Established dedicated nuclear magnetic resonance microscopy hardware (solenoidal radiofrequency microcoils and planar field gradients) and methods (constant time imaging) were adapted to the specific needs of hair MRI. Images were produced at a spatial resolution high enough to resolve the inner structure of the hair, showing contrast between cortex and medulla. Quantitative evaluation of a scan series with different echo times provided a T*(2) value of 2.6 ms for the cortex and a water content of about 90% for hairs saturated with water. The demonstration of the feasibility of hair MRI potentially adds a new tool to the large variety of analytical methods used nowadays in the development of hair care products.

  8. Quantitative validation of a nonlinear histology-MRI coregistration method using Generalized Q-sampling Imaging in complex human cortical white matter.

    PubMed

    Gangolli, Mihika; Holleran, Laurena; Hee Kim, Joong; Stein, Thor D; Alvarez, Victor; McKee, Ann C; Brody, David L

    2017-03-29

    Advanced diffusion MRI methods have recently been proposed for detection of pathologies such as traumatic axonal injury and chronic traumatic encephalopathy which commonly affect complex cortical brain regions. However, radiological-pathological correlations in human brain tissue that detail the relationship between the multi-component diffusion signal and underlying pathology are lacking. We present a nonlinear voxel based two dimensional coregistration method that is useful for matching diffusion signals to quantitative metrics of high resolution histological images. When validated in ex vivo human cortical tissue at a 250 × 250 x 500 μm spatial resolution, the method proved robust in correlations between generalized q-sampling imaging and histologically based white matter fiber orientations, with r = 0.94 for the primary fiber direction and r = 0.88 for secondary fiber direction in each voxel. Importantly, however, the correlation was substantially worse with reduced spatial resolution or with fiber orientations derived using a diffusion tensor model. Furthermore, we have detailed a quantitative histological metric of white matter fiber integrity termed power coherence capable of distinguishing between architecturally complex but intact white matter from disrupted white matter regions. These methods may allow for more sensitive and specific radiological-pathological correlations of neurodegenerative diseases affecting complex gray and white matter.

  9. MRI Biomarkers in Oncology Clinical Trials

    PubMed Central

    Abramson, Richard G.; Arlinghaus, Lori; Dula, Adrienne; Quarles, C. Chad; Stokes, Ashley; Weis, Jared; Whisenant, Jennifer; Chekmenev, Eduard Y.; Zhukov, Igor; Williams, Jason; Yankeelov, Thomas

    2015-01-01

    Quantitative magnetic resonance imaging (MRI) techniques have the ability to quantitatively report various pathophysiological processes associated with cancer. These measures have been shown to provide complementary information to that typically obtained from standard morphologically based criteria (e.g., size) and, furthermore, have been shown to outperform sized based measures in certain applications. In this review, we discuss eight areas of quantitative MRI that are either currently employed in clinical trials, or are emerging as promising techniques for both diagnosing cancer as well as assessing—or even predicting—the response of cancer to various therapies. The currently employed methods include the response evaluation criteria in solid tumors (RECIST), dynamic susceptibility MRI (DSC-MRI), dynamic contrast enhanced MRI (DCE-MRI), and diffusion weighted imaging (DWI). The emerging techniques covered are chemical exchange saturation transfer MRI (CEST-MRI), elastography, hyperpolarized MRI, and multi-parameter MRI. After a brief introduction to each technique, we present a small number of illustrative applications before noting the existing limitations of each method and what must be done to move each to more routine clinical application. PMID:26613873

  10. How to scan polymer gels with MRI?

    NASA Astrophysics Data System (ADS)

    De Deene, Y.

    2013-06-01

    The absorbed radiation dose fixated in a polymer gel dosimeter can be read out by several methods such as magnetic resonance imaging (MRI), optical CT, X-ray CT and ultrasound with MRI being the first method that was explored. Although MRI was considered as an elegant scanning technique, readily available in most hospitals, it was later found that using a non-optimized imaging protocol may result in unacceptable deviations in the obtained dose distribution. Although most medical physicists have an understanding of the basic principles of magnetic resonance imaging (MRI), the optimization of quantitative imaging sequences and protocols is often perceived as the work of MRI experts. In this paper, we aim at providing the reader with some easy guidelines in how to obtain reliable quantitative MRI maps.

  11. A comparison of MRI tissue relaxometry and ROI methods used to determine regional brain iron concentrations in restless legs syndrome

    PubMed Central

    Moon, Hye-Jin; Chang, Yongmin; Lee, Yeong Seon; Song, Huijin; Chang, Hyuk Won; Ku, Jeonghun; Allen, Richard P; Earley, Christopher J; Cho, Yong Won

    2015-01-01

    Purpose Magnetic resonance imaging relaxometry studies differed on the relaxometry methods and their approaches to determining the regions of interest (ROIs) in restless legs syndrome (RLS) patients. These differences could account for the variable and inconsistent results found across these studies. The aim of this study was to assess the relationship between the different relaxometry methods and different ROI approaches using each of these methods on a single population of controls and RLS subjects. Methods A 3.0-T magnetic resonance imaging with the gradient-echo sampling of free induction decay and echo pulse sequence was used. The regional brain “iron concentrations” were determined using three relaxometry metrics (R2, R2*, and R2′) through two different ROI methods. The substantia nigra (SN) was the primary ROI with red nucleus, caudate, putamen, and globus pallidus as the secondary ROIs. Results Thirty-seven RLS patients and 40 controls were enrolled. The iron concentration as determined by R2 did not correlate with either of the other two methods, while R2* and R2′ showed strong correlations, particularly for the substantia nigra and red nucleus. In the fixed-shape ROI method, the RLS group showed a lower iron index compared to the control group in the substantia nigra and several other regions. With the semi-automated ROI method, however, only the red nucleus showed a significant difference between the two groups. Conclusion Both the relaxometry and ROI determination methods significantly influenced the outcome of studies that used these methods to estimate regional brain iron concentrations. PMID:26257527

  12. 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

  13. [Recent advances in newborn MRI].

    PubMed

    Morel, B; Hornoy, P; Husson, B; Bloch, I; Adamsbaum, C

    2014-07-01

    The accurate morphological exploration of the brain is a major challenge in neonatology that advances in magnetic resonance imaging (MRI) can now provide. MRI is the gold standard if an hypoxic ischemic pathology is suspected in a full term neonate. In prematures, the specific role of MRI remains to be defined, secondary to US in any case. We present a state of the art of hardware and software technical developments in MRI. The increase in magnetic field strength (3 tesla) and the emergence of new MRI sequences provide access to new information. They both have positive and negative consequences on the daily clinical data acquisition use. The semiology of brain imaging in full term newborns and prematures is more extensive and complex and thereby more difficult to interpret. The segmentation of different brain structures in the newborn, even very premature, is now available. It is now possible to dissociate the cortex and basal ganglia from the cerebral white matter, to calculate the volume of anatomical structures, which improves the morphometric quantification and the understanding of the normal and abnormal brain development. MRI is a powerful tool to analyze the neonatal brain. The relevance of the diagnostic contribution requires an adaptation of the parameters of the sequences to acquire and of the image processing methods.

  14. 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.

  15. 3D Segmentation with an application of level set-method using MRI volumes for image guided surgery.

    PubMed

    Bosnjak, A; Montilla, G; Villegas, R; Jara, I

    2007-01-01

    This paper proposes an innovation in the application for image guided surgery using a comparative study of three different method of segmentation. This segmentation method is faster than the manual segmentation of images, with the advantage that it allows to use the same patient as anatomical reference, which has more precision than a generic atlas. This new methodology for 3D information extraction is based on a processing chain structured of the following modules: 1) 3D Filtering: the purpose is to preserve the contours of the structures and to smooth the homogeneous areas; several filters were tested and finally an anisotropic diffusion filter was used. 2) 3D Segmentation. This module compares three different methods: Region growing Algorithm, Cubic spline hand assisted, and Level Set Method. It then proposes a Level Set-based on the front propagation method that allows the making of the reconstruction of the internal walls of the anatomical structures of the brain. 3) 3D visualization. The new contribution of this work consists on the visualization of the segmented model and its use in the pre-surgery planning.

  16. Technical aspects and evaluation methodology for the application of two automated brain MRI tumor segmentation methods in radiation therapy planning.

    PubMed

    Beyer, Gloria P; Velthuizen, Robert P; Murtagh, F Reed; Pearlman, James L

    2006-11-01

    The purpose of this study was to design the steps necessary to create a tumor volume outline from the results of two automated multispectral magnetic resonance imaging segmentation methods and integrate these contours into radiation therapy treatment planning. Algorithms were developed to create a closed, smooth contour that encompassed the tumor pixels resulting from two automated segmentation methods: k-nearest neighbors and knowledge guided. These included an automatic three-dimensional (3D) expansion of the results to compensate for their undersegmentation and match the extended contouring technique used in practice by radiation oncologists. Each resulting radiation treatment plan generated from the automated segmentation and from the outlining by two radiation oncologists for 11 brain tumor patients was compared against the volume and treatment plan from an expert radiation oncologist who served as the control. As part of this analysis, a quantitative and qualitative evaluation mechanism was developed to aid in this comparison. It was found that the expert physician reference volume was irradiated within the same level of conformity when using the plans generated from the contours of the segmentation methods. In addition, any uncertainty in the identification of the actual gross tumor volume by the segmentation methods, as identified by previous research into this area, had small effects when used to generate 3D radiation therapy treatment planning due to the averaging process in the generation of margins used in defining a planning target volume.

  17. 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.

  18. 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.

  19. 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

  20. An active contour-based atlas registration model applied to automatic subthalamic nucleus targeting on MRI: method and validation.

    PubMed

    Duay, Valérie; Bresson, Xavier; Castro, Javier Sanchez; Pollo, Claudio; Cuadra, Meritxell Bach; Thiran, Jean-Philippe

    2008-01-01

    This paper presents a new non parametric atlas registration framework, derived from the optical flow model and the active contour theory, applied to automatic subthalamic nucleus (STN) targeting in deep brain stimulation (DBS) surgery. In a previous work, we demonstrated that the STN position can be predicted based on the position of surrounding visible structures, namely the lateral and third ventricles. A STN targeting process can thus be obtained by registering these structures of interest between a brain atlas and the patient image. Here we aim to improve the results of the state of the art targeting methods and at the same time to reduce the computational time. Our simultaneous segmentation and registration model shows mean STN localization errors statistically similar to the most performing registration algorithms tested so far and to the targeting expert's variability. Moreover, the computational time of our registration method is much lower, which is a worthwhile improvement from a clinical point of view.

  1. A novel phase-unwrapping method based on pixel clustering and local surface fitting with application to Dixon water-fat MRI.

    PubMed

    Cheng, Junying; Mei, Yingjie; Liu, Biaoshui; Guan, Jijing; Liu, Xiaoyun; Wu, Ed X; Feng, Qianjin; Chen, Wufan; Feng, Yanqiu

    2017-03-01

    To develop and evaluate a novel 2D phase-unwrapping method that works robustly in the presence of severe noise, rapid phase changes, and disconnected regions. The MR phase map usually varies rapidly in regions adjacent to wraps. In contrast, the phasors can vary slowly, especially in regions distant from tissue boundaries. Based on this observation, this paper develops a phase-unwrapping method by using a pixel clustering and local surface fitting (CLOSE) approach to exploit different local variation characteristics between the phase and phasor data. The CLOSE approach classifies pixels into easy-to-unwrap blocks and difficult-to-unwrap residual pixels first, and then sequentially performs intrablock, interblock, and residual-pixel phase unwrapping by a region-growing surface-fitting method. The CLOSE method was evaluated on simulation and in vivo water-fat Dixon data, and was compared with phase region expanding labeler for unwrapping discrete estimates (PRELUDE). In the simulation experiment, the mean error ratio by CLOSE was less than 1.50%, even in areas with signal-to-noise ratio equal to 0.5, phase changes larger than π, and disconnected regions. For 350 in vivo knee and ankle images, the water-fat swap ratio of CLOSE was 4.29%, whereas that of PRELUDE was 25.71%. The CLOSE approach can correctly unwrap phase with high robustness, and benefit MRI applications that require phase unwrapping. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  2. The method of educational assessment affects children's neural processing and performance: behavioural and fMRI Evidence

    NASA Astrophysics Data System (ADS)

    Howard, Steven J.; Burianová, Hana; Calleia, Alysha; Fynes-Clinton, Samuel; Kervin, Lisa; Bokosmaty, Sahar

    2017-08-01

    Standardised educational assessments are now widespread, yet their development has given comparatively more consideration to what to assess than how to optimally assess students' competencies. Existing evidence from behavioural studies with children and neuroscience studies with adults suggest that the method of assessment may affect neural processing and performance, but current evidence remains limited. To investigate the impact of assessment methods on neural processing and performance in young children, we used functional magnetic resonance imaging to identify and quantify the neural correlates during performance across a range of current approaches to standardised spelling assessment. Results indicated that children's test performance declined as the cognitive load of assessment method increased. Activation of neural nodes associated with working memory further suggests that this performance decline may be a consequence of a higher cognitive load, rather than the complexity of the content. These findings provide insights into principles of assessment (re)design, to ensure assessment results are an accurate reflection of students' true levels of competency.

  3. Cyclic generalized projection MRI.

    PubMed

    Sarty, Gordon E

    2015-04-01

    Progress in the development of portable MRI hinges on the ability to use lightweight magnets that have non-uniform magnetic fields. An image encoding method and mathematical procedure for recovering the image from the NMR signal from non-uniform magnets with closed isomagnetic contours is given. Individual frequencies in an NMR signal from an object in a non-uniform magnetic field give rise to integrals of the object along contours of constant magnetic field: generalized projections. With closed isomagnetic field contours a simple, cyclic, direct reconstruction of the image from the generalized projections is possible when the magnet and RF transmit coil are held fixed relative to the imaged object while the RF receive coil moves. Numerical simulations, using the Shepp and Logan mathematical phantom, were completed to show that the mathematical method works and to illustrate numerical limitations. The method is numerically verified and exact reconstruction demonstrated for discrete mathematical image phantoms. Correct knowledge of the RF receive field is necessary or severe image distortions will result. The cyclic mathematical reconstruction method presented here will be useful for portable MRI schemes that use non-uniform magnets with closed isomagnetic contours along with mechanically or electronically moving the RF receive coils.

  4. 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.

  5. Repeatability of a dual gradient-recalled echo MRI method for monitoring post-isometric contraction blood volume and oxygenation changes.

    PubMed

    Sanchez, O A; Louie, E A; Copenhaver, E A; Damon, B M

    2009-08-01

    The purpose of this study was to assess the repeatability of a dual gradient-recalled echo (GRE) muscle functional MRI technique. On 2 days, subjects (n = 8) performed 10 s isometric dorsiflexion contractions under conditions of: (1) maximal voluntary contraction (MVC), (2) 50% MVC (50% MVC), or (3) 50% MVC with concurrent proximal arterial cuff occlusion (50% MVC(cuff)). Functional MRI data were acquired using single-slice dual GRE (TR/TE = 1000/6, 46 ms)-echo planar imaging for 20 s before, during, and for 180 s after each contraction. The mean signal intensity (SI) time courses at each TE (SI(6) and SI(46), reflecting variations in blood volume and %HbO(2), respectively) from the tibialis anterior (TA) and extensor digitorum longus (EDL) muscles were characterized with the post-contraction change in SI and the time-to-peak SI (DeltaSI and TTP, respectively). DeltaSI(6) following an MVC was 36% higher than that obtained after a 50% MVC (p = 0.048). For DeltaSI(6), the highest intraclass correlation coefficients (ICCs) were observed for the TA muscle in the 50% MVC and MVC conditions, with values of 0.83 (p = 0.01) and 0.88 (p = 0.005), respectively. Bland-Altman plots revealed repeatability coefficients (RCs) for the 50% MVC and MVC conditions in the TA muscle of 1.9 and 1.4, respectively. The most repeatable measures for DeltaSI(46) were obtained for the 50% MVC and MVC conditions in the EDL muscle (p = 0.01 and p = 0.04, respectively). Bland-Altman plots revealed RC's for 50% MVC and MVC conditions in the EDL muscle of 3.9 and 5.7, respectively. DeltaSI(6) and DeltaSI(46) increased as a function of the contraction intensity. The repeatability of the method depends on the muscle and contraction condition being evaluated, and in general, is higher following an MVC. 2009 John Wiley & Sons, Ltd.

  6. Repeatability of a Dual Gradient-Recalled Echo MRI Method for Monitoring Post-Isometric Contraction Blood Volume and Oxygenation Changes

    PubMed Central

    Sanchez, O.A.; Louie, E.A.; Copenhaver, E.A.; Damon, B.M.

    2015-01-01

    The purpose of this study was to assess the repeatability of a dual gradient-recalled echo (GRE) muscle functional MRI technique. On two days, subjects (n=8) performed 10 s isometric dorsiflexion contractions under conditions of: 1) maximal voluntary contraction (MVC), 2) 50% MVC (50%MVC) or 3) 50% MVC with concurrent proximal arterial cuff occlusion (50%MVCcuff). Functional MRI data were acquired using single-slice dual GRE (TR/TE=1000/6, 46 ms) EPI for 20 seconds before, during, and for 180 seconds after each contraction. The mean signal intensity (SI) time courses at each TE (SI6 and SI46, reflecting variations in blood volume and %HbO2, respectively) from the tibialis anterior (TA) and extensor digitorum (EDL) muscles were characterized with the post-contraction change in SI and the time to peak SI (ΔSI and TTP, respectively). ΔSI6 and ΔSI46 were 36% and 31% higher following an MVC than after a 50%MVC (p = 0.05 and p = 0.07 respectively). For ΔSI6 the highest intraclass correlation coefficients (ICC) were observed for the TA muscle at the 50%MVC and MVC condition, with values of 0.83 (p = 0.01) and 0.88 (p = 0.005), respectively. Bland-Altman plots revealed repeatability coefficients (RC) for the 50%MVC and MVC conditions in the TA muscle of 1.9 and 1.4, respectively. The most repeatable measures for ΔSI46 were obtained for the 50%MVC and MVC conditions in the EDL muscle (p = 0.01 and p = 0.04, respectively). Bland-Altman plots revealed RC’s for 50%MVC and MVC conditions in the EDL muscle of 3.9 and 5.7, respectively. ΔSI6 and ΔSI46 increased as a function of contraction intensity. The repeatability of the method depends on the muscle and contraction condition being evaluated, and in general, is higher following an MVC. PMID:19382156

  7. 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

  8. [Anatomic variants of Meckel's cave on MRI].

    PubMed

    Benoudiba, F; Hadj-Rabia, M; Iffenecker, C; Fuerxer, F; Bekkali, F; Francke, J P; Doyon, D

    1998-10-01

    Magnetic resonance imaging (MRI) gives an accurate analysis of Meckel's cave variability. Images were acquired in 50 patients with several sections for anatomical comparison. Using several sections, MRI is a suitable method for better analysis of the trigeminal cistern. The most frequent findings are symmetrical trigeminal cisterns. Expansion of Meckel's cave or its disappearance has pathological significance.

  9. Noise cancellation signal processing method and computer system for improved real-time electrocardiogram artifact correction during MRI data acquisition.

    PubMed

    Odille, Freddy; Pasquier, Cédric; Abächerli, Roger; Vuissoz, Pierre-André; Zientara, Gary P; Felblinger, Jacques

    2007-04-01

    A system was developed for real-time electrocardiogram (ECG) analysis and artifact correction during magnetic resonance (MR) scanning, to improve patient monitoring and triggering of MR data acquisitions. Based on the assumption that artifact production by magnetic field gradient switching represents a linear time invariant process, a noise cancellation (NC) method is applied to ECG artifact linear prediction. This linear prediction is performed using a digital finite impulse response (FIR) matrix, that is computed employing ECG and gradient waveforms recorded during a training scan. The FIR filters are used during further scanning to predict artifacts by convolution of the gradient waveforms. Subtracting the artifacts from the raw ECG signal produces the correction with minimal delay. Validation of the system was performed both off-line, using prerecorded signals, and under actual examination conditions. The method is implemented using a specially designed Signal Analyzer and Event Controller (SAEC) computer and electronics. Real-time operation was demonstrated at 1 kHz with a delay of only 1 ms introduced by the processing. The system opens the possibility of automatic monitoring algorithms for electrophysiological signals in the MR environment.

  10. A novel method to decrease electric field and SAR using an external high dielectric sleeve at 3 T head MRI: numerical and experimental results.

    PubMed

    Park, Bu S; Rajan, Sunder S; Guag, Joshua W; Angelone, Leonardo M

    2015-04-01

    Materials with high dielectric constant (HDC) have been used in high field MRI to decrease specific absorption rate (SAR), increase magnetic field intensity, and increase signal-to-noise ratio. In previous studies, the HDC materials were placed inside the RF coil decreasing the space available. This study describes an alternative approach that considers an HDC-based sleeve placed outside the RF coil. The effects of an HDC on the electromagnetic (EM) field were studied using numerical simulations with a coil unloaded and loaded with a human head model. In addition, experimental EM measurements at 128 MHz were performed inside a custom-made head coil, fitted with a distilled water sleeve. The numerical simulations showed up to 40% decrease in maximum 10 g-avg. SAR on the surface of the head model with an HDC material of barium titanate. Experimental measurements also showed up to 20% decrease of maximum electric field using an HDC material of distilled water. The proposed method can be incorporated in the design of high field transmit RF coils.

  11. Maximum entropy spherical deconvolution for diffusion MRI.

    PubMed

    Alexander, Daniel C

    2005-01-01

    This paper proposes a maximum entropy method for spherical deconvolution. Spherical deconvolution arises in various inverse problems. This paper uses the method to reconstruct the distribution of microstructural fibre orientations from diffusion MRI measurements. Analysis shows that the PASMRI algorithm, one of the most accurate diffusion MRI reconstruction algorithms in the literature, is a special case of the maximum entropy spherical deconvolution. Experiments compare the new method to linear spherical deconvolution, used previously in diffusion MRI, and to the PASMRI algorithm. The new method compares favourably both in simulation and on standard brain-scan data.

  12. A comparison of three clustering methods for finding subgroups in MRI, SMS or clinical data: SPSS TwoStep Cluster analysis, Latent Gold and SNOB.

    PubMed

    Kent, Peter; Jensen, Rikke K; Kongsted, Alice

    2014-10-02

    There are various methodological approaches to identifying clinically important subgroups and one method is to identify clusters of characteristics that differentiate people in cross-sectional and/or longitudinal data using Cluster Analysis (CA) or Latent Class Analysis (LCA). There is a scarcity of head-to-head comparisons that can inform the choice of which clustering method might be suitable for particular clinical datasets and research questions. Therefore, the aim of this study was to perform a head-to-head comparison of three commonly available methods (SPSS TwoStep CA, Latent Gold LCA and SNOB LCA). The performance of these three methods was compared: (i) quantitatively using the number of subgroups detected, the classification probability of individuals into subgroups, the reproducibility of results, and (ii) qualitatively using subjective judgments about each program's ease of use and interpretability of the presentation of results.We analysed five real datasets of varying complexity in a secondary analysis of data from other research projects. Three datasets contained only MRI findings (n = 2,060 to 20,810 vertebral disc levels), one dataset contained only pain intensity data collected for 52 weeks by text (SMS) messaging (n = 1,121 people), and the last dataset contained a range of clinical variables measured in low back pain patients (n = 543 people). Four artificial datasets (n = 1,000 each) containing subgroups of varying complexity were also analysed testing the ability of these clustering methods to detect subgroups and correctly classify individuals when subgroup membership was known. The results from the real clinical datasets indicated that the number of subgroups detected varied, the certainty of classifying individuals into those subgroups varied, the findings had perfect reproducibility, some programs were easier to use and the interpretability of the presentation of their findings also varied. The results from the artificial datasets

  13. MRI in guiding and assessing intramyocardial therapy.

    PubMed

    Saeed, M; Saloner, D; Weber, O; Martin, A; Henk, C; Higgins, C

    2005-05-01

    Cardiovascular intervention, using MRI guidance, is challenging for clinical applications. Real-time imaging sequences with high spatial resolution are needed for monitoring intramyocardial delivery of drug, gene, or stem cell therapies. New generation MR scanners make local intramyocardial and vascular wall therapies feasible. Contrast-enhanced MRI is used for assessing myocardial ischemia, infarction, and scar tissue. Active (microcoils) and passive (T1 and T2* mechanisms) tracking methods have been used for visualization of endovascular catheters. Safety issues related to potential heating of endovascular devices is still a major obstacle for MRI-guided interventions. Fabrication of MRI-compatible interventional devices is limited. Noninvasive imaging strategies will be critical in defining spatial and temporal characteristics of angiogenesis and myocardial repair as well as in assessing the efficacy of new therapies in ischemic heart disease. MRI contrast media improve the capability of MRI by delineating the target and vascular tree. Labeling stem cells enables MRI to trace distribution, differentiation, and survival in myocardium and vascular wall. In the long term, MRI in guiding and assessing intramyocardial therapy may circumvent the limitations of peripherally administered cell therapy, X-ray angiography, and nuclear imaging. MRI represents a highly attractive discipline whose systematic development will foster the implementation of new cardiac and vascular therapies.

  14. MRI Safety during Pregnancy

    MedlinePlus

    ... 20 to 40 minutes. top of page Contrast material For some MRI exams, a contrast material called gadolinium will need to be injected into a vein in the arm. While contrast material sometimes improves the MRI images, during pregnancy the ...

  15. Sinus MRI scan

    MedlinePlus

    ... sinuses. The test is noninvasive. MRI uses powerful magnets and radio waves instead of radiation. Signals from ... in the eyes. Because the MRI contains a magnet, metal-containing objects such as pens, pocketknives, and ...

  16. Arm MRI scan

    MedlinePlus

    ... arm MRI (magnetic resonance imaging) scan uses strong magnets to create pictures of the upper and lower ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  17. Magnetic Resonance Imaging (MRI)

    MedlinePlus

    ... an image. Repeated exposure can be harmful.An MRI scan takes longer to perform (30 to 60 minutes, ... a treatment plan.Depending on your symptoms, an MRI will scan a specific portion of your body to diagnose: ...

  18. MRI Safety during Pregnancy

    MedlinePlus

    ... 20 to 40 minutes. top of page Contrast material For some MRI exams, a contrast material called gadolinium will need to be injected into a vein in the arm. While contrast material sometimes improves the MRI images, during pregnancy the ...

  19. On the construction of a ground truth framework for evaluating voxel-based diffusion tensor MRI analysis methods.

    PubMed

    Van Hecke, Wim; Sijbers, Jan; De Backer, Steve; Poot, Dirk; Parizel, Paul M; Leemans, Alexander

    2009-07-01

    Although many studies are starting to use voxel-based analysis (VBA) methods to compare diffusion tensor images between healthy and diseased subjects, it has been demonstrated that VBA results depend heavily on parameter settings and implementation strategies, such as the applied coregistration technique, smoothing kernel width, statistical analysis, etc. In order to investigate the effect of different parameter settings and implementations on the accuracy and precision of the VBA results quantitatively, ground truth knowledge regarding the underlying microstructural alterations is required. To address the lack of such a gold standard, simulated diffusion tensor data sets are developed, which can model an array of anomalies in the diffusion properties of a predefined location. These data sets can be employed to evaluate the numerous parameters that characterize the pipeline of a VBA algorithm and to compare the accuracy, precision, and reproducibility of different post-processing approaches quantitatively. We are convinced that the use of these simulated data sets can improve the understanding of how different diffusion tensor image post-processing techniques affect the outcome of VBA. In turn, this may possibly lead to a more standardized and reliable evaluation of diffusion tensor data sets of large study groups with a wide range of white matter altering pathologies. The simulated DTI data sets will be made available online (http://www.dti.ua.ac.be).

  20. Comparing different analysis methods for quantifying the MRI amide proton transfer (APT) effect in hyperacute stroke patients.

    PubMed

    Tee, Y K; Harston, G W J; Blockley, N; Okell, Thomas W; Levman, J; Sheerin, F; Cellerini, M; Jezzard, P; Kennedy, J; Payne, S J; Chappell, M A

    2014-09-01

    Amide proton transfer (APT) imaging is a pH mapping method based on the chemical exchange saturation transfer phenomenon that has potential for penumbra identification following stroke. The majority of the literature thus far has focused on generating pH-weighted contrast using magnetization transfer ratio asymmetry analysis instead of quantitative pH mapping. In this study, the widely used asymmetry analysis and a model-based analysis were both assessed on APT data collected from healthy subjects (n = 2) and hyperacute stroke patients (n = 6, median imaging time after onset = 2 hours 59 minutes). It was found that the model-based approach was able to quantify the APT effect with the lowest variation in grey and white matter (≤ 13.8 %) and the smallest average contrast between these two tissue types (3.48 %) in the healthy volunteers. The model-based approach also performed quantitatively better than the other measures in the hyperacute stroke patient APT data, where the quantified APT effect in the infarct core was consistently lower than in the contralateral normal appearing tissue for all the patients recruited, with the group average of the quantified APT effect being 1.5 ± 0.3 % (infarct core) and 1.9 ± 0.4 % (contralateral). Based on the fitted parameters from the model-based analysis and a previously published pH and amide proton exchange rate relationship, quantitative pH maps for hyperacute stroke patients were generated, for the first time, using APT imaging.

  1. Perfusion MRI: The Five Most Frequently Asked Clinical Questions

    PubMed Central

    Essig, Marco; Nguyen, Thanh Binh; Shiroishi, Mark S.; Saake, Marc; Provenzale, James M.; Enterline, David S.; Anzalone, Nicoletta; Dörfler, Arnd; Rovira, Àlex; Wintermark, Max; Law, Meng

    2013-01-01

    OBJECTIVE This article addresses questions that radiologists frequently ask when planning, performing, processing, and interpreting MRI perfusion studies in CNS imaging. CONCLUSION Perfusion MRI is a promising tool in assessing stroke, brain tumors, and neurodegenerative diseases. Most of the impediments that have limited the use of perfusion MRI can be overcome to allow integration of these methods into modern neuroimaging protocols. PMID:23971482

  2. [MRI of the pineal gland].

    PubMed

    Langevad, Line; Madsen, Camilla Gøbel; Siebner, Hartwig; Garde, Ellen

    2014-11-10

    The pineal gland (CP) is located centrally in the brain and produces melatonin. Cysts and concrements are frequent findings on MRI but their significance is still unclear. The visualization of CP is difficult due to its location and surrounding structures and so far, no standardized method exists. New studies suggest a correlation between CP-morphology and melatonin secretion as well as a connection between melatonin, disturbed circadian rhythm, and the development of cancer and cardiovascular diseases, underlining the need for a standardized approach to CP on MRI.

  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. Cardiovascular MRI in thalassemia major.

    PubMed

    Wood, John C; Noetzli, Leila

    2010-08-01

    MRI assessment of myocardial iron and function has revolutionized the treatment of thalassemia major patients. While knowledge of somatic iron stores is vital for iron chelation management, it does not adequately monitor cardiac risk. MRI monitoring of cardiac T2* allows preclinical recognition of myocardial iron, stratifies prospective cardiac risk, and tracks response to modifications in iron chelation therapy. MRI assessment of cardiac function complements T2* measurements by offering highly accurate and reproducible assessments of ventricular function. This manuscript describes the historical context of cardiac toxicity in thalassemia major, the introduction of cardiac T2* methods in the early 2000s, and the impact of these techniques on patient care as well as our fundamental understanding of iron cardiomyopathy. Technical details regarding T2* image acquisition and postprocessing are also discussed. As barriers to widespread implementation are being overcome, cardiac T2* is rapidly transitioning from a clinical research tool to the standard of care.

  5. Osteitis and synovitis, but not bone erosion, is associated with proteoglycan loss and microstructure damage in the cartilage of patients with rheumatoid arthritis.

    PubMed

    Herz, Barbara; Albrecht, Andreas; Englbrecht, Matthias; Welsch, Götz H; Uder, Michael; Renner, Nina; Schlechtweg, Philipp; Paul, Dominik; Lauer, Lars; Engelke, Klaus; Janka, Rolf; Rech, Jürgen; Schett, Georg; Finzel, Stephanie

    2014-06-01

    To investigate the relation between anatomic changes of the synovium, the bone, the bone marrow and the cartilage to biochemical properties of the cartilage in patients with rheumatoid arthritis (RA). 33 patients with RA received 3-T MRI scans of the metacarpophalangeal joints. Two independent methods, (A) the delayed gadolinium enhanced MRI of the cartilage (dGEMRIC, T2-mapping), which was used to assess the biochemical properties of the cartilage; (B) synovitis, osteitis and bone erosions were quantified according to the RA MRI scoring (RAMRIS) method and cartilage thickness (CT), interbone joint space (IBJS, distance between proximal and distal bone surface) and intercartilage joint space (ICJS, distance between proximal and distal cartilage surface) were measured. Biochemical changes of the cartilage, corresponding to low dGEMRIC and high T2 values, were more likely to be seen in joints with decreased IBJS and ICJS as well as decreased CT. For instance, dGEMRIC was directly correlated to the IBJS (p=0.001) and ICJS (p=0.001), whereas T2 mapping was inversely correlated to IBJS and ICJS (both p=0.017). Moreover, the degree of osteitis, and to some extent synovitis, was correlated to biochemical cartilage changes as measured by dGEMRIC (p=0.003) or the T2 mapping (p=0.013). By contrast, bone erosions did not correlate to the degree of biochemical cartilage changes. These data support the concept that synovitis and osteitis may be two main triggers for cartilage damage. Thus, the actual inflammatory state of a joint, but not so much the degree of bone erosion, appears to influence cartilage properties in RA.

  6. 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

  7. Evaluation of MRI-TRUS fusion versus cognitive registration accuracy for MRI-targeted, TRUS-guided prostate biopsy.

    PubMed

    Cool, Derek W; Zhang, Xuli; Romagnoli, Cesare; Izawa, Jonathan I; Romano, Walter M; Fenster, Aaron

    2015-01-01

    The purpose of this article is to compare transrectal ultrasound (TRUS) biopsy accuracies of operators with different levels of prostate MRI experience using cognitive registration versus MRI-TRUS fusion to assess the preferred method of TRUS prostate biopsy for MRI-identified lesions. SUBJECTS AND METHODS; One hundred patients from a prospective prostate MRI-TRUS fusion biopsy study were reviewed to identify all patients with clinically significant prostate adenocarcinoma (PCA) detected on MRI-targeted biopsy. Twenty-five PCA tumors were incorporated into a validated TRUS prostate biopsy simulator. Three prostate biopsy experts, each with different levels of experience in prostate MRI and MRI-TRUS fusion biopsy, performed a total of 225 simulated targeted biopsies on the MRI lesions as well as regional biopsy targets. Simulated biopsies performed using cognitive registration with 2D TRUS and 3D TRUS were compared with biopsies performed under MRI-TRUS fusion. Two-dimensional and 3D TRUS sampled only 48% and 45% of clinically significant PCA MRI lesions, respectively, compared with 100% with MRI-TRUS fusion. Lesion sampling accuracy did not statistically significantly vary according to operator experience or tumor volume. MRI-TRUS fusion-naïve operators showed consistent errors in targeting of the apex, midgland, and anterior targets, suggesting that there is biased error in cognitive registration. The MRI-TRUS fusion expert correctly targeted the prostate apex; however, his midgland and anterior mistargeting was similar to that of the less-experienced operators. MRI-targeted TRUS-guided prostate biopsy using cognitive registration appears to be inferior to MRI-TRUS fusion, with fewer than 50% of clinically significant PCA lesions successfully sampled. No statistically significant difference in biopsy accuracy was seen according to operator experience with prostate MRI or MRI-TRUS fusion.

  8. 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.

  9. 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

  10. WE-B-BRD-00: MRI for Radiation Oncology

    SciTech Connect

    2015-06-15

    The use of MRI in radiation therapy is rapidly increasing. Applications vary from the MRI simulator, to the MRI fused with CT, and to the integrated MRI+RT system. Compared with the standard MRI QA, a broader scope of QA features has to be defined in order to maximize the benefits of using MRI in radiation therapy. These QA features include geometric fidelity, image registration, motion management, cross-system alignment, and hardware interference. Advanced MRI techniques require a specific type of QA, as they are being widely used in radiation therapy planning, dose calculations, post-implant dosimetry, and prognoses. A vigorous and adaptive QA program is crucial to defining the responsibility of the entire radiation therapy group and detecting deviations from the performance of high-quality treatment. As a drastic departure from CT simulation, MRI simulation requires changes in the work flow of treatment planning and image guidance. MRI guided radiotherapy platforms are being developed and commercialized to take the advantage of the advance in knowledge, technology and clinical experience. This symposium will from an educational perspective discuss the scope and specific issues related to MRI guided radiotherapy. Learning Objectives: Understand the difference between a standard and a radiotherapy-specific MRI QA program. Understand the effects of MRI artifacts (geometric distortion and motion) on radiotherapy. Understand advanced MRI techniques (ultrashort echo, fast MRI including dynamic MRI and 4DMRI, diffusion, perfusion, and MRS) and related QA. Understand the methods to prepare MRI for treatment planning (electron density assignment, multimodality image registration, segmentation and motion management). Current status of MRI guided treatment platforms. Dr. Jihong Wang has a research grant with Elekta-MRL project. Dr. Ke Sheng receives research grants from Varian Medical systems.

  11. Hyperpolarization MRI

    PubMed Central

    Miloushev, Vesselin Z.; Keshari, Kayvan R.; Holodny, Andrei I.

    2016-01-01

    Hyperpolarization is a novel technology that can dramatically increase signal to noise in magnetic resonance. The method is being applied to small injectable endogenous molecules, which can be used to monitor transient in vivo metabolic events, in real time. The emergence of hyperpolarized 13C-labeled probes, specifically 13C pyruvate, has enabled monitoring of core cellular metabolic events. Neuro-oncological applications have been demonstrated in preclinical models. Many more applications of this technology are envisioned, with transformative potential in magnetic resonance imaging. PMID:26848559

  12. Validation of Sodium MRI of Intervertebral Disc

    PubMed Central

    Wang, Chenyang; McArdle, Erin; Fenty, Matthew; Witschey, Walter; Elliott, Mark; Sochor, Matthew; Reddy, Ravinder; Borthakur, Arijitt

    2009-01-01

    Study Design This study demonstrated the diagnostic potential of sodium MRI for non-invasive quantification of PG in the intervertebral discs. Objective To determine the existence of a linear correlation between intervertebral disc [Na] measured from sodium MRI and [PG] measurement from DMMB assay. Summary of Background Data Previous studies have shown the possibility of quantifying [Na] in vivo using sodium MRI, however none has shown a direct linear correlation between [Na] measured from sodium MRI and [PG]. Methods 3D sodium MRI images of bovine discs were acquired and converted into [Na] maps. Samples were systematically removed from the discs for DMMB assay. The removal locations were photographically recorded and applied to the [Na] maps to extract the [Na] measurements for comparison. In vivo sodium MRI scans were also carried out on a pair of symptomatic and asymptomatic subjects. Results The linear regression fit of [Na] versus [PG] data yielded a significant linear correlation coefficient of 0.71. The in vivo sodium MRI image of the symptomatic subject showed significant [Na] decrease when compared to that of the asymptomatic subject. Conclusion Sodium MRI's specificity for PG in the intervertebral discs makes it a promising diagnostic tool for the earlier phase of disc degeneration. PMID:20147881

  13. Functional MRI for Surgery of Gliomas.

    PubMed

    Castellano, Antonella; Cirillo, Sara; Bello, Lorenzo; Riva, Marco; Falini, Andrea

    2017-08-23

    Advanced neuroimaging techniques such as functional MRI (fMRI) and diffusion MR tractography have been increasingly used at every stage of the surgical management of brain gliomas, as a means to improve tumor resection while preserving brain functions. This review provides an overview of the last advancements in the field of functional MRI techniques, with a particular focus on their current clinical use and reliability in the preoperative and intraoperative setting, as well as their future perspectives for personalized multimodal management of patients with gliomas. fMRI and diffusion MR tractography give relevant insights on the anatomo-functional organization of eloquent cortical areas and subcortical connections near or inside a tumor. Task-based fMRI and diffusion tensor imaging (DTI) tractography have proven to be valid and highly sensitive tools for localizing the distinct eloquent cortical and subcortical areas before surgery in glioma patients; they also show good accuracy when compared with intraoperative stimulation mapping data. Resting-state fMRI functional connectivity as well as new advanced HARDI (high angular resolution diffusion imaging) tractography methods are improving and reshaping the role of functional MRI for surgery of gliomas, with potential benefit for personalized treatment strategies. Noninvasive functional MRI techniques may offer the opportunity to perform a multimodal assessment in brain tumors, to be integrated with intraoperative mapping and clinical data for improving surgical management and oncological and functional outcome in patients affected by gliomas.

  14. Recent Advances in MRI of Articular Cartilage

    PubMed Central

    Gold, Garry E.; Chen, Christina A.; Koo, Seungbum; Hargreaves, Brian A.; Bangerter, Neal K.

    2010-01-01

    OBJECTIVE MRI is the most accurate noninvasive method available to diagnose disorders of articular cartilage. Conventional 2D and 3D approaches show changes in cartilage morphology. Faster 3D imaging methods with isotropic resolution can be reformatted into arbitrary planes for improved detection and visualization of pathology. Unique contrast mechanisms allow us to probe cartilage physiology and detect changes in cartilage macromolecules. CONCLUSION MRI has great promise as a noninvasive comprehensive tool for cartilage evaluation. PMID:19696274

  15. Vessel wall characterization using quantitative MRI: what's in a number?

    PubMed

    Coolen, Bram F; Calcagno, Claudia; van Ooij, Pim; Fayad, Zahi A; Strijkers, Gustav J; Nederveen, Aart J

    2017-08-14

    The past decade has witnessed the rapid development of new MRI technology for vessel wall imaging. Today, with advances in MRI hardware and pulse sequences, quantitative MRI of the vessel wall represents a real alternative to conventional qualitative imaging, which is hindered by significant intra- and inter-observer variability. Quantitative MRI can measure several important morphological and functional characteristics of the vessel wall. This review provides a detailed introduction to novel quantitative MRI methods for measuring vessel wall dimensions, plaque composition and permeability, endothelial shear stress and wall stiffness. Together, these methods show the versatility of non-invasive quantitative MRI for probing vascular disease at several stages. These quantitative MRI biomarkers can play an important role in the context of both treatment response monitoring and risk prediction. Given the rapid developments in scan acceleration techniques and novel image reconstruction, we foresee the possibility of integrating the acquisition of multiple quantitative vessel wall parameters within a single scan session.

  16. [Temporomandibular joint: MRI diagnostics].

    PubMed

    Kress, B; Schmitter, M

    2005-09-01

    MRI of the temporomandibular joint (TMJ) requires 1.5 T. The radiologist must be familiar with the anatomy and pathology of the TMJ. This review gives a description of MRI protocols for the TMJ, and MRI anatomy and pathology of the TMJ (open and closed mouth) by means of MR images and drawings. Diagnosing of the TMJ related diseases depends on standardized clinical and MR examinations. Therefore close interdisciplinary cooperation between dentist and radiologist is necessary.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. Cranial magnetic resonance imaging (MRI) in elderly American Indians: Design, methods, and implementation of the Cerebrovascular Disease and its Consequences in American Indians Study

    PubMed Central

    Suchy-Dicey, Astrid M.; Shibata, Dean; Best, Lyle G.; Verney, Steven P.; Longstreth, W.T.; Lee, Elisa T.; Okin, Peter M.; Devereux, Richard; O’Leary, Marcia; Ali, Tauqeer; Jensen, Paul N.; Muller, Clemma; Nelson, Lonnie A.; Rhoades, Everett; Madhyastha, Tara; Grabowski, Thomas J.; Beauchamp, Norman; Umans, Jason G.; Buchwald, Dedra

    2016-01-01

    The Cerebrovascular Disease and Its Consequences in American Indians (CDCAI) Study recruited surviving members of a 20-year, longitudinal, population-based cohort of American Indians focused on cardiovascular disease, its risk factors, and its consequences. The goal of CDCAI Study is to characterize the burden, risk factors, and manifestations of vascular brain injury identified on cranial magnetic resonance imaging (MRI). CDCAI Study investigators enrolled 1,033 participants aged 60 years and older from 11 American Indian communities and tribes in the Northern Plains, Southern Plains, and Southwestern U.S. In addition to cranial MRI performed according to standardized protocols, participants underwent extensive medical interview, clinical examination, neurocognitive testing, physical function evaluation, electrocardiogram, and provided blood and urine specimens. Participants also self-administered questionnaires covering demographics, quality of life, and medical history. This report describes the design, implementation, and some of the unique challenges of this study and data collection. PMID:27603047

  2. MRI of the Musculoskeletal System

    MedlinePlus

    ... does not completely surround you. Some newer MRI machines have a larger diameter bore which can be ... size patients or patients with claustrophobia. Other MRI machines are open on the sides (open MRI). Open ...

  3. Magnetic Resonance Imaging (MRI) - Spine

    MedlinePlus

    ... does not completely surround you. Some newer MRI machines have a larger diameter bore which can be ... size patients or patients with claustrophobia. Other MRI machines are open on the sides (open MRI). Open ...

  4. Comparison of conventional DCE-MRI and a novel golden-angle radial multicoil compressed sensing method for the evaluation of breast lesion conspicuity.

    PubMed

    Heacock, Laura; Gao, Yiming; Heller, Samantha L; Melsaether, Amy N; Babb, James S; Block, Tobias K; Otazo, Ricardo; Kim, Sungheon G; Moy, Linda

    2017-06-01

    To compare a novel multicoil compressed sensing technique with flexible temporal resolution, golden-angle radial sparse parallel (GRASP), to conventional fat-suppressed spoiled three-dimensional (3D) gradient-echo (volumetric interpolated breath-hold examination, VIBE) MRI in evaluating the conspicuity of benign and malignant breast lesions. Between March and August 2015, 121 women (24-84 years; mean, 49.7 years) with 180 biopsy-proven benign and malignant lesions were imaged consecutively at 3.0 Tesla in a dynamic contrast-enhanced (DCE) MRI exam using sagittal T1-weighted fat-suppressed 3D VIBE in this Health Insurance Portability and Accountability Act-compliant, retrospective study. Subjects underwent MRI-guided breast biopsy (mean, 13 days [1-95 days]) using GRASP DCE-MRI, a fat-suppressed radial "stack-of-stars" 3D FLASH sequence with golden-angle ordering. Three readers independently evaluated breast lesions on both sequences. Statistical analysis included mixed models with generalized estimating equations, kappa-weighted coefficients and Fisher's exact test. All lesions demonstrated good conspicuity on VIBE and GRASP sequences (4.28 ± 0.81 versus 3.65 ± 1.22), with no significant difference in lesion detection (P = 0.248). VIBE had slightly higher lesion conspicuity than GRASP for all lesions, with VIBE 12.6% (0.63/5.0) more conspicuous (P < 0.001). Masses and nonmass enhancement (NME) were more conspicuous on VIBE (P < 0.001), with a larger difference for NME (14.2% versus 9.4% more conspicuous). Malignant lesions were more conspicuous than benign lesions (P < 0.001) on both sequences. GRASP DCE-MRI, a multicoil compressed sensing technique with high spatial resolution and flexible temporal resolution, has near-comparable performance to conventional VIBE imaging for breast lesion evaluation. 3 Technical Efficacy: Stage 3 J. MAGN. RESON. IMAGING 2017;45:1746-1752. © 2016 International Society for Magnetic Resonance in Medicine.

  5. Fundamentals of tracer kinetics for dynamic contrast-enhanced MRI.

    PubMed

    Koh, Tong San; Bisdas, Sotirios; Koh, Dow Mu; Thng, Choon Hua

    2011-12-01

    Tracer kinetic methods employed for quantitative analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) share common roots with earlier tracer studies involving arterial-venous sampling and other dynamic imaging modalities. This article reviews the essential foundation concepts and principles in tracer kinetics that are relevant to DCE MRI, including the notions of impulse response and convolution, which are central to the analysis of DCE MRI data. We further examine the formulation and solutions of various compartmental models frequently used in the literature. Topics of recent interest in the processing of DCE MRI data, such as the account of water exchange and the use of reference tissue methods to obviate the measurement of an arterial input, are also discussed. Although the primary focus of this review is on the tracer models and methods for T(1) -weighted DCE MRI, some of these concepts and methods are also applicable for analysis of dynamic susceptibility contrast-enhanced MRI data.

  6. Recommendations for real-time speech MRI.

    PubMed

    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. © 2015 Wiley Periodicals, Inc.

  7. 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

  8. MRI Scans - Multiple Languages

    MedlinePlus

    ... español) Ukrainian (українська ) Arabic (العربية) Expand Section MRI (Magnetic Resonance Imaging) - العربية (Arabic) Bilingual PDF Health Information Translations Chinese, Simplified (Mandarin dialect) (简体中文) Expand Section MRI ( ...

  9. Current status of magnetic resonance imaging (MRI) and ultrasonography fusion software platforms for guidance of prostate biopsies.

    PubMed

    Logan, Jennifer K; Rais-Bahrami, Soroush; Turkbey, Baris; Gomella, Andrew; Amalou, Hayet; Choyke, Peter L; Wood, Bradford J; Pinto, Peter A

    2014-11-01

    Prostate MRI is currently the best diagnostic imaging method for detecting PCa. Magnetic resonance imaging (MRI)/ultrasonography (US) fusion allows the sensitivity and specificity of MRI to be combined with the real-time capabilities of transrectal ultrasonography (TRUS). Multiple approaches and techniques exist for MRI/US fusion and include direct 'in bore' MRI biopsies, cognitive fusion, and MRI/US fusion via software-based image coregistration platforms. © 2013 The Authors. BJU International © 2013 BJU International.

  10. Resting state BOLD fMRI for pre-surgical planning

    PubMed Central

    Kamran, Mudassar; Hacker, Carl D; Allen, Monica G; Mitchell, Timothy J; Leuthardt, Eric C; Snyder, Abraham Z; Shimony, Joshua S

    2014-01-01

    SYNOPSIS Resting state functional MRI (rsfMRI) measures spontaneous fluctuations in the BOLD signal and can be used to elucidate the brain’s functional organization. It can be used to simultaneously assess multiple distributed resting state networks. Unlike task fMRI, rsfMRI does not require task performance and thus can be performed in any subject that can obtain an MRI scan. In this article we present a brief introduction of rsfMRI processing methods followed by a detailed discussion on the use of rsfMRI in pre-surgical planning. Example cases are provided to highlight the strengths and limitations of the technique. PMID:25441506

  11. Current Status of MRI and Ultrasound Fusion Software Platforms for Guidance of Prostate Biopsies

    PubMed Central

    Logan, Jennifer K; Rais-Bahrami, Soroush; Turkbey, Baris; Gomella, Andrew; Amalou, Hayet; Choyke, Peter L; Wood, Bradford J; Pinto, Peter A

    2015-01-01

    • Prostate MRI is currently the best diagnostic imaging method for detecting prostate cancer • Magnetic Resonance Imaging-Ultrasound (MRI/US) fusion allows the sensitivity and specificity of MRI to be combined with real time capabilities of transrectal ultrasound (TRUS). • Multiple approaches and techniques exist for MRI/US fusion and include (1) direct “in bore” MR biopsies, (2) cognitive fusion, and (3) MRI/US fusion via software-based image co-registration platforms. PMID:24298917

  12. 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

  13. A Novel MRI Marker for Prostate Brachytherapy

    SciTech Connect

    Frank, Steven J. Stafford, R. Jason; Bankson, James A.; Li Chun; Swanson, David A.; Kudchadker, Rajat J.; Martirosyan, Karen S.

    2008-05-01

    Purpose: Magnetic resonance imaging (MRI) is the optimal imaging modality for the prostate and surrounding critical organ structures. However, on MRI, the titanium radioactive seeds used for brachytherapy appear as black holes (negative contrast) and cannot be accurately localized. We sought to develop an encapsulated contrast agent marker (ECAM) with high-signal intensity on MRI to permit accurate localization of radioactive seeds with MRI during and after prostate brachytherapy. Methods and Materials: We investigated several agents with paramagnetic and superparamagnetic properties. The agents were injected into titanium, acrylic, and glass seeds, which were linked together in various combinations and imaged with MRI. The agent with the greatest T1-weighted signal was tested further in a canine prostate and agarose phantom. Studies were performed on a 1.5-T clinical MRI scanner. Results: The cobalt-chloride complex contrast (C4) agent with stoichiometry (CoCl{sub 2}){sub 0.8}(C{sub 2}H{sub 5}NO{sub 2}){sub 0.2} had the greatest T1-weighted signal (positive contrast) with a relaxivity ratio >1 (r{sub 2}/r{sub 1} = 1.21 {+-} 0.29). Acrylic-titanium and glass-titanium seed strands were clearly visualized with the encapsulated contrast agent marker. Conclusion: We have developed a novel ECAM that permits positive identification of the radioactive seeds used for prostate brachytherapy on MRI. Preclinical in vitro phantom studies and in vivo canine studies are needed to further optimize MRI sequencing techniques to facilitate MRI-based dosimetry.

  14. The cerebral network’s reconstruction by MRI methods and the hemodynamics study of small laboratory animal in type 1 diabetes

    NASA Astrophysics Data System (ADS)

    Akulov, A.; Cherevko, A.; Parshin, D.; Tur, D.; Yankova, G.

    2017-08-01

    The blood realizes the transport of substances, which are necessary for livelihoods, throughout the body. The assumption about the relationship some disease and structure of vasculature (in particular of brain) is natural. In the paper we consider models of Willis’ circle for two groups of laboratory mice - one control group and another with diabetes. Vascular net obtained as a result of preprocessing MRI data. The purpose of the work is to determine the effect of type 1 diabetes on the properties of the laboratory mice vasculature.

  15. 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.

  16. The PRESTO technique for fMRI

    PubMed Central

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

    2012-01-01

    In the early days of BOLD fMRI, the acquisition of T2* 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 T2* weighted scanning available on standard clinical scanning. 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

  17. Advanced flow MRI: emerging techniques and applications

    PubMed Central

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

    2016-01-01

    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

  18. 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. Published by Elsevier Inc.

  19. In vivo prostate cancer detection and grading using restriction spectrum imaging-MRI

    PubMed Central

    McCammack, KC; Kane, CJ; Parsons, JK; White, NS; Schenker-Ahmed, NM; Kuperman, JM; Bartsch, H; Desikan, RS; Rakow-Penner, RA; Adams, D; Liss, MA; Mattrey, RF; Bradley, WG; Margolis, DJA; Raman, SS; Shabaik, A; Dale, AM; Karow, DS

    2017-01-01

    BACKGROUND Magnetic resonance imaging (MRI) is emerging as a robust, noninvasive method for detecting and characterizing prostate cancer (PCa), but limitations remain in its ability to distinguish cancerous from non-cancerous tissue. We evaluated the performance of a novel MRI technique, restriction spectrum imaging (RSI-MRI), to quantitatively detect and grade PCa compared with current standard-of-care MRI. METHODS In a retrospective evaluation of 33 patients with biopsy-proven PCa who underwent RSI-MRI and standard MRI before radical prostatectomy, receiver-operating characteristic (ROC) curves were performed for RSI-MRI and each quantitative MRI term, with area under the ROC curve (AUC) used to compare each term’s ability to differentiate between PCa and normal prostate. Spearman rank-order correlations were performed to assess each term’s ability to predict PCa grade in the radical prostatectomy specimens. RESULTS RSI-MRI demonstrated superior differentiation of PCa from normal tissue, with AUC of 0.94 and 0.85 for RSI-MRI and conventional diffusion MRI, respectively (P = 0.04). RSI-MRI also demonstrated superior performance in predicting PCa aggressiveness, with Spearman rank-order correlation coefficients of 0.53 (P = 0.002) and − 0.42 (P = 0.01) for RSI-MRI and conventional diffusion MRI, respectively, with tumor grade. CONCLUSIONS RSI-MRI significantly improves upon current noninvasive PCa imaging and may potentially enhance its diagnosis and characterization. PMID:26754261

  20. Measuring eye states in functional MRI.

    PubMed

    Brodoehl, Stefan; Witte, Otto W; Klingner, Carsten M

    2016-07-13

    In many functional magnetic resonance imaging (fMRI) studies, experimental design often depends on the eye state (i.e., whether the participants had their eyes open or closed). Closed eyes during an fMRI is the general convention, particularly when patients are in a resting-state, but the eye state is difficult to verify. Although knowledge of the impact of the eye state on brain activity is steadily growing, only a few research groups have implemented standardized procedures to monitor eye movements and eye state. These procedures involve advanced methods that are costly (e.g., fMRI-compatible cameras) and often time-consuming (e.g., EEG/EOG). We present a simple method that distinguishes open from closed eyes utilizing functional MR images alone. The utility of this method was demonstrated on fMRI data from 14 healthy subjects who had to open and close their eyes according to a predetermined protocol (3.0 T MRI scanner, EPI sequence with 3 × 3 × 3 mm voxels, TR 2.52 s). The method presented herein is capable of extracting the movement direction of the eyes. All described methods are applicable for pre- and post-normalized MR images and are freely available through a MATLAB toolbox.

  1. MRI of the Breast

    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 ...

  2. MRI of the Prostate

    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 ...

  3. 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 ...

  4. Cervical MRI scan

    MedlinePlus

    ... magnetic resonance imaging) scan uses energy from strong magnets to create pictures of the part of the ... in your eyes) Because the MRI contains strong magnets, metal objects are not allowed into the room ...

  5. 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 ...

  6. 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 ...

  7. MRI of the Breast

    MedlinePlus

    ... of the breast uses a powerful magnetic field, radio waves and a computer to produce detailed pictures of ... scans, MRI does not utilize ionizing radiation. Instead, radio waves redirect alignment of hydrogen atoms that naturally exist ...

  8. A new approach for radiosynoviorthesis: A dose-optimized planning method based on Monte Carlo simulation and synovial measurement using 3D slicer and MRI.

    PubMed

    Torres Berdeguez, Mirta Bárbara; Thomas, Sylvia; Rafful, Patricia; Arruda Sanchez, Tiago; Medeiros Oliveira Ramos, Susie; Souza Albernaz, Marta; Vasconcellos de Sá, Lidia; Lopes de Souza, Sergio Augusto; Mas Milian, Felix; Silva, Ademir Xavier da

    2017-07-01

    Recently, there has been a growing interest in a methodology for dose planning in radiosynoviorthesis to substitute fixed activity. Clinical practice based on fixed activity frequently does not embrace radiopharmaceutical dose optimization in patients. The aim of this paper is to propose and discuss a dose planning methodology considering the radiological findings of interest obtained by three-dimensional magnetic resonance imaging combined with Monte Carlo simulation in radiosynoviorthesis treatment applied to hemophilic arthropathy. The parameters analyzed were: surface area of the synovial membrane (synovial size), synovial thickness and joint effusion obtained by 3D MRI of nine knees from nine patients on a SIEMENS AVANTO 1.5 T scanner using a knee coil. The 3D Slicer software performed both the semiautomatic segmentation and quantitation of these radiological findings. A Lucite phantom 3D MRI validated the quantitation methodology. The study used Monte Carlo N-Particle eXtended code version 2.6 for calculating the S-values required to set up the injected activity to deliver a 100 Gy absorbed dose at a determined synovial thickness. The radionuclides assessed were: 90Y, 32P, 188Re, 186Re, 153Sm, and 177Lu, and the present study shows their effective treatment ranges. The quantitation methodology was successfully tested, with an error below 5% for different materials. S-values calculated could provide data on the activity to be injected into the joint, considering no extra-articular leakage from joint cavity. Calculation of effective treatment range could assist with the therapeutic decision, with an optimized protocol for dose prescription in RSO. Using 3D Slicer software, this study focused on segmentation and quantitation of radiological features such as joint effusion, synovial size, and thickness, all obtained by 3D MRI in patients' knees with hemophilic arthropathy. The combination of synovial size and thickness with the parameters obtained by Monte Carlo

  9. Temperature mapping of thermal ablation using MRI.

    PubMed

    Samset, Eigil

    2006-01-01

    MRI is a unique tool for minimally invasive thermal ablation in that it can provide both targeting, monitoring and control during the procedure. Monitoring is achieved by using MRI temperature mapping. In this review the relevant physics is explained as a background to the state-of-the-art methods for computing temperature maps as well as the more cutting edge methods. The review covers both methods to monitor heating and cooling of tissue and explains temperature mapping using Proton Resonance Frequency shift, T1 mapping, diffusion mapping, R2* mapping and thermal models.

  10. MRI-guided brachytherapy

    PubMed Central

    Tanderup, Kari; Viswanathan, Akila; Kirisits, Christian; Frank, Steven J.

    2014-01-01

    The application of MRI-guided brachytherapy has demonstrated significant growth during the last two decades. Clinical improvements in cervix cancer outcomes have been linked to the application of repeated MRI for identification of residual tumor volumes during radiotherapy. This has changed clinical practice in the direction of individualized dose administration, and mounting evidence of improved clinical outcome with regard to local control, overall survival as well as morbidity. MRI-guided prostate HDR and LDR brachytherapy has improved the accuracy of target and organs-at-risk (OAR) delineation, and the potential exists for improved dose prescription and reporting for the prostate gland and organs at risk. Furthermore, MRI-guided prostate brachytherapy has significant potential to identify prostate subvolumes and dominant lesions to allow for dose administration reflecting the differential risk of recurrence. MRI-guided brachytherapy involves advanced imaging, target concepts, and dose planning. The key issue for safe dissemination and implementation of high quality MRI-guided brachytherapy is establishment of qualified multidisciplinary teams and strategies for training and education. PMID:24931089

  11. 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.

  12. 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.

  13. 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