pinecone/core-2020-05-10-deduplication huggingface dataset:
Fast image reconstruction with L2-regularization

Purpose
We introduce L2-regularized reconstruction algorithms with closed-form solutions that achieve dramatic computational speed-up relative to state of the art L1- and L2-based iterative algorithms while maintaining similar image quality for various applications in MRI reconstruction.
Materials and Methods
We compare fast L2-based methods to state of the art algorithms employing iterative L1- and L2-regularization in numerical phantom and in vivo data in three applications; (i) Fast Quantitative Susceptibility Mapping (QSM), (ii) Lipid artifact suppression in Magnetic Resonance Spectroscopic Imaging (MRSI), and (iii) Diffusion Spectrum Imaging (DSI). In all cases, proposed L2-based methods are compared with the state of the art algorithms, and two to three orders of magnitude speed up is demonstrated with similar reconstruction quality.
Results
The closed-form solution developed for regularized QSM allows processing of a three-dimensional volume under 5 s, the proposed lipid suppression algorithm takes under 1 s to reconstruct single-slice MRSI data, while the PCA based DSI algorithm estimates diffusion propagators from undersampled q-space for a single slice under 30 s, all running in Matlab using a standard workstation.
Conclusion
For the applications considered herein, closed-form L2-regularization can be a faster alternative to its iterative counterpart or L1-based iterative algorithms, without compromising image quality.National Institute for Biomedical Imaging and Bioengineering (U.S.) (Grant NIBIB K99EB012107)National Institutes of Health (U.S.) (Grant NIH R01 EB007942)National Institute for Biomedical Imaging and Bioengineering (U.S.) (Grant NIBIB R01EB006847)Grant K99/R00 EB008129National Center for Research Resources (U.S.) (Grant NCRR P41RR14075)National Institutes of Health (U.S.) (Blueprint for Neuroscience Research U01MH093765)Siemens CorporationSiemens-MIT AllianceMIT-Center for Integration of Medicine and Innovative Technology (Medical Engineering Fellowship
Aqueductal cerebrospinal fluid pulsatility in healthy individuals is affected by impaired cerebral venous outflow

yesTo investigate cerebrospinal fluid (CSF) dynamics in the aqueduct of Sylvius (AoS) in chronic cerebrospinal venous insufficiency (CCSVI)-positive and -negative healthy individuals using cine phase contrast imaging.
Materials and Methods

Fifty-one healthy individuals (32 CCSVI-negative and 19 age-matched CCSVI-positive subjects) were examined using Doppler sonography (DS). Diagnosis of CCSVI was established if subjects fulfilled ≥2 venous hemodynamic criteria on DS. CSF flow and velocity measures were quantified using a semiautomated method and compared with clinical and routine 3T MRI outcomes.
Results

CCSVI was associated with increased CSF pulsatility in the AoS. Net positive CSF flow was 32% greater in the CCSVI-positive group compared with the CCSVI-negative group (P = 0.008). This was accompanied by a 28% increase in the mean aqueductal characteristic signal (ie, the AoS cross-sectional area over the cardiac cycle) in the CCSVI-positive group compared with the CCSVI-negative group (P = 0.021).
Conclusion

CSF dynamics are altered in CCSVI-positive healthy individuals, as demonstrated by increased pulsatility. This is accompanied by enlargement of the AoS, suggesting that structural changes may be occurring in the brain parenchyma of CCSVI-positive healthy individual
Multimodal MRI can identify perfusion and metabolic changes in the invasive margin of glioblastomas

Purpose: Invasion of normal brain is a cardinal feature of glioblastomas (GBM) and a major cause of treatment failure. Diffusion tensor MR (DTI) can identify invasive regions. The aim of this study was to use perfusion and MR spectroscopy to compare the DTI-defined invasive and non-invasive regions. Materials and Methods: 50 GBM patients were imaged pre-operatively at 3 T with anatomic sequences, DTI, dynamic susceptibility perfusion MR (DSCI) and multivoxel spectroscopy. The DTI and DSCI data were co-registered to the spectroscopy data and regions of interest were made in the invasive (determined by DTI), non-invasive regions and normal brain. Values of relative cerebral blood volume (rCBV), N-acetyl aspartate (NAA), myoinositol (mI), total choline (Cho) and glutamate+glutamine (Glx) normalized to creatine (Cr) and Cho/NAA were measured at each ROI. Results: Invasive regions showed significant increases in rCBV suggesting angiogenesis (invasive rCBV 1.64 [95%CI 1.5–1.76] vs. non-invasive 1.14 [1.09-1.18]; P<0.001), Cho/Cr (invasive 0.42 [0.38–0.46] vs. non-invasive 0.35 [0.31-0.38]; P=0.02) and Cho/NAA (invasive 0.54 [0.41-0.68] vs. non-invasive 0.37 [0.29-0.45]; P=<0.03) suggesting proliferation, and Glx/Cr (invasive 1.54 [1.27-1.82] vs. non-invasive 1.3 [1.13-1.47]; P=0.028) suggesting glutamate release; and a significantly reduced NAA/Cr (invasive 0.95 [0.85-1.05] vs. non-invasive 1.19 [1.06-1.31]; P=0.008). The mI/Cr was not different between the three ROIs (invasive 1.2 [0.99-1.41] vs. non-invasive 1.3 [1.14-1.46]; P=0.68). In the non-invasive regions, the values were not different from normal brain. Conclusions: Combining DTI to identify the invasive region with perfusion and spectroscopy, we can identify changes in invasive regions not seen in non-invasive regions.This study was funded from a National Institutes of Health Research Clinician Scientist FellowshipThis is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/jmri.2499
Distortion correction of echo-planar diffusion-weighted images of uterine cervix

PurposeTo investigate the clinical utility of the reverse gradient algorithm in correcting distortions in diffusion-weighted images of the cervix and for increasing diagnostic performance. Materials and MethodsForty-one patients ages 25-72 years (mean 40 11 years) with suspected or early stage cervical cancer were imaged at 3T using an endovaginal coil. T-2-weighted (W) and diffusion-weighted images with right and left phase-encode gradient directions were obtained coronal to the cervix (b = 0, 100, 300, 500, 800 s mm(-2)). Differences in angle of the endocervical canal to the x-axis between T2W and right-gradient, left-gradient, and corrected images were measured. Uncorrected and corrected images were assessed for diagnostic performance when viewed together with T2W images by two independent observers against subsequent histology. ResultsThe angles of the endocervical canal relative to the x-axis were significantly different between the T2W images and the right-gradient images (P=0.007), approached significance for left-gradient images (P=0.055), and were not significantly different after correction (P=0.95). Corrected images enabled a definitive diagnosis in 34% (n=14) of patients classified as equivocal on uncorrected images. Tumor volume in this subset was 0.18 +/- 0.44 cm(3) (mean +/- SD; sensitivity of detection 100% [8/8], specificity 50% [3/6] for an experienced observer). Correction did not improve diagnostic performance for the less-experienced observer. ConclusionDistortion-corrected diffusion-weighted images improved correspondence with T2W images and diagnostic performance in a third of cases. J. Magn. Reson. Imaging 2016;43:1218-1223
Quantitative analysis of tibial subchondral bone:Texture analysis outperforms conventional trabecular microarchitecture analysis

BACKGROUND: The aim of this study was to compare two different methods of quantitative assessment of tibial subchondral bone in osteoarthritis (OA): statistical texture analysis (sTA) and trabecular microarchitecture analysis (tMA). METHODS: Asymptomatic controls aged 20-30 (n = 10), patients aged 40-50 with chronic knee pain but without established OA (n = 10) and patients aged 55-85 with advanced OA scheduled for knee replacement (n = 10) underwent knee MR imaging at 3 Tesla with a three-dimensional gradient echo sequence to allow sTA and tMA. tMA and sTA features were calculated using region of interest creation in the medial (MT) and lateral (LT) tibial subchondral bone. Features were compared between groups using one-way analysis of variance. The two most discriminating tMA and sTA features were used to construct exploratory discriminant functions to assess the ability of the two methods to classify participants. RESULTS: No tMA features were significantly different between groups at either MT or LT. 17/20 and 11/20 sTA features were significantly different between groups at the MT/LT, respectively (P < 0.001). Discriminant functions created using tMA features classified 12/30 participants correctly (40% accuracy; 95% confidence interval [CI], 22-58%) based on MT data and 9/30 correctly (30%,; 95% CI, 14-46) based on LT data. Discriminant functions using sTA features classified 16/30 participants correctly (53%; 95% CI, 35-71) based on MT data and 14/30 correctly (47%; 95% CI, 29-65) based on LT data. CONCLUSION: sTA features showed more significant differences between the three study groups and improved classification accuracy compared with tMA features. J. Magn. Reson. Imaging 2015
In vivo γ-aminobutyric acid measurement in rats with spectral editing at 4.7T

Purpose

To evaluate the feasibility of spectral editing for quantification of γ-aminobutyric acid (GABA) in the rat brain and to determine whether altered GABA concentration in the ventral striatum is a neural endophenotype associated with trait-like impulsive behavior.

Materials and Methods

Spectra were acquired at 4.7T for 23 male Lister-hooded rats that had been previously screened for extremely low and high impulsivity phenotypes on an automated behavioral task (n = 11 low-impulsive; n = 12 high-impulsive). Voxels of 3 × 7 × 4 mm3 (84 μL) centered bilaterally across the ventral striatum were used to evaluate GABA concentration ratios.

Results

Quantifiable GABA signals in the ventral striatum were obtained for all rats. Mean-edited GABA to n-acetyl aspartate (NAA) ratios in the ventral striatum were 0.22 (95% confidence interval [CI] [0.18, 0.25]). Mean GABA/NAA ratios in this region were significantly decreased by 28% in high-impulsive rats compared to low-impulsive rats (P = 0.02; 95% CI [–53%, –2%]).

Conclusion

These findings demonstrate that spectral editing at 4.7T is a feasible method to assess in vivo GABA concentrations in the rat brain. The results show that diminished GABA content in the ventral striatum may be a neural endophenotype associated with impulsivity. J. Magn. Reson. Imaging 2015.This study was funded by the UK Medical Research Council (G0701500) and by a joint award from the Medical Research Council (G1000183) and Wellcome Trust (093875/Z/10/Z) in support of the Behavioural and Clinical Neuroscience Institute at Cambridge University. BJ is supported by grants from the AXA Research Fund and the Australian National Health and Medical Research Council (1016313).This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/jmri.2509
Dynamic contrast-enhanced MRI: Study of inter-software accuracy and reproducibility using simulated and clinical data

International audiencePURPOSE: To test the reproducibility and accuracy of pharmacokinetic parameter measurements on five analysis software packages (SPs) for dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), using simulated and clinical data. MATERIALS AND METHODS: This retrospective study was Institutional Review Board-approved. Simulated tissues consisted of pixel clusters of calculated dynamic signal changes for combinations of Tofts model pharmacokinetic parameters (volume transfer constant [K(trans) ], extravascular extracellular volume fraction [ve ]), longitudinal relaxation time (T1 ). The clinical group comprised 27 patients treated for rectal cancer, with 36 3T DCE-MR scans performed between November 2012 and February 2014, including dual-flip-angle T1 mapping and a dynamic postcontrast T1 -weighted, 3D spoiled gradient-echo sequence. The clinical and simulated images were postprocessed with five SPs to measure K(trans) , ve , and the initial area under the gadolinium curve (iAUGC). Modified Bland-Altman analysis was conducted, intraclass correlation coefficients (ICCs) and within-subject coefficients of variation were calculated. RESULTS: Thirty-one examinations from 23 patients were of sufficient technical quality and postprocessed. Measurement errors were observed on the simulated data for all the pharmacokinetic parameters and SPs, with a bias ranging from -0.19 min(-1) to 0.09 min(-1) for K(trans) , -0.15 to 0.01 for ve , and -0.65 to 1.66 mmol.L(-1) .min for iAUGC. The ICC between SPs revealed moderate agreement for the simulated data (K(trans) : 0.50; ve : 0.67; iAUGC: 0.77) and very poor agreement for the clinical data (K(trans) : 0.10; ve : 0.16; iAUGC: 0.21). CONCLUSION: Significant errors were found in the calculated DCE-MRI pharmacokinetic parameters for the perfusion analysis SPs, resulting in poor inter-software reproducibility. J. Magn. Reson. Imaging 201
Repeatability and Sensitivity of T-2* Measurements in Patients With Head and Neck Squamous Cell Carcinoma at 3T

Purpose: To determine whether quantitation of T-2* is sufficiently repeatable and sensitive to detect clinically relevant oxygenation levels in head and neck squamous cell carcinoma (HNSCC) at 3T. Materials and Methods: Ten patients with newly diagnosed locally advanced HNSCC underwent two magnetic resonance imaging (MRI) scans between 24 and 168 hours apart prior to chemoradiotherapy treatment. A multiple gradient echo sequence was used to calculate T-2* maps. A quadratic function was used to model the blood transverse relaxation rate as a function of blood oxygenation. A set of published coefficients measured at 3T were incorporated to account for tissue hematocrit levels and used to plot the dependence of fractional blood oxygenation (Y) on T-2* values, together with the corresponding repeatability range. Repeatability of T-2* using Bland-Altman analysis, and calculation of limits of agreement (LoA), was used to assess the sensitivity, defined as the minimum difference in fractional blood oxygenation that can be confidently detected. Results: T-2* LoA for 22 outlined tumor volumes were 13%. The T-2* dependence of fractional blood oxygenation increases monotonically, resulting in increasing sensitivity of the method with increasing blood oxygenation. For fractional blood oxygenation values above 0.11, changes in T-2* were sufficient to detect differences in blood oxygenation greater than 10% (Delta T-2* > LoA for Delta Y > 0.1). Conclusion: Quantitation of T-2* at 3T can detect clinically relevant changes in tumor oxygenation within a wide range of blood volumes and oxygen tensions, including levels reported in HNSCC
Acceleration of skeletal age MR examination using compressed sensing

PurposeTo examine the feasibility of accelerating magnetic resonance (MR) image acquisition for children using compressed sensing (CS). Skeletal age assessment using MRI sometimes suffers from motion artifacts because of the long scan time in children. Reducing image acquisition time may provide benefits by reducing motion artifacts, increasing efficiency of examination, and creating a stress-free environment.Materials and MethodsUndersampling patterns for CS were optimized and CS-based examination with the acceleration factors of 3 (CS3, 55 seconds per scan) and 4 (CS4, 41 seconds per scan) was performed for 59 subjects (35 boys and 24 girls; mean age, 9.1 years; age range, 4.4–15.3 years) using a 0.3T scanner. The skeletal age was assessed by two raters (A and B).ResultsThe interrater and intrarater reproducibility in skeletal age assessment was high (Pearson\u27s r = 0.966 [CS3(A1) vs. CS3(A2)], 0.962 [CS4(A1) vs. CS4(A2)], 0.935 [CS3(A1) vs. CS3(B)], and 0.964 [CS4(A1) vs. CS4(B)]; P < 0.001). The errors in skeletal age assessed on the basis of CS-reconstructed images were similar to those assessed on the basis of fully Nyquist-sampled images.ConclusionThese results demonstrate the validity and reliability of skeletal age examination accelerated by CS-MRI. We conclude that the acceleration factor of 3 was optimal. J. Magn. Reson. Imaging 2016;44:204–211
Diffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering?

PURPOSE\ud
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To investigate if image registration of diffusion tensor imaging (DTI) allows omitting respiratory triggering for both transplanted and native kidneys MATERIALS AND METHODS: Nine kidney transplant recipients and eight healthy volunteers underwent renal DTI on a 3T scanner with and without respiratory triggering. DTI images were registered using a multimodal nonrigid registration algorithm. Apparent diffusion coefficient (ADC), the contribution of perfusion (FP ), and the fractional anisotropy (FA) were determined. Relative root mean square errors (RMSE) of the fitting and the standard deviations of the derived parameters within the regions of interest (SDROI ) were evaluated as quality criteria.\ud
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RESULTS\ud
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Registration significantly reduced RMSE in all DTI-derived parameters of triggered and nontriggered measurements in cortex and medulla of both transplanted and native kidneys (P < 0.05 for all). In addition, SDROI values were lower with registration for all 16 parameters in transplanted kidneys (14 of 16 SDROI values were significantly reduced, P < 0.04) and for 15 of 16 parameters in native kidneys (9 of 16 SDROI values were significantly reduced, P < 0.05). Comparing triggered versus nontriggered DTI in transplanted kidneys revealed no significant difference for RMSE (P > 0.14) and for SDROI (P > 0.13) of all parameters. In contrast, in native kidneys relative RMSE from triggered scans were significantly lower than those from nontriggered scans (P < 0.02), while SDROI was slightly higher in triggered compared to nontriggered measurements in 15 out of 16 comparisons (significantly for two, P < 0.05).\ud
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CONCLUSION\ud
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Registration improves the quality of DTI in native and transplanted kidneys. Diffusion parameters in renal allografts can be measured without respiratory triggering. In native kidneys, respiratory triggering appears advantageous. J. Magn. Reson. Imaging 2016
Quantitative BOLD imaging at 3T: Temporal changes in hepatocellular carcinoma and fibrosis following oxygen challenge

Purpose: To evaluate the utility of oxygen challenge and report on temporal changes in blood oxygenation level-dependent (BOLD) contrast in normal liver, hepatocellular carcinoma (HCC) and background fibrosis.  

Materials and Methods: Eleven volunteers (9 male and 2 female, mean age 33.5, range 27–41 years) and 10 patients (9 male and 1 female, mean age 68.9, range 56–87 years) with hepatocellular carcinoma on a background of diffuse liver disease were recruited. Imaging was performed on a 3T system using a multi-phase, multi-echo, fast gradient echo sequence. Oxygen was administered via a Hudson mask after two minutes free-breathing. Paired t-tests were performed to determine if the mean pre- and post-O2 differences were statistically significant. 

Results: In patients with liver fibrosis (n=8) the change in T2* following O2 administration was elevated (0.88±0.582ms, range 0.03–1.69ms) and the difference was significant (p=0.004). The magnitude of the BOLD response in patients with HCC (n=10) was larger, however the response was more variable (1.07±1.458ms, range -0.93–3.26 ms), the difference was borderline significant (p=0.046).  The BOLD response in the volunteer cohort was not significant (p=0.121, 0.59±1.162 ms, range -0.81–2.44 ms).

Conclusions:  This work demonstrates that the BOLD response following oxygen challenge within cirrhotic liver is consistent with a breakdown in vascular autoregulatory mechanisms. Similarly the elevated BOLD response within HCC is consistent with the abnormal capillary vasculature within tumors and the arterialization of the blood supply. Our results suggest that oxygen challenge may prove a viable BOLD contrast mechanism in the liver.This study was supported by the Addenbrooke’s Charitable Trust, Cambridge’s Experimental Cancer Medicine Centre and a NIHR comprehensive Biomedical Research Centre award to Cambridge University Hospitals NHS Foundation Trust in partnership with the University of Cambridge.This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1002/jmri.2518
Breath-hold MR measurements of fat fraction, T1 , and T2 * of water and fat in vertebral bone marrow

International audienceTo assess the feasibility of measuring the fat fraction, T1 and T2 * relaxation times of water and fat signals in vertebral bone marrow using breath-hold magnetic resonance imaging (MRI) gradient echo images of the spine. MRI experiments were performed at 1.5T on eight healthy volunteers (35.1 ± 15.7 years, five men and three women) using two sagittal four-echo 3D gradient echo volumetric interpolated breath-hold examination (VIBE Dixon) sequences acquired at two different flip angles (5° and 15°). The water/fat decomposition was performed in the vertebral bodies of L1 to L5 by fitting the signal to a function that depends on the echo time and the flip angle to calculate the fat fraction (FF) and T1 and T2 * relaxation times of water and fat signals. Repeatability was assessed by scanning one volunteer six times. The mean fat fraction over L1 to L5 was 33 ± 8%. The mean T1 and T2 * of water and fat signals were respectively T1w = 701 ± 151 msec, T2 *w = 13.7 ± 2.9 msec, T1f = 334 ± 113 msec, and T2 *f = 11.4 ± 2.7 msec. When considering each vertebra separately, the fat fraction increased from L1 to L5 and the T1w decreased from L1 to L5. The mean coefficients of variation obtained from the repeatability study were 8% (FF), 11% (T1w ), 17% (T1f ), 8% (T2 *w ), and 27% (T2 *f ). The method introduced in the current study allows for the measurement of the fat fraction and water and fat relaxation times, with a total acquisition time of less than 40 seconds. J. Magn. Reson. Imaging 2016
3T MRI investigation of cardiac left ventricular structure and function in a UK population : he Tayside screening for the prevention of cardiac events (TASCFORCE) study

Contract grant sponsor: Souter Charitable Trust, and Chest, Heart and Stroke Scotland; Contract grant sponsor: Wellcome Trust; contract grant number: WT 085664 (Clinical Research Fellowship to J.W-McC.)Purpose : To scan a volunteer population using 3.0T magnetic resonance imaging (MRI). MRI of the left ventricular (LV) structure and function in healthy volunteers has been reported extensively at 1.5T. Materials and Methods : A population of 1528 volunteers was scanned. A standardized approach was taken to acquire steady-state free precession (SSFP) LV data in the short-axis plane, and images were quantified using commercial software. Six observers undertook the segmentation analysis. Results : Mean values (±standard deviation, SD) were: ejection fraction (EF) = 69 ± 6%, end diastolic volume index (EDVI) = 71 ± 13 ml/m2 , end systolic volume index (ESVI) = 22 ± 7 ml/m2 , stroke volume index (SVI) = 49 ± 8 ml/m2 , and LV mass index (LVMI) = 55 ± 12 g/m2 . The mean EF was slightly larger for females (69%) than for males (68%), but all other variables were smaller for females (EDVI 68v77 ml/m2 , ESVI 21v25 ml/m2 , SVI 46v52 ml/m2 , LVMI 49v64 g/m2, all P < 0.05). The mean LV volume data mostly decreased with each age decade (EDVI males: -2.9 ± 1.3 ml/m2 , females: -3.1 ± 0.8 ml/m2 ; ESVI males: -1.3 ± 0.7 ml/m2 , females: -1.7 ± 0.5 ml/m2 ; SVI males: -1.7 ± 0.9 ml/m2 , females: -1.4 ± 0.6 ml/m2 ; LVMI males: -1.6 ± 1.1 g/m2 , females: -0.2 ± 0.6 g/m2 but the mean EF was virtually stable in males (0.6 ± 0.6%) and rose slightly in females (1.2 ± 0.5%) with age. Conclusion : LV reference ranges are provided in this population-based MR study at 3.0T. The variables are similar to those described at 1.5T, including variations with age and gender. These data may help to support future population-based MR research studies that involve the use of 3.0T MRI scanners.Publisher PDFPeer reviewe