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Hierarchical spherical deformation for cortical surface registration.
Lyu I, Kang H, Woodward ND, Styner MA, Landman BA
(2019) Med Image Anal 57: 72-88
MeSH Terms: Algorithms, Anatomic Landmarks, Brain Mapping, Datasets as Topic, Humans, Image Enhancement, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging
Show Abstract · Added January 31, 2020
We present hierarchical spherical deformation for a group-wise shape correspondence to address template selection bias and to minimize registration distortion. In this work, we aim at a continuous and smooth deformation field to guide accurate cortical surface registration. In conventional spherical registration methods, a global rigid alignment and local deformation are independently performed. Motivated by the composition of precession and intrinsic rotation, we simultaneously optimize global rigid rotation and non-rigid local deformation by utilizing spherical harmonics interpolation of local composite rotations in a single framework. To this end, we indirectly encode local displacements by such local composite rotations as functions of spherical locations. Furthermore, we introduce an additional regularization term to the spherical deformation, which maximizes its rigidity while reducing registration distortion. To improve surface registration performance, we employ the second order approximation of the energy function that enables fast convergence of the optimization. In the experiments, we validate our method on healthy normal subjects with manual cortical surface parcellation in registration accuracy and distortion. We show an improved shape correspondence with high accuracy in cortical surface parcellation and significantly low registration distortion in surface area and edge length. In addition to validation, we discuss parameter tuning, optimization, and implementation design with potential acceleration.
Copyright © 2019 Elsevier B.V. All rights reserved.
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1 Members
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9 MeSH Terms
Registration-based image enhancement improves multi-atlas segmentation of the thalamic nuclei and hippocampal subfields.
Bao S, Bermudez C, Huo Y, Parvathaneni P, Rodriguez W, Resnick SM, D'Haese PF, McHugo M, Heckers S, Dawant BM, Lyu I, Landman BA
(2019) Magn Reson Imaging 59: 143-152
MeSH Terms: Algorithms, Brain Mapping, Hippocampus, Humans, Image Enhancement, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Temporal Lobe, Thalamic Nuclei
Show Abstract · Added March 26, 2019
Magnetic resonance imaging (MRI) is an important tool for analysis of deep brain grey matter structures. However, analysis of these structures is limited due to low intensity contrast typically found in whole brain imaging protocols. Herein, we propose a big data registration-enhancement (BDRE) technique to augment the contrast of deep brain structures using an efficient large-scale non-rigid registration strategy. Direct validation is problematic given a lack of ground truth data. Rather, we validate the usefulness and impact of BDRE for multi-atlas (MA) segmentation on two sets of structures of clinical interest: the thalamic nuclei and hippocampal subfields. The experimental design compares algorithms using T1-weighted 3 T MRI for both structures (and additional 7 T MRI for the thalamic nuclei) with an algorithm using BDRE. As baseline comparisons, a recent denoising (DN) technique and a super-resolution (SR) method are used to preprocess the original 3 T MRI. The performance of each MA segmentation is evaluated by the Dice similarity coefficient (DSC). BDRE significantly improves mean segmentation accuracy over all methods tested for both thalamic nuclei (3 T imaging: 9.1%; 7 T imaging: 15.6%; DN: 6.9%; SR: 16.2%) and hippocampal subfields (3 T T1 only: 8.7%; DN: 8.4%; SR: 8.6%). We also present DSC performance for each thalamic nucleus and hippocampal subfield and show that BDRE can help MA segmentation for individual thalamic nuclei and hippocampal subfields. This work will enable large-scale analysis of clinically relevant deep brain structures from commonly acquired T1 images.
Copyright © 2019 Elsevier Inc. All rights reserved.
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9 MeSH Terms
Enhancing Parathyroid Gland Visualization Using a Near Infrared Fluorescence-Based Overlay Imaging System.
McWade MA, Thomas G, Nguyen JQ, Sanders ME, Solórzano CC, Mahadevan-Jansen A
(2019) J Am Coll Surg 228: 730-743
MeSH Terms: Adult, Aged, Equipment Design, Female, Fluorescence, Humans, Image Enhancement, Male, Middle Aged, Optical Imaging, Parathyroid Diseases, Parathyroid Glands, Parathyroidectomy, Phantoms, Imaging, Spectroscopy, Near-Infrared, Surgery, Computer-Assisted, Thyroid Diseases, Thyroidectomy
Show Abstract · Added April 2, 2019
BACKGROUND - Misidentifying parathyroid glands (PGs) during thyroidectomies or parathyroidectomies could significantly increase postoperative morbidity. Imaging systems based on near infrared autofluorescence (NIRAF) detection can localize PGs with high accuracy. These devices, however, depict NIRAF images on remote display monitors, where images lack spatial context and comparability with actual surgical field of view. In this study, we designed an overlay tissue imaging system (OTIS) that detects tissue NIRAF and back-projects the collected signal as a visible image directly onto the surgical field of view instead of a display monitor, and tested its ability for enhancing parathyroid visualization.
STUDY DESIGN - The OTIS was first calibrated with a fluorescent ink grid and initially tested with parathyroid, thyroid, and lymph node tissues ex vivo. For in vivo measurements, the surgeon's opinion on tissue of interest was first ascertained. After the surgeon looked away, the OTIS back-projected visible green light directly onto the tissue of interest, only if the device detected relatively high NIRAF as observed in PGs. System accuracy was determined by correlating NIRAF projection with surgeon's visual confirmation for in situ PGs or histopathology report for excised PGs.
RESULTS - The OTIS yielded 100% accuracy when tested ex vivo with parathyroid, thyroid, and lymph node specimens. Subsequently, the device was evaluated in 30 patients who underwent thyroidectomy and/or parathyroidectomy. Ninety-seven percent of exposed tissue of interest was visualized correctly as PGs by the OTIS, without requiring display monitors or contrast agents.
CONCLUSIONS - Although OTIS holds novel potential for enhancing label-free parathyroid visualization directly within the surgical field of view, additional device optimization is required for eventual clinical use.
Copyright © 2019 American College of Surgeons. Published by Elsevier Inc. All rights reserved.
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18 MeSH Terms
Exact Topological Inference for Paired Brain Networks Persistent Homology.
Chung MK, Vilalta-Gil V, Lee H, Rathouz PJ, Lahey BB, Zald DH
(2017) Inf Process Med Imaging 2017: 299-310
MeSH Terms: Algorithms, Brain, Brain Mapping, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 21, 2018
We present a novel framework for characterizing paired brain networks using techniques in hyper-networks, sparse learning and persistent homology. The framework is general enough for dealing with any type of paired images such as twins, multimodal and longitudinal images. The exact nonparametric statistical inference procedure is derived on testing monotonic graph theory features that do not rely on time consuming permutation tests. The proposed method computes the exact probability in quadratic time while the permutation tests require exponential time. As illustrations, we apply the method to simulated networks and a twin fMRI study. In case of the latter, we determine the statistical significance of the heritability index of the large-scale reward network where every voxel is a network node.
0 Communities
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9 MeSH Terms
CEST imaging of fast exchanging amine pools with corrections for competing effects at 9.4 T.
Zhang XY, Wang F, Li H, Xu J, Gochberg DF, Gore JC, Zu Z
(2017) NMR Biomed 30:
MeSH Terms: Algorithms, Amines, Animals, Artifacts, Biomarkers, Tumor, Brain Neoplasms, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Molecular Imaging, Proton Magnetic Resonance Spectroscopy, Rats, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 13, 2017
Chemical exchange saturation transfer (CEST) imaging of fast exchanging amine protons at 3 ppm offset from the water resonant frequency is of practical interest, but quantification of fast exchanging pools by CEST is challenging. To effectively saturate fast exchanging protons, high irradiation powers need to be applied, but these may cause significant direct water saturation as well as non-specific semi-solid magnetization transfer (MT) effects, and thus decrease the specificity of the measured signal. In addition, the CEST signal may depend on the water longitudinal relaxation time (T ), which likely varies between tissues and with pathology, further reducing specificity. Previously, an analysis of the asymmetry of saturation effects (MTR ) has been commonly used to quantify fast exchanging amine CEST signals. However, our results show that MTR is greatly affected by the above factors, as well as asymmetric MT and nuclear Overhauser enhancement (NOE) effects. Here, we instead applied a relatively more specific inverse analysis method, named AREX (apparent exchange-dependent relaxation), that has previously been applied only to slow and intermediate exchanging solutes. Numerical simulations and controlled phantom experiments show that, although MTR depends on T and semi-solid content, AREX acquired in steady state does not, which suggests that AREX is more specific than MTR . By combining with a fitting approach instead of using the asymmetric analysis to obtain reference signals, AREX can also avoid contaminations from asymmetric MT and NOE effects. Animal experiments show that these two quantification methods produce differing contrasts between tumors and contralateral normal tissues in rat brain tumor models, suggesting that conventional MTR applied in vivo may be influenced by variations in T , semi-solid content, or NOE effect. Thus, the use of MTR may lead to misinterpretation, while AREX with corrections for competing effects likely enhances the specificity and accuracy of quantification to fast exchanging pools.
Copyright © 2017 John Wiley & Sons, Ltd.
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3 Members
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14 MeSH Terms
Accuracy in the quantification of chemical exchange saturation transfer (CEST) and relayed nuclear Overhauser enhancement (rNOE) saturation transfer effects.
Zhang XY, Wang F, Li H, Xu J, Gochberg DF, Gore JC, Zu Z
(2017) NMR Biomed 30:
MeSH Terms: Algorithms, Amines, Animals, Artifacts, Biomarkers, Tumor, Brain Neoplasms, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Molecular Imaging, Proton Magnetic Resonance Spectroscopy, Rats, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 13, 2017
Accurate quantification of chemical exchange saturation transfer (CEST) effects, including dipole-dipole mediated relayed nuclear Overhauser enhancement (rNOE) saturation transfer, is important for applications and studies of molecular concentration and transfer rate (and thereby pH or temperature). Although several quantification methods, such as Lorentzian difference (LD) analysis, multiple-pool Lorentzian fits, and the three-point method, have been extensively used in several preclinical and clinical applications, the accuracy of these methods has not been evaluated. Here we simulated multiple-pool Z spectra containing the pools that contribute to the main CEST and rNOE saturation transfer signals in the brain, numerically fit them using the different methods, and then compared their derived CEST metrics with the known solute concentrations and exchange rates. Our results show that the LD analysis overestimates contributions from amide proton transfer (APT) and intermediate exchanging amine protons; the three-point method significantly underestimates both APT and rNOE saturation transfer at -3.5 ppm (NOE(-3.5)). The multiple-pool Lorentzian fit is more accurate than the other two methods, but only at lower irradiation powers (≤1 μT at 9.4 T) within the range of our simulations. At higher irradiation powers, this method is also inaccurate because of the presence of a fast exchanging CEST signal that has a non-Lorentzian lineshape. Quantitative parameters derived from in vivo images of rodent brain tumor obtained using an irradiation power of 1 μT were also compared. Our results demonstrate that all three quantification methods show similar contrasts between tumor and contralateral normal tissue for both APT and the NOE(-3.5). However, the quantified values of the three methods are significantly different. Our work provides insight into the fitting accuracy obtainable in a complex tissue model and provides guidelines for evaluating other newly developed quantification methods.
Copyright © 2017 John Wiley & Sons, Ltd.
0 Communities
3 Members
0 Resources
14 MeSH Terms
New resonator geometries for ICE decoupling of loop arrays.
Yan X, Gore JC, Grissom WA
(2017) J Magn Reson 277: 59-67
MeSH Terms: Algorithms, Computer Simulation, Electromagnetic Fields, Image Enhancement, Magnetic Resonance Imaging, Phantoms, Imaging
Show Abstract · Added April 6, 2017
RF arrays with a large number of independent coil elements are advantageous for parallel transmission (pTx) and reception at high fields. One of the main challenges in designing RF arrays is to minimize the electromagnetic (EM) coupling between the coil elements. The induced current elimination (ICE) method, which uses additional resonator elements to cancel coils' mutual EM coupling, has proven to be a simple and efficient solution for decoupling microstrip, L/C loop, monopole and dipole arrays. However, in previous embodiments of conventional ICE decoupling, the decoupling elements acted as "magnetic-walls" with low transmit fields and consequently low MR signal near them. To solve this problem, new resonator geometries including overlapped and perpendicular decoupling loops are proposed. The new geometries were analyzed theoretically and validated in EM simulations, bench tests and MR experiments. The isolation between two closely-placed loops could be improved from about -5dB to <-45dB by using the new geometries.
Copyright © 2017 Elsevier Inc. All rights reserved.
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1 Members
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6 MeSH Terms
30-Second bound and pore water concentration mapping of cortical bone using 2D UTE with optimized half-pulses.
Manhard MK, Harkins KD, Gochberg DF, Nyman JS, Does MD
(2017) Magn Reson Med 77: 945-950
MeSH Terms: Algorithms, Body Water, Cortical Bone, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Porosity, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Computer-Assisted
Show Abstract · Added February 27, 2017
PURPOSE - MRI of cortical bone has the potential to offer new information about fracture risk. Current methods are typically performed with 3D acquisitions, which suffer from long scan times and are generally limited to extremities. This work proposes using 2D UTE with half pulses for quantitatively mapping bound and pore water in cortical bone.
METHODS - Half-pulse 2D UTE methods were implemented on a 3T Philips Achieva scanner using an optimized slice-select gradient waveform, with preparation pulses to selectively image bound or pore water. The 2D methods were quantitatively compared with previously implemented 3D methods in the tibia in five volunteers.
RESULTS - The mean difference between bound and pore water concentration acquired from 3D and 2D sequences was 0.6 and 0.9 mol H/L (3 and 12%, respectively). While 2D pore water methods tended to slightly overestimate concentrations relative to 3D methods, differences were less than scan-rescan uncertainty and expected differences between healthy and fracture-prone bones.
CONCLUSION - Quantitative bound and pore water concentration mapping in cortical bone can be accelerated by 2 orders of magnitude using 2D protocols with optimized half-pulse excitation. Magn Reson Med 77:945-950, 2017. © 2017 International Society for Magnetic Resonance in Medicine.
© 2017 International Society for Magnetic Resonance in Medicine.
2 Communities
1 Members
0 Resources
11 MeSH Terms
Cerebral hemodynamics and pseudo-continuous arterial spin labeling considerations in adults with sickle cell anemia.
Juttukonda MR, Jordan LC, Gindville MC, Davis LT, Watchmaker JM, Pruthi S, Donahue MJ
(2017) NMR Biomed 30:
MeSH Terms: Adult, Anemia, Sickle Cell, Blood Flow Velocity, Cerebral Angiography, Cerebrovascular Circulation, Contrast Media, Female, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Angiography, Male, Reproducibility of Results, Sensitivity and Specificity, Spin Labels
Show Abstract · Added March 24, 2020
Sickle cell anemia (SCA) is a genetic disorder resulting in reduced oxygen carrying capacity and elevated stroke risk. Pseudo-continuous arterial spin labeling (pCASL) measures of cerebral blood flow (CBF) may have relevance for stroke risk assessment; however, the effects of elevated flow velocity and reduced bolus arrival time (BAT) on CBF quantification in SCA patients have not been thoroughly characterized, and pCASL model parameters used in healthy adults are often applied to patients with SCA. Here, cervical arterial flow velocities and pCASL labeling efficiencies were computed in adults with SCA (n = 19) and age- and race-matched controls without sickle trait (n = 7) using pCASL in sequence with phase contrast MR angiography (MRA). Controls (n = 7) and a subgroup of patients (n = 8) also underwent multi-post-labeling-delay pCASL for BAT assessment. Mean flow velocities were elevated in SCA adults (velocity = 28.3 ± 4.1 cm/s) compared with controls (velocity = 24.5 ± 3.8 cm/s), and mean pCASL labeling efficiency (α) was reduced in SCA adults (α = 0.72) relative to controls (α = 0.91). In patients, mean whole-brain CBF from phase contrast MRA was 91.8 ± 18.1 ml/100 g/min, while mean pCASL CBF when assuming a constant labeling efficiency of 0.86 was 75.2 ± 17.3 ml/100 g/min (p < 0.01), resulting in a mean absolute quantification error of 23% when a labeling efficiency appropriate for controls was assumed. This difference cannot be accounted for by BAT (whole-brain BAT: control, 1.13 ± 0.06 s; SCA, 1.02 ± 0.09 s) or tissue T variation. In conclusion, BAT variation influences pCASL quantification less than elevated cervical arterial velocity and labeling efficiency variation in SCA adults; thus, a lower labeling efficiency (α = 0.72) or subject-specific labeling efficiency should be incorporated for SCA patients.
Copyright © 2017 John Wiley & Sons, Ltd.
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MeSH Terms
Chemical exchange saturation transfer of the cervical spinal cord at 7 T.
Dula AN, Pawate S, Dethrage LM, Conrad BN, Dewey BE, Barry RL, Smith SA
(2016) NMR Biomed 29: 1249-57
MeSH Terms: Adult, Algorithms, Cervical Cord, Female, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Imaging, Male, Middle Aged, Multiple Sclerosis, Relapsing-Remitting, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added April 6, 2017
High-magnetic-field (7 T) chemical exchange saturation transfer (CEST) MRI provides information on the tissue biochemical environment. Multiple sclerosis (MS) affects the entire central nervous system, including the spinal cord. Optimal CEST saturation parameters found via simulation were implemented for CEST MRI in 10 healthy controls and 10 patients with MS, and the results were examined using traditional asymmetry analysis and a Lorentzian fitting method. In addition, T1 - and T2 *-weighted images were acquired for lesion localization and the transmitted B1 (+) field was evaluated to guide imaging parameters. Distinct spectral features for all tissue types studied were found both up- and downfield from the water resonance. The z spectra in healthy subjects had the expected z spectral shape with CEST effects apparent from 2.0 to 4.5 ppm. The z spectra from patients with MS demonstrated deviations from this expected normal shape, indicating this method's sensitivity to known pathology as well as to tissues appearing normal on conventional MRI. Examination of the calculated CESTasym revealed increased asymmetry around the amide proton resonance (Δω = 3.5 ppm), but it was apparent that this measure is complicated by detail in the CEST spectrum upfield from water, which is expected to result from the nuclear Overhauser effect. The z spectra upfield (negative ppm range) were also distinct between healthy and diseased tissue, and could not be ignored, particularly when considering the conventional asymmetry analysis used to quantify the CEST effect. For all frequencies greater than +1 ppm, the Lorentzian differences (and z spectra) for lesions and normal-appearing white matter were distinct from those for healthy white matter. The increased frequency separation and signal-to-noise ratio, in concert with prolonged T1 at 7 T, resulted in signal enhancements necessary to detect subtle tissue changes not possible at lower field strengths. This study presents CEST imaging metrics that may be sensitive to the extensive and temporally varying biochemical neuropathology of MS in the spinal cord. Copyright © 2016 John Wiley & Sons, Ltd.
Copyright © 2016 John Wiley & Sons, Ltd.
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13 MeSH Terms