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102


Rapid quantitative magnetization transfer imaging: Utilizing the hybrid state and the generalized Bloch model

Assländer, Jakob; Gultekin, Cem; Mao, Andrew; Zhang, Xiaoxia; Duchemin, Quentin; Liu, Kangning; Charlson, Robert W; Shepherd, Timothy M; Fernandez-Granda, Carlos; Flassbeck, Sebastian
PURPOSE/OBJECTIVE:To explore efficient encoding schemes for quantitative magnetization transfer (qMT) imaging with few constraints on model parameters. THEORY AND METHODS/METHODS:We combine two recently proposed models in a Bloch-McConnell equation: the dynamics of the free spin pool are confined to the hybrid state, and the dynamics of the semi-solid spin pool are described by the generalized Bloch model. We numerically optimize the flip angles and durations of a train of radio frequency pulses to enhance the encoding of three qMT parameters while accounting for all eight parameters of the two-pool model. We sparsely sample each time frame along this spin dynamics with a three-dimensional radial koosh-ball trajectory, reconstruct the data with subspace modeling, and fit the qMT model with a neural network for computational efficiency. RESULTS:We extracted qMT parameter maps of the whole brain with an effective resolution of 1.24 mm from a 12.6-min scan. In lesions of multiple sclerosis subjects, we observe a decreased size of the semi-solid spin pool and longer relaxation times, consistent with previous reports. CONCLUSION/CONCLUSIONS:The encoding power of the hybrid state, combined with regularized image reconstruction, and the accuracy of the generalized Bloch model provide an excellent basis for efficient quantitative magnetization transfer imaging with few constraints on model parameters.
PMID: 38073093
ISSN: 1522-2594
CID: 5589482

On multi-path longitudinal spin relaxation in brain tissue

Assländer, Jakob; Mao, Andrew; Beck, Erin S; Rosa, Francesco La; Charlson, Robert W; Shepherd, Timothy M; Flassbeck, Sebastian
The purpose of this paper is to confirm previous reports that identified magnetization transfer (MT) as an inherent driver of longitudinal relaxation in brain tissue by asserting a substantial difference between the $T_1$ relaxation times of the free and the semi-solid spin pools. Further, we aim to identify an avenue towards the quantification of these relaxation processes on a voxel-by-voxel basis in a clinical imaging setting, i.e. with a nominal resolution of 1mm isotropic and full brain coverage in 12min. To this end, we optimized a hybrid-state pulse sequence for mapping the parameters of an unconstrained MT model. We scanned 4 people with relapsing-remitting multiple sclerosis (MS) and 4 healthy controls with this pulse sequence and estimated $T_1^f \approx 1.90$s and $T_1^s \approx 0.327$s for the free and semi-solid spin pool of healthy WM, respectively, confirming previous reports and questioning the commonly used assumptions $T_1^s = T_1^f$ or $T_1^s = 1$s. Further, we estimated a fractional size of the semi-solid spin pool of $m_0^s \approx 0.202$, which is larger than previously assumed. An analysis of $T_1^f$ in normal appearing white matter revealed statistically significant differences between individuals with MS and controls. In conclusion, we confirm that longitudinal spin relaxation in brain tissue is dominated by MT and that the hybrid state facilitates a voxel-wise fit of the unconstrained MT model, which enables the analysis of subtle neurodegeneration.
PMCID:9882584
PMID: 36713253
ISSN: 2331-8422
CID: 5473602

Improved reconstruction of crossing fibers in the mouse optic pathways with orientation distribution function fingerprinting

Filipiak, Patryk; Sajitha, Thajunnisa A; Shepherd, Timothy M; Clarke, Kamri; Goldman, Hannah; Placantonakis, Dimitris G; Zhang, Jiangyang; Chan, Kevin C; Boada, Fernando E; Baete, Steven H
PURPOSE/OBJECTIVE:The accuracy of diffusion MRI tractography reconstruction decreases in the white matter regions with crossing fibers. The optic pathways in rodents provide a challenging structure to test new diffusion tractography approaches because of the small crossing volume within the optic chiasm and the unbalanced 9:1 proportion between the contra- and ipsilateral neural projections from the retina to the lateral geniculate nucleus, respectively. METHODS: RESULTS:ODF-FP outperformed by over 100% all the tested methods in terms of the ratios between the contra- and ipsilateral segments of the reconstructed optic pathways as well as the spatial overlap between tractography and MEMRI. CONCLUSION/CONCLUSIONS:In this challenging model system, ODF-Fingerprinting reduced uncertainty of diffusion tractography for complex structural formations of fiber bundles.
PMID: 37927121
ISSN: 1522-2594
CID: 5612792

Comparison of Dentatorubrothalamic Tractography Methods Based on the Anatomy of the Rubral Wing

Berger, Assaf; Chung, Jongchul; Schnurman, Zane; Stepanov, Valentin; Pan, Ling; Shepherd, Timothy M; Mogilner, Alon
BACKGROUND AND OBJECTIVES/OBJECTIVE:Precise localization of the dentatorubrothalamic (DRT) tract can facilitate anatomic targeting in MRI-guided high-intensity focused ultrasound (HIFU) thalamotomy and thalamic deep brain stimulation for tremor. The anatomic segment of DRT fibers adjacent to the ventral intermediate nucleus of the thalamus (VIM), referred to as the rubral wing (RW), may be directly visualized on the fast gray matter acquisition T1 inversion recovery. We compared reproducibility, lesion overlap, and clinical outcomes when reconstructing the DRT tract using a novel anatomically defined RW region of interest, DRT-RW, to an existing tractography method based on the posterior subthalamic area region of interest (DRT-PSA). METHODS:We reviewed data of 23 patients with either essential tremor (n = 18) or tremor-predominant Parkinson's disease (n = 5) who underwent HIFU thalamotomy, targeting the VIM. DRT tractography, ipsilateral to the lesion, was created based on either DRT-PSA or DRT-RW. Volume sections of each tract were created and dice similarity coefficients were used to measure spatial overlap between the 2 tractographies. Post-HIFU lesion size and location (on postoperative T2 MRI) was correlated with tremor outcomes and side effects for both DRT tractography methods and the RW itself. RESULTS:DRT-PSA passed through the RW and DRT-RW intersected with the ROIs of the DRT-PSA in all 23 cases. A higher percentage of the RW was ablated in patients who achieved tremor control (18.9%, 95% CI 15.1, 22.7) vs those without tremor relief (6.7%, 95% CI% 0, 22.4, P = .017). In patients with tremor control 6 months postoperatively (n = 12), those with side effects (n = 6) had larger percentages of their tracts ablated in comparison with those without side effects in both DRT-PSA (44.8, 95% CI 31.8, 57.8 vs 24.2%, 95% CI 12.4, 36.1, P = .025) and DRT-RW (35.4%, 95% CI 21.5, 49.3 vs 21.7%, 95% CI 12.7, 30.8, P = .030). CONCLUSION/CONCLUSIONS:Tractography of the DRT could be reconstructed by direct anatomic visualization of the RW on fast gray matter acquisition T1 inversion recovery-MRI. Anatomic planning is expected to be quicker, more reproducible, and less operator-dependent.
PMID: 38289086
ISSN: 2332-4260
CID: 5627462

Tractography passes the test: Results from the diffusion-simulated connectivity (disco) challenge

Girard, Gabriel; Rafael-Patiño, Jonathan; Truffet, Raphaël; Aydogan, Dogu Baran; Adluru, Nagesh; Nair, Veena A; Prabhakaran, Vivek; Bendlin, Barbara B; Alexander, Andrew L; Bosticardo, Sara; Gabusi, Ilaria; Ocampo-Pineda, Mario; Battocchio, Matteo; Piskorova, Zuzana; Bontempi, Pietro; Schiavi, Simona; Daducci, Alessandro; Stafiej, Aleksandra; Ciupek, Dominika; Bogusz, Fabian; Pieciak, Tomasz; Frigo, Matteo; Sedlar, Sara; Deslauriers-Gauthier, Samuel; Kojčić, Ivana; Zucchelli, Mauro; Laghrissi, Hiba; Ji, Yang; Deriche, Rachid; Schilling, Kurt G; Landman, Bennett A; Cacciola, Alberto; Basile, Gianpaolo Antonio; Bertino, Salvatore; Newlin, Nancy; Kanakaraj, Praitayini; Rheault, Francois; Filipiak, Patryk; Shepherd, Timothy M; Lin, Ying-Chia; Placantonakis, Dimitris G; Boada, Fernando E; Baete, Steven H; Hernández-Gutiérrez, Erick; Ramírez-Manzanares, Alonso; Coronado-Leija, Ricardo; Stack-Sánchez, Pablo; Concha, Luis; Descoteaux, Maxime; Mansour L, Sina; Seguin, Caio; Zalesky, Andrew; Marshall, Kenji; Canales-Rodríguez, Erick J; Wu, Ye; Ahmad, Sahar; Yap, Pew-Thian; Théberge, Antoine; Gagnon, Florence; Massi, Frédéric; Fischi-Gomez, Elda; Gardier, Rémy; Haro, Juan Luis Villarreal; Pizzolato, Marco; Caruyer, Emmanuel; Thiran, Jean-Philippe
Estimating structural connectivity from diffusion-weighted magnetic resonance imaging is a challenging task, partly due to the presence of false-positive connections and the misestimation of connection weights. Building on previous efforts, the MICCAI-CDMRI Diffusion-Simulated Connectivity (DiSCo) challenge was carried out to evaluate state-of-the-art connectivity methods using novel large-scale numerical phantoms. The diffusion signal for the phantoms was obtained from Monte Carlo simulations. The results of the challenge suggest that methods selected by the 14 teams participating in the challenge can provide high correlations between estimated and ground-truth connectivity weights, in complex numerical environments. Additionally, the methods used by the participating teams were able to accurately identify the binary connectivity of the numerical dataset. However, specific false positive and false negative connections were consistently estimated across all methods. Although the challenge dataset doesn't capture the complexity of a real brain, it provided unique data with known macrostructure and microstructure ground-truth properties to facilitate the development of connectivity estimation methods.
PMID: 37330025
ISSN: 1095-9572
CID: 5609102

Editorial for "Synthetic MRI With MR-STAT: Results From a Clinical Trial" [Editorial]

Cloos, Martijn A; Shepherd, Timothy M
PMID: 36326570
ISSN: 1522-2586
CID: 5358702

Surgical cytoreduction of deep-seated high-grade glioma through tubular retractor

Hajtovic, Sabastian; Sun, James; Multani, Jasjit S; Herrmann, Linda L; Britton, Hannah; Gautreaux, Jose; Tortolero, Lea; Harrison, Gillian; Golfinos, John G; Shepherd, Timothy M; Tanweer, Omar; Placantonakis, Dimitris G
OBJECTIVE:Maximal safe resection is the goal of surgical treatment for high-grade glioma (HGG). Deep-seated hemispheric gliomas present a surgical challenge due to safety concerns and previously were often considered inoperable. The authors hypothesized that use of tubular retractors would allow resection of deep-seated gliomas with an acceptable safety profile. The purpose of this study was to describe surgical outcomes and survival data after resection of deep-seated HGG with stereotactically placed tubular retractors, as well as to discuss the technical advances that enable such procedures. METHODS:This is a retrospective review of 20 consecutive patients who underwent 22 resections of deep-seated hemispheric HGG with the Viewsite Brain Access System by a single surgeon. Patient demographics, survival, tumor characteristics, extent of resection (EOR), and neurological outcomes were recorded. Cannulation trajectories and planned resection volumes depended on the relative location of white matter tracts extracted from diffusion tractography. The surgical plans were designed on the Brainlab system and preoperatively visualized on the Surgical Theater virtual reality SNAP platform. Volumetric assessment of EOR was obtained on the Brainlab platform and confirmed by a board-certified neuroradiologist. RESULTS:Twenty adult patients (18 with IDH-wild-type glioblastomas and 2 with IDH-mutant grade IV astrocytomas) and 22 surgeries were included in the study. The cohort included both newly diagnosed (n = 17; 77%) and recurrent (n = 5; 23%) tumors. Most tumors (64%) abutted the ventricular system. The average preoperative and postoperative tumor volumes measured 33.1 ± 5.3 cm3 and 15.2 ± 5.1 cm3, respectively. The median EOR was 93%. Surgical complications included 2 patients (10%) who developed entrapment of the temporal horn, necessitating placement of a ventriculoperitoneal shunt; 1 patient (5%) who suffered a wound infection and pulmonary embolus; and 1 patient (5%) who developed pneumonia. In 2 cases (9%) patients developed new permanent visual field deficits, and in 5 cases (23%) patients experienced worsening of preoperative deficits. Preoperative neurological or cognitive deficits remained the same in 9 cases (41%) and improved in 7 (32%). The median overall survival was 14.4 months in all patients (n = 20) and in the newly diagnosed IDH-wild-type glioblastoma group (n = 16). CONCLUSIONS:Deep-seated HGGs, which are surgically challenging and frequently considered inoperable, are amenable to resection through tubular retractors, with an acceptable safety profile. Such cytoreductive surgery may allow these patients to experience an overall survival comparable to those with more superficial tumors.
PMID: 36334293
ISSN: 1933-0693
CID: 5358912

MRI-Visible Anatomy of the Basal Ganglia and Thalamus

Hoch, Michael J; Shepherd, Timothy M
Conventional MR imaging does not discriminate basal ganglia and thalamic internal anatomy well. Radiology reports describe anatomic locations but not specific functional structures. Functional neurosurgery uses indirect targeting based on commissural coordinates or atlases that do not fully account for individual variability. We describe innovative MR imaging sequences that improve the visualization of normal anatomy in this complex brain region and may increase our understanding of basal ganglia and thalamic function. Better visualization also may improve treatments for movement disorders and other emerging functional neurosurgery targets. We aim to provide an accessible review of the most clinically-relevant neuroanatomy within the thalamus and basal ganglia.
PMID: 35843660
ISSN: 1557-9867
CID: 5278552

MRI-Visible Anatomy of the Brainstem

Shepherd, Timothy M; Hoch, Michael J
Human brainstem internal anatomy is intricate, complex, and essential to normal brain function. The brainstem is affected by stroke, multiple sclerosis, and most neurodegenerative diseases-a 1-mm focus of pathologic condition can have profound clinical consequences. Unfortunately, detailed internal brainstem anatomy is difficult to see with conventional MRI sequences. We review normal brainstem anatomy visualized on widely available clinical 3-T MRI scanners using fast gray matter acquisition T1 inversion recovery, probabilistic diffusion tractography, neuromelanin, and susceptibility-weighted imaging. Better anatomic localization using these recent innovations improves our ability to diagnose, localize, and treat brainstem diseases. We aim to provide an accessible review of the most clinically relevant brainstem neuroanatomy.
PMID: 35843662
ISSN: 1557-9867
CID: 5278562

Performance of orientation distribution function-fingerprinting with a biophysical multicompartment diffusion model

Filipiak, Patryk; Shepherd, Timothy; Lin, Ying-Chia; Placantonakis, Dimitris G; Boada, Fernando E; Baete, Steven H
PURPOSE/OBJECTIVE:Orientation Distribution Function (ODF) peak finding methods typically fail to reconstruct fibers crossing at shallow angles below 40°, leading to errors in tractography. ODF-Fingerprinting (ODF-FP) with the biophysical multicompartment diffusion model allows for breaking this barrier. METHODS:A randomized mechanism to generate a multidimensional ODF-dictionary that covers biologically plausible ranges of intra- and extra-axonal diffusivities and fraction volumes is introduced. This enables ODF-FP to address the high variability of brain tissue. The performance of the proposed approach is evaluated on both numerical simulations and a reconstruction of major fascicles from high- and low-resolution in vivo diffusion images. RESULTS:ODF-FP with the suggested modifications correctly identifies fibers crossing at angles as shallow as 10 degrees in the simulated data. In vivo, our approach reaches 56% of true positives in determining fiber directions, resulting in visibly more accurate reconstruction of pyramidal tracts, arcuate fasciculus, and optic radiations than the state-of-the-art techniques. Moreover, the estimated diffusivity values and fraction volumes in corpus callosum conform with the values reported in the literature. CONCLUSION/CONCLUSIONS:The modified ODF-FP outperforms commonly used fiber reconstruction methods at shallow angles, which improves deterministic tractography outcomes of major fascicles. In addition, the proposed approach allows for linearization of the microstructure parameters fitting problem.
PMID: 35225365
ISSN: 1522-2594
CID: 5174102