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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: 5576662

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

Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI

Maffei, Chiara; Girard, Gabriel; Schilling, Kurt G; Aydogan, Dogu Baran; Adluru, Nagesh; Zhylka, Andrey; Wu, Ye; Mancini, Matteo; Hamamci, Andac; Sarica, Alessia; Teillac, Achille; Baete, Steven H; Karimi, Davood; Yeh, Fang-Cheng; Yildiz, Mert E; Gholipour, Ali; Bihan-Poudec, Yann; Hiba, Bassem; Quattrone, Andrea; Quattrone, Aldo; Boshkovski, Tommy; Stikov, Nikola; Yap, Pew-Thian; de Luca, Alberto; Pluim, Josien; Leemans, Alexander; Prabhakaran, Vivek; Bendlin, Barbara B; Alexander, Andrew L; Landman, Bennett A; Canales-Rodríguez, Erick J; Barakovic, Muhamed; Rafael-Patino, Jonathan; Yu, Thomas; Rensonnet, Gaëtan; Schiavi, Simona; Daducci, Alessandro; Pizzolato, Marco; Fischi-Gomez, Elda; Thiran, Jean-Philippe; Dai, George; Grisot, Giorgia; Lazovski, Nikola; Puch, Santi; Ramos, Marc; Rodrigues, Paulo; Prčkovska, Vesna; Jones, Robert; Lehman, Julia; Haber, Suzanne N; Yendiki, Anastasia
Limitations in the accuracy of brain pathways reconstructed by diffusion MRI (dMRI) tractography have received considerable attention. While the technical advances spearheaded by the Human Connectome Project (HCP) led to significant improvements in dMRI data quality, it remains unclear how these data should be analyzed to maximize tractography accuracy. Over a period of two years, we have engaged the dMRI community in the IronTract Challenge, which aims to answer this question by leveraging a unique dataset. Macaque brains that have received both tracer injections and ex vivo dMRI at high spatial and angular resolution allow a comprehensive, quantitative assessment of tractography accuracy on state-of-the-art dMRI acquisition schemes. We find that, when analysis methods are carefully optimized, the HCP scheme can achieve similar accuracy as a more time-consuming, Cartesian-grid scheme. Importantly, we show that simple pre- and post-processing strategies can improve the accuracy and robustness of many tractography methods. Finally, we find that fiber configurations that go beyond crossing (e.g., fanning, branching) are the most challenging for tractography. The IronTract Challenge remains open and we hope that it can serve as a valuable validation tool for both users and developers of dMRI analysis methods.
PMID: 35636227
ISSN: 1095-9572
CID: 5235852

Reproducibility of the Standard Model of diffusion in white matter on clinical MRI systems

Coelho, Santiago; Baete, Steven H; Lemberskiy, Gregory; Ades-Aaron, Benjamin; Barrol, Genevieve; Veraart, Jelle; Novikov, Dmitry S; Fieremans, Els
Estimating intra- and extra-axonal microstructure parameters, such as volume fractions and diffusivities, has been one of the major efforts in brain microstructure imaging with MRI. The Standard Model (SM) of diffusion in white matter has unified various modeling approaches based on impermeable narrow cylinders embedded in locally anisotropic extra-axonal space. However, estimating the SM parameters from a set of conventional diffusion MRI (dMRI) measurements is ill-conditioned. Multidimensional dMRI helps resolve the estimation degeneracies, but there remains a need for clinically feasible acquisitions that yield robust parameter maps. Here we find optimal multidimensional protocols by minimizing the mean-squared error of machine learning-based SM parameter estimates for two 3T scanners with corresponding gradient strengths of 40 and 80mT/m. We assess intra-scanner and inter-scanner repeatability for 15-minute optimal protocols by scanning 20 healthy volunteers twice on both scanners. The coefficients of variation all SM parameters except free water fraction are ≲10% voxelwise and 1-4% for their region-averaged values. As the achieved SM reproducibility outcomes are similar to those of conventional diffusion tensor imaging, our results enable robust in vivo mapping of white matter microstructure in neuroscience research and in the clinic.
PMID: 35545197
ISSN: 1095-9572
CID: 5214502

Three-Dimensional Printed Anatomic Models Derived From Magnetic Resonance Imaging Data: Current State and Image Acquisition Recommendations for Appropriate Clinical Scenarios

Talanki, Varsha R; Peng, Qi; Shamir, Stephanie B; Baete, Steven H; Duong, Timothy Q; Wake, Nicole
Three-dimensional (3D) printing technologies have been increasingly utilized in medicine over the past several years and can greatly facilitate surgical planning thereby improving patient outcomes. Although still much less utilized compared to computed tomography (CT), magnetic resonance imaging (MRI) is gaining traction in medical 3D printing. The purpose of this study was two-fold: 1) to determine the prevalence in the existing literature of using MRI to create 3D printed anatomic models for surgical planning and 2) to provide image acquisition recommendations for appropriate clinical scenarios where MRI is the most suitable imaging modality. The workflow for creating 3D printed anatomic models from medical imaging data is complex and involves image segmentation of the regions of interest and conversion of that data into 3D surface meshes, which are compatible with printing technologies. CT is most commonly used to create 3D printed anatomic models due to the high image quality and relative ease of performing image segmentation from CT data. As compared to CT datasets, 3D printing using MRI data offers advantages since it provides exquisite soft tissue contrast needed for accurate organ segmentation and it does not expose patients to unnecessary ionizing radiation. MRI, however, often requires complicated imaging techniques and time-consuming postprocessing procedures to generate high-resolution 3D anatomic models needed for 3D printing. Despite these challenges, 3D modeling and printing from MRI data holds great clinical promises thanks to emerging innovations in both advanced MRI imaging and postprocessing techniques. EVIDENCE LEVEL: 2 TECHNICAL EFFICATCY: 5.
PMID: 34046959
ISSN: 1522-2586
CID: 4888362

T1 and T2 quantification using magnetic resonance fingerprinting in mild traumatic brain injury

Gerhalter, Teresa; Cloos, Martijn; Chen, Anna M; Dehkharghani, Seena; Peralta, Rosemary; Babb, James S; Zarate, Alejandro; Bushnik, Tamara; Silver, Jonathan M; Im, Brian S; Wall, Stephen; Baete, Steven; Madelin, Guillaume; Kirov, Ivan I
OBJECTIVES/OBJECTIVE:To assess whether MR fingerprinting (MRF)-based relaxation properties exhibit cross-sectional and prospective correlations with patient outcome and compare the results with those from DTI. METHODS:from MRF were compared in 12 gray and white matter regions with Mann-Whitney tests. Bivariate associations between MR measures and outcome were assessed using the Spearman correlation and logistic regression. RESULTS:, accounted for five of the six MR measures with the highest utility for identification of non-recovered patients at timepoint 2 (AUC > 0.80). CONCLUSION/CONCLUSIONS:, FA, and ADC for predicting 3-month outcome after mTBI. KEY POINTS/CONCLUSIONS:, and FA.
PMID: 34410458
ISSN: 1432-1084
CID: 5006382

Lower extremity MRI following 10-week supervised exercise intervention in patients with diabetic peripheral neuropathy

Brown, Ryan; Sharafi, Azadeh; Slade, Jill M; Convit, Antonio; Davis, Nathan; Baete, Steven; Milton, Heather; Mroczek, Kenneth J; Kluding, Patricia M; Regatte, Ravinder R; Parasoglou, Prodromos; Rao, Smita
INTRODUCTION/BACKGROUND:The purpose of this study was to characterize using MRI the effects of a 10-week supervised exercise program on lower extremity skeletal muscle composition, nerve microarchitecture, and metabolic function in individuals with diabetic peripheral neuropathy (DPN). RESEARCH DESIGN AND METHODS/METHODS:) and once following intervention to measure relaxation times (T1, T1ρ, and T2), phosphocreatine recovery, fat fraction, and diffusion parameters. RESULTS:and postintervention MRI metrics were: calf adipose infiltration -2.6%±6.4%, GM T1ρ -4.1%±7.7%, GM T2 -3.5%±6.4%, and gastrocnemius lateral T2 -4.6±7.4%. Insignificant changes were observed in gastrocnemius phosphocreatine recovery rate constant (p>0.3) and tibial nerve fractional anisotropy (p>0.6) and apparent diffusion coefficient (p>0.4). CONCLUSIONS:The 10-week supervised exercise intervention program successfully reduced adiposity and altered resting tissue properties in the lower leg in DPN. Gastrocnemius mitochondrial oxidative capacity and tibial nerve microarchitecture changes were not observed, either due to lack of response to therapy or to lack of measurement sensitivity.
PMID: 34518157
ISSN: 2052-4897
CID: 5012272

Cortical and subcortical signatures of conscious object recognition

Levinson, Max; Podvalny, Ella; Baete, Steven H; He, Biyu J
The neural mechanisms underlying conscious recognition remain unclear, particularly the roles played by the prefrontal cortex, deactivated brain areas and subcortical regions. We investigated neural activity during conscious object recognition using 7 Tesla fMRI while human participants viewed object images presented at liminal contrasts. Here, we show both recognized and unrecognized images recruit widely distributed cortical and subcortical regions; however, recognized images elicit enhanced activation of visual, frontoparietal, and subcortical networks and stronger deactivation of the default-mode network. For recognized images, object category information can be decoded from all of the involved cortical networks but not from subcortical regions. Phase-scrambled images trigger strong involvement of inferior frontal junction, anterior cingulate cortex and default-mode network, implicating these regions in inferential processing under increased uncertainty. Our results indicate that content-specific activity in both activated and deactivated cortical networks and non-content-specific subcortical activity support conscious recognition.
PMID: 34006884
ISSN: 2041-1723
CID: 4877132

Global decrease in brain sodium concentration after mild traumatic brain injury

Gerhalter, Teresa; Chen, Anna M; Dehkharghani, Seena; Peralta, Rosemary; Adlparvar, Fatemeh; Babb, James S; Bushnik, Tamara; Silver, Jonathan M; Im, Brian S; Wall, Stephen P; Brown, Ryan; Baete, Steven H; Kirov, Ivan I; Madelin, Guillaume
The pathological cascade of tissue damage in mild traumatic brain injury is set forth by a perturbation in ionic homeostasis. However, whether this class of injury can be detected in vivo and serve as a surrogate marker of clinical outcome is unknown. We employ sodium MRI to test the hypotheses that regional and global total sodium concentrations: (i) are higher in patients than in controls and (ii) correlate with clinical presentation and neuropsychological function. Given the novelty of sodium imaging in traumatic brain injury, effect sizes from (i), and correlation types and strength from (ii), were compared to those obtained using standard diffusion imaging metrics. Twenty-seven patients (20 female, age 35.9 ± 12.2 years) within 2 months after injury and 19 controls were scanned with proton and sodium MRI at 3 Tesla. Total sodium concentration, fractional anisotropy and apparent diffusion coefficient were obtained with voxel averaging across 12 grey and white matter regions. Linear regression was used to obtain global grey and white matter total sodium concentrations. Patient outcome was assessed with global functioning, symptom profiles and neuropsychological function assessments. In the regional analysis, there were no statistically significant differences between patients and controls in apparent diffusion coefficient, while differences in sodium concentration and fractional anisotropy were found only in single regions. However, for each of the 12 regions, sodium concentration effect sizes were uni-directional, due to lower mean sodium concentration in patients compared to controls. Consequently, linear regression analysis found statistically significant lower global grey and white matter sodium concentrations in patients compared to controls. The strongest correlation with outcome was between global grey matter sodium concentration and the composite z-score from the neuropsychological testing. In conclusion, both sodium concentration and diffusion showed poor utility in differentiating patients from controls, and weak correlations with clinical presentation, when using a region-based approach. In contrast, sodium linear regression, capitalizing on partial volume correction and high sensitivity to global changes, revealed high effect sizes and associations with patient outcome. This suggests that well-recognized sodium imbalances in traumatic brain injury are (i) detectable non-invasively; (ii) non-focal; (iii) occur even when the antecedent injury is clinically mild. Finally, in contrast to our principle hypothesis, patients' sodium concentrations were lower than controls, indicating that the biological effect of traumatic brain injury on the sodium homeostasis may differ from that in other neurological disorders. Note: This figure has been annotated.
PMID: 33928248
ISSN: 2632-1297
CID: 4852212

Mapping brain-behavior networks using functional and structural connectome fingerprinting in the HCP dataset

Lin, Ying-Chia; Baete, Steven H; Wang, Xiuyuan; Boada, Fernando E
INTRODUCTION/BACKGROUND:Connectome analysis of the human brain's structural and functional architecture provides a unique opportunity to understand the organization of the brain's functional architecture. In previous studies, connectome fingerprinting using brain functional connectivity profiles as an individualized trait was able to predict an individual's neurocognitive performance from the Human Connectome Project (HCP) neurocognitive datasets. MATERIALS AND METHODS/METHODS:In the present study, we extend connectome fingerprinting from functional connectivity (FC) to structural connectivity (SC), identifying multiple relationships between behavioral traits and brain connectivity. Higher-order neurocognitive tasks were found to have a weaker association with structural connectivity than its functional connectivity counterparts. RESULTS:Neurocognitive tasks with a higher sensory footprint were, however, found to have a stronger association with structural connectivity than their functional connectivity counterparts. Language behavioral measurements had a particularly stronger correlation, especially between performance on the picture language test (Pic Vocab) and both FC (r = .28, p < .003) and SC (r = 0.27, p < .00077). CONCLUSIONS:At the neural level, we found that the pattern of structural brain connectivity related to high-level language performance is consistent with the language white matter regions identified in presurgical mapping. We illustrate how this approach can be used to generalize the connectome fingerprinting framework to structural connectivity and how this can help understand the connections between cognitive behavior and the white matter connectome of the brain.
PMID: 32351025
ISSN: 2162-3279
CID: 4412612