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Roadmap of the challenges of microstructure biophysical modeling. The main objective of this review is to propose a roadmap for development of a reliable biophysical model of diffusion in a given tissue. Discrete steps along this course are shown above, although the entire process is very much a continuous and iterative process of validation, adaptation, and application

Challenges for biophysical modeling of microstructure

Dec. 9, 2020—Ileana O. Jelescu, Marco Palombo, Francesca Bagnato, Kurt G. Schilling. “Challenges for biophysical modeling of microstructure”. (2020) Journal of Neuroscience Methods 108861. Full text: https: https://www.sciencedirect.com/science/article/pii/S0165027020302843 Abstract The biophysical modeling efforts in diffusion MRI have grown considerably over the past 25 years. In this review, we dwell on the various challenges along the journey of...

Qualitative comparison of tracer and tractography for PCG injection. Tracer digitized on the reference atlas [and reproduced from Schmahmann and Pandya (2006), with permission] is shown alongside the anatomically matched b0 slice with streamlines shown in black (only streamlines within ± 1 slice are displayed) for both the manual-based dissection and the template-based dissection

Brain connections derived from diffusion MRI tractography can be highly anatomically accurate – if we know where white matter pathways start, where they end, and where they don’t go

Aug. 25, 2020—Kurt G Schilling, Laurent Petit, Francois Rheault, Samuel Remedios, Carlo Pierpaoli, Adam W Anderson, Bennett A Landman, Maxime Descoteaux. “Brain connections derived from diffusion MRI tractography can be highly anatomically accurate – if we know where white matter pathways start, where they end, and where they don’t go”. Brain Struct Funct (2020). https://doi.org/10.1007/s00429-020-02129-z Full text: https://link.springer.com/article/10.1007/s00429-020-02129-z Abstract MR...

Figure 4. The response function varies across brain regions. Three locations in the same monkey brain (monkey #2) are shown, along with the histological fiber orientation distribution, signal, and derived response function for all 9 voxels. In addition, the average response function for each z-stack is shown in two views.

Histologically derived fiber response functions for diffusion MRI vary across white matter fibers – an ex vivo validation study in the squirrel monkey brain

Aug. 25, 2020—Kurt G Schilling, Yurui Gao, Iwona Stepniewska, Vaibhav Janve, Bennett A. Landman, Adam W. Anderson. “Histologically derived fiber response functions for diffusion MRI vary across white matter fibers – an ex vivo validation study in the squirrel monkey brain”. NMR in Biomedicine. 2019 Jun;32(6):e4090. doi: 10.1002/nbm.4090. Epub 2019 Mar 25. Full text: https://pubmed.ncbi.nlm.nih.gov/30908803/ Abstract Understanding the...

Fig 8. External dataset validation.
External validation of corrected b0’s after applying the synthesized b0 distortion correction pipeline with data from open-sourced studies. The distorted (“D”) and undistorted (“U”) b0 images are shown alongside T1 images. In all cases, effective distortion correction is visually apparent (distortions indicated by arrows).

Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps

Aug. 25, 2020—Kurt G Schilling*, Justin Blaber*, Colin Hansen, Leon Cai, Baxter Rogers, Adam W Anderson, Seth A Smith, Praitayini Kanakaraj, Tonia Rex, Susan M. Resnick, Andrea T. Shafer, Laurie Cutting, Neil Woodward, David Zald, Bennett A Landman.“ Distortion correction of diffusion weighted MRI without reverse phase-encoding scans or field-maps ”. PLoS ONE 15(7): e0236418. https://doi.org/10.1371/journal.pone.0236418 Full text: https:...

Diffusion MRI microstructural models in the cervical spinal cord – application, normative values, and correlations with histological analysis

Dec. 16, 2019—Kurt G. Schilling, Samantha By, Haley Feiler, Bailey Box, Kristin P. O’Grady, Atlee Witt, Bennett A. Landman, Seth A. Smith. “Diffusion MRI microstructural models in the cervical spinal cord – application, normative values, and correlations with histological analysis”. NeuroImage. doi: 10.1016/j.neuroimage.2019.116026. 2019. Full text: https://www.ncbi.nlm.nih.gov/pubmed/31326569 Abstract Multi-compartment tissue modeling using diffusion magnetic resonance imaging has proven...

Fig. 2. Distortion and correction in diffusion MRI. (A) EPI susceptibility distortion occurs along the phase encode direction, with phase encoding in the posterior (PE-P) direction leading to displacements of identical distance but opposite direction of that in the anterior (PE-A) direction. (B) State of the art distortion correction (topup) typically uses distortions in two opposite directions to iteratively estimate the undistorted image. (C) The proposed method uses an undistorted T1-weighted image to synthesize an undistorted volume with b0 contrast, which can be used to correct the distorted (in this case, PE-P) image without requiring an additional phase encoding acquisition. The blue circles highlight areas of observable signal distortion. Yellow arrows indicate phase encode direction. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Synthesized b0 for diffusion distortion correction (Synb0-DisCo).

Dec. 16, 2019—Kurt G Schilling, Yuankai Huo, Allen Newton, Colin Hansen, Vishwesh Nath, Andrea T. Shafer, Owen Williams, Susan M. Resnick, Baxter Rogers, Adam W Anderson, Bennett A Landman. “Synthesized b0 for diffusion distortion correction (Synb0-DisCo).” Magnetic Resonance Imaging. 2019 May 7. pii: S0730-725X(18)30617-9. doi: 10.1016/j.mri.2019.05.008 Full text: https://www.ncbi.nlm.nih.gov/pubmed/?term=Synthesized+b0+for+diffusion+distortion+correction+(Synb0-DisCo). Abstract Diffusion magnetic resonance images typically suffer from spatial...

Fig. 1. Effects of incorrect b-vector tables. Diffusion encoded color (DEC) maps and vector maps are shown for a correct gradient table (A), a table with a flipped component (B), and one with permuted components (C). With a flipped component, the DEC map may appear correct, but unit vectors will be flipped in one plane (coronal plane in this example), and will appear correct in another (axial). For a permuted table, both the color maps and vectors will be erroneous. In both (B) and (C), directions are incorrect, and subsequent analysis and tractography will also be erroneous. DEC and vector maps are colored red, green, and blue for diffusion primarily in the right/left, anterior/posterior, and superior/inferior directions, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

A fiber coherence index for quality control of B-table orientation in diffusion MRI scans.

May. 16, 2019—Kurt G Schilling, Fang-Cheng Yeh, Vishwesh Nath, Colin Hansen, Owen Williams, Susan Resnick, Adam W. Anderson, Bennett A. Landman. “A fiber coherence index for quality control of B-table orientation in diffusion MRI scans”. Magnetic Resonance Imaging. 2019. doi: 10.1016/j.mri.2019.01.018 Full text: https://www.ncbi.nlm.nih.gov/pubmed/?term=fiber+coherence+b-table Abstract Purpose The diffusion MRI “b-vector” table describing the diffusion sensitization direction can be flipped and...

Response functions estimated using conventional methods differ from the histologically derived response functions. Kernels estimated using the highest FA voxels, the iterative calibration method, and modeled from the diffusion tensor are shown in two views. The average histologically derived response function for each monkey (across 6 z stacks) is shown (monkeys 1–3 correspond to A‐C) along with the mean (red) and mean ± standard deviation (gray) surfaces to highlight variability. Note that differences in magnitude are due to differing normalization in our work and in MRTrix3. Shape, and not magnitude, determines the final FOD shape

Histologically derived fiber response functions for diffusion MRI vary across white matter fibers-An ex vivo validation study in the squirrel monkey brain.

Mar. 16, 2019—Kurt G. Schilling, Yurui Gao, Iwona Stepniewska, Vaibhav Janve, Bennett A. Landman, Adam W. Anderson. “Histologically derived fiber response functions for diffusion MRI vary across white matter fibers – an ex vivo validation study in the squirrel monkey brain”. NMR in Biomedicine. 2019 Jun;32(6):e4090. doi: 10.1002/nbm.4090. Epub 2019 Mar 25. Full text: https://www.ncbi.nlm.nih.gov/pubmed/30908803 Abstract Understanding the...