Fiber Tracking

Before practicum on Friday, please complete following:

• Watch a video about tractography

• Read [2. Challenges in mapping brain pathways] and [6. Fiber tracking methods] of a review paper.

During practicum on Friday:

Review of last weeks materials (5 min)

• Commissural pathway (X-axis): pathways connecting left-right cortical regions
• Association pathway (Y-axis): pathways connecting cortical regions within the same hemisphere
  • dorsal: AF, SLF, FAT
  • ventral: IFOF, UF, ILF, MdLF, VOF
  • medial: cingulum
• Projection pathway (Z-axis) pathways connecting cortical regions to basal ganglia (caudate, putamen, globus pallidus), thalamus, brainstem nuclei

Introduction to tractography (15 min)

• First tractography by Basser ISMRM 1998, Poupon et al MICCAI 1998, Mori et al Ann Neuro 1999, Conturo et al PNAS 1999.
• Fiber tracking method
  • Input: (1) local fiber orientation(s), a.k.a. fixel (2) termination metrics, e.g., anisotropy
  • Output: sequences of 3D coordinates
  • Deterministic vs probablistic

Local fiber orientations derived from dMRI

source: http://jmahaffy.sdsu.edu/courses/f00/math122/lectures/num_method_diff_equations/nummethod_diffeq.html

• Hands-on:
  • 100206.src.gz.gqi.1.7.fib.gz
  • fiber tracking using GUI
    • anisotropy threshold
    • angular threshold
    • step size
    • minimum and maximum length
  • fiber tracking using CLI

dsi_studio --action=trk --source=*.fib.gz --parameter_id=c9A99193Fb803FdbF041b96438813cb01cbaCDCC4C3Ec > log.txt

Errors in tractography (15 min)

• What is good/bad tractography?

reference: Fernandez-Miranda JC,Neurosurgery. 2012 Aug 1;71(2):430-53.

• Error near the brain surface
  • Mostly due to DWI processing and modeling
    • eddy current or susceptibility distortion
    • diffusion models
  • Solutions: (1) better acquisition (2) better modeling
• Error in deeper white matter
  • Mostly due to limitations in fiber tracking algorithms
    • false routing (a.k.a crossing/branching problem)
    • gyral bias
  • Solutions: (1) better spatial resolution (2) atlas-guided false fiber eliminations

reference: Yeh, Fang-Cheng, et al. “Tractography methods and findings in brain tumors and traumatic brain injury.” NeuroImage 245 (2021): 118651.

reference: Wu, Ye, et al. “Mitigating gyral bias in cortical tractography via asymmetric fiber orientation distributions.” Medical image analysis 59 (2020): 101543.

Region-based fiber tracking (15 min)

• Hands-on:
  • the template-space FIB file ICBM152_2mm.fib.gz
  • 100206.src.gz.gqi.1.7.fib.gz
• Demonstrate Region types: seed, ROI, ROA, END, terminative
  • ROI: a filtering region that filters IN tracks
  • ROA: a filtering region that filters OUT tracks
  • Seed: the starting location of fiber tracking
  • END: a filtering region that filters IN tracks ending in the region
  • Not-END: a filtering region that filters OUT tracks ending in the region
  • Terminative: cut tracks that enters the region
• Recommended steps to find a pathway between left and right V1
  1. Assign HCP_MMP:L_V1 and HCP_MMP:L_V2 as ROIs
  2. Adding seed regions to speed up
  3. Adding negated-dilated NOA
  4. Adding ROA/END/NOT END to refine
• Fiber tracking using CLI
  • Rename the regions files to include “mni” in the file name, and DSI Studio will load it as an MNI regions

2 ROIs

dsi_studio --action=trk --source=*.fib.gz --parameter_id=c9A99193Fb803FdbF041b96438813cb01cbaCDCC4C3Ec --roi=HCP-MMP:L_V1 --roi2=HCP-MMP:R_V1

2 ROIs + seed

dsi_studio --action=trk --source=*.fib.gz --parameter_id=c9A99193Fb803FdbF041b96438813cb01cbaCDCC4C3Ec --roi=HCP-MMP:L_V1 --roi2=HCP-MMP:R_V1 --seed=tract_mni.nii.gz

3 ROIs + seed + NOA

dsi_studio --action=trk --source=*.fib.gz --parameter_id=c9A99193Fb803FdbF041b96438813cb01cbaCDCC4C3Ec --roi=HCP-MMP:L_V1 --roi2=HCP-MMP:R_V1 --seed=tract_mni.nii.gz --roa=tract_mni.nii.gz,dilation,dilation,dilation,dilation,dilation,dilation,negate

• Examples (Optional)
  • Region Manual(source: Schneider lab)
  • TractEM

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Assignment:

1. Combine automatic fiber tracking and region-based fiber tracking

1. Use automatic fiber tracking to map left corticospinal tracts on 100206.src.gz.gqi.1.7.fib.gz
2. Identify false results and use MNI-space ROI or ROA regions to improve the tractogram.
3. Use command line to repeat the same on subject-space FIB file(Download 3~5 FIB files)

2. Mapping difficult pathways using region-based fiber tracking

1. Download HCP1065 1-mm FIB file
2. Use region-based fiber tracking, map the orbital connections in nuclei 5.
3. Use region-based fiber tracking, map the temporal connections in nuclei 5.
4. Use region-based fiber tracking, map the occipital connections in nuclei 5.