Fiber Tracking

Before practicum on Friday, please complete following:

During practicum on Friday:

Review of last weeks materials (5 min)

Introduction to tractography (15 min)

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Local fiber orientations derived from dMRI

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

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

Errors in tractography (15 min)

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

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)

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

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

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  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.