Fiber Tracking

Fiber tracking is a technique used in diffusion MRI to reconstruct the pathways of nerve fibers within the brain. It is based on the principle that water molecules tend to diffuse more readily along the axons of nerve fibers than across them. By measuring the diffusion of water molecules using diffusion MRI and applying advanced computational techniques, it is possible to create 3D reconstructions of the pathways of nerve fibers within the brain, known as “tracts.”

Before practicum on Friday, please complete following:

During practicum on Friday:

Review of last weeks materials (5 min)

Introduction to tractography (15 min)


Local fiber orientations derived from dMRI



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


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.