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:

1.Introduction to tractography

• Fiber tracking method
  • Input: local fiber orientations (a.k.a. fixel)
  • Output: sequences of 3D coordinates
  • Deterministic vs probablistic

Local fiber orientations derived from dMRI

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

• Hands-on: tracking parameters
  • 100206.src.gz.gqi.1.7.fib.gz
  • Parameters
    • Anisotropy threshold
    • Angular threshold
    • Step size
    • Minimum and maximum length

2.Limitations

• false routing and premature termination:

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

source: https://www.nature.com/articles/s41467-017-01285-x/figures/7

• gyral bias

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

3.Region types used in fiber tracking

• Hands-on: region-based fiber tracking
  • Load HCP1065.1mm.fib.gz
  • Demonstrate Region types: seed, ROI, ROA, END, terminative
    • Seed: the starting location of fiber tracking
    • ROI: a filtering region that filters IN tracks
    • ROA: a filtering region that filters OUT tracks
    • 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

4.Fiber tracking protocols

• Region Manual(source: Schneider lab)
• TractEM
• Hands-on: mapping left arcuate fasciculus
  • Load HCP1065.1mm.fib.gz by clicking “StepT3: Fiber Tracking & Visualization”.
  • According to page 17 of the Region Manual, in order to generate raw left arcuate fasciculus, we need:
    • ROIs: ArcuateCoronal_left, ArcuateAxial_left
    • ROAs: SagittalROA, ExternalCapsule_left

  • To draw region ArcuateCoronal_left, for example, steps include:

    1. Look up Table of Contents in page 2, find Regions - ArcuateCoronal_SIDE (AC) - page 63.
    2. Turn to page 63, follow the instructions of how to draw ArcuateCoronal_SIDE to identify the region looked for.
    3. Remember to define the type of the region drawn, either ROI or ROA in the GUI. In the region window, click Type and then select ROI/ROA.
    4. After creating all the ROIs and ROAs, hit Fiber Tracking in the Tracts window.
  • Save regions using [Regions][Save Checked Regions in Multiple Files]
  • Repeat the mapping on 100206.src.gz.gqi.1.7.fib.gz by loading the saved regions from [Regions Misc][Open MNI Regions]

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Assignment:

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

1. Use [AutoTract] to map left corticospinal tracts on 100206.src.gz.gqi.1.7.fib.gz

2. Identify false results and use ROI-based fiber tracking to improve the results.

3. [Optional] write a script to map CST in multiple FIB files(Download 3~5 FIB files)

   • rename the regions files to include “mni” in the file name, and DSI Studio will load it as MNI regions
   • examples

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.