Before practicum on Friday, please complete following:
- Watch a video about tractography
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
- Anisotropy threshold
- Angular threshold
- Step size
- Minimum and maximum length
- 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.
- 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)
- 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:
- Look up Table of Contents in page 2, find Regions - ArcuateCoronal_SIDE (AC) - page 63.
- Turn to page 63, follow the instructions of how to draw ArcuateCoronal_SIDE to identify the region looked for.
- 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.
- 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]
1. Combine automatic fiber tracking and region-based fiber tracking
Use [AutoTract] to map left corticospinal tracts on 100206.src.gz.gqi.1.7.fib.gz
Identify false results and use ROI-based fiber tracking to improve the results.
[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
2. Mapping difficult pathways using region-based fiber tracking
Download HCP1065 1-mm FIB file
Use region-based fiber tracking, map the orbital connections in nuclei 5.
Use region-based fiber tracking, map the temporal connections in nuclei 5.
Use region-based fiber tracking, map the occipital connections in nuclei 5.