This repository contains scripts to reconstruct trigeminal nerve pathways using diffusion MRI tractography.
The pipeline currently includes two main steps:
- First-order trigeminal tractography
- Second-order trigeminal tractography
The scripts should be run in this order:
trigeminal_first_order.sh
trigeminal_second_order.sh
The following software must be installed before running the scripts:
- Scilpy 2.2.0
- ANTs
- FreeSurfer >= 7.0
The file aparc.DKTatlas+aseg.mgz is generated by FreeSurfer >= 7.0. It is not included in older FreeSurfer outputs. If needed, FreeSurfer can be run through CBRAIN:
https://cbrain.ca/
Each subject folder should contain FreeSurfer outputs and TractoFlow outputs.
Expected structure:
[input]
├── sub-01
│ ├── freesurfer
│ │ └── aparc.DKTatlas+aseg.mgz
│ └── tractoflow
│ ├── sub-01__fa.nii.gz
│ ├── sub-01__fodf.nii.gz
│ └── sub-01__t1_warped.nii.gz
│
├── sub-02
│ ├── freesurfer
│ │ └── aparc.DKTatlas+aseg.mgz
│ └── tractoflow
│ ├── sub-02__fa.nii.gz
│ ├── sub-02__fodf.nii.gz
│ └── sub-02__t1_warped.nii.gz
The first-order script reconstructs three bilateral trigeminal components:
- Mesencephalic tract
- Spinal tract
- Remaining principal sensory/motor component
The script performs tractography from the cerebellar peduncle region, applies ROI-based filtering, segments the bundles, filters them by length, removes outliers, and saves the final bundles in both MNI space and original subject space.
bash trigeminal_first_order.sh \
-s path/to/input/sub-01 \
-m ROIs_clean \
-o my_results \
-t 10 \
-f 0.15 \
-n 20000 \
-g true-s Path to one subject folder
-m Path to the MNI-space ROI folder, usually ROIs_clean/
-o Output directory
-t Number of threads
-p Step size for tracking
-e Maximum angle/theta for tracking
-f FA threshold
-n Total number of seeds per voxel for first-order tracking
-g Use GPU if set to true
If -p and -e are not provided, the script runs ensemble tractography using:
step size = 0.1, 0.5, 1.0
theta = 20, 30, 40
If both -p and -e are provided, the script runs only one tracking combination.
Default values:
FA threshold = 0.15
npv_first_order = 20000
For HCP data, an FA threshold of 0.20 can be used. For clinical data, a lower threshold such as 0.15 may be more appropriate because of reduced anisotropy.
The following figures illustrate the first-order trigeminal probabilistic templates and reconstructed pathways.
The second-order script should be run after the first-order script. It uses the first-order final bundles to generate seeding masks and reconstruct second-order trigeminal pathways. The script reconstructs pathways related to:
- DTTT ipsilateral CS
- DTTT ipsilateral dPSN
- DTTT contralateral CS
- VTTT contralateral OS/IS
- VTTT contralateral vPSN
bash trigeminal_second_order.sh \
-s path/to/input \
-m ROIs_clean \
-o my_results \
-g true-s Path to the input folder containing all subject folders
-m Path to the MNI-space ROI folder, usually ROIs_clean/
-o Output directory
-g Use GPU if set to true
FA threshold = 0.20
npv_from_spinal_track_long = 1000
npv_from_spinal_track_short = 100
npv_from_thalamus_track = 500
For each subject, the pipeline creates outputs in both original subject space and MNI space.
Example:
my_results/
└── sub-01
├── orig_space
│ ├── rois
│ ├── tracking_first_order
│ ├── tracking_second_order
│ └── transfo
└── mni_space
├── rois
├── tracking_first_order
└── tracking_second_order
After running both first-order and second-order scripts, the MNI-space folder should look like:
sub-01/mni_space/
├── rois
├── tracking_first_order
└── tracking_second_order
The original-space folder should look like:
sub-01/orig_space/
├── rois
├── tracking_first_order
├── tracking_second_order
└── transfo
The tracking_first_order/ folder contains the first-order trigeminal bundles.
The tracking_second_order/ folder contains the second-order trigeminal pathways.
The atlas/ folder contains atlas-derived files.
Current structure:
atlas/
├── bundles_mask/
├── proba/
│ └── first_order/
└── trks/
└── first_order/
The probabilistic maps are stored in:
atlas/proba/first_order/
The binary mask files are stored in:
atlas/bundles_mask/
The tractography files are expected in:
atlas/trks/first_order/
Apply atlas
trigeminal_apply_atlas.sh
-s path/to/input
-m ROIs_clean/
-o my_results
-a atlas/
-t 30 \ # Number of threads -g true # Use GPU
The first-order script must be completed before running the second-order script, because the second-order script uses the final first-order spinal and remaining component bundles to generate seeding masks.