trigeminal

This repo allows you to run a pipeline to track the trigeminal nerves.
There are two scripts that need to be run one after the other.

You will need scilpy 2.2.0 and ANTs to be installed in order to run these scripts.

The aparc.DKTatlas+aseg.mgz comes from Freesurfer >= 7.0 version. It is not
included in older versions of Freesurfer output. You can use https://cbrain.ca/
to run freesurfer effectively.

trigeminal_first_order.sh
trigeminal_second_order.sh

Input 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
    .
    .

Examples

First order

trigeminal_first_order.sh \
    -s path/to/input \
    -m ROIs_clean \
    -o my_results \
    -t 10 \ # Number of threads
    -g true # Use GPU

Second order

trigeminal_second_order.sh \
    -s path/to/input \
    -m ROIs_clean \
    -o my_results \
    -t 10 \ # Number of threads
    -g true # Use GPU

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

mdesco/trigeminal