(t1w)=

# T1w

(t1w-preproc)=

## Preprocessing

1. Run freesurfer and manual interventions

2. Setup

   ```bash
   module load bashHelperKennedyRodrigue
   root_dir='get_root_dir kenrod'
   code_dir="${root_dir}/software/scripts/eep170030/study-jlbs/mri/anat/T1w"
   ```

3. Convert freesurfer ROIs from surfaces to volumes

   ```bash
   bash ${code_dir}/s01_freesurfer_roi_from_surface_to_volume_faster.sh
   ```

   ROIs:

   - `brainmask.mgz`
   - `aparc+aseg.mgz`
   - `aparc.a2009s+aseg.mgz`
   - `wmparc.mgz`

4. Warp volumetric ROIs from freesurfer-space to native T1w space

   ```bash
   bash ${code_dir}/s02_warp_freesurfer_roi_from-fsnative_to-T1w-native.sh
   ```

5. Preprocess T1w

   ```bash
   bash ${code_dir}/s03_preprocess_T1w.sh
   ```

   The code performs the following:

   - brain extraction (using ANTs, FSL, and Freesurfer)
   - combines brain masks
   - warps the brain to MNI152 space
   - creates tissue segments (FSL's fast)