T1w

Preprocessing

1. Run freesurfer and manual interventions

2. Setup

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

5. Preprocess T1w

   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)