mri

T1w

T1w Pipeline Description

1. Freesurfer processing

   1. Freesurfer’s recon-all

   2. QC and, if necessary, add control points and run specific recon-all function

2. Post-freesurfer processing

   1. Convert T1w and segmentations from .mgz to .nii

   2. Create individual ROIs from DK Atlas (aparc+aseg), Destrieux Atlas (aparc.a2009s+aseg), and white matter parcellation (wmparc)

   3. Reorient T1w to MNI152

   4. Warp T1w from fsnative to T1w

   5. Extract brain (ANT’s antsBrainExtraction, FSL’s bet, and hd-bet; combine masks with freesurfer’s DK Atlas to create final brain mask)

   6. Warp T1w from native to MNI152

   7. Segment tissue (fsl’s fast)