FreeSurfer performs the whole cortical reconstruction process and generates it their unique FreeSurfer file format using the command recon-all.
Running whole pre-processing pipeline automatically
You can automatically run the whole process (without manual editing/manual checks):
with a niftii file
| Code Block |
|---|
recon-all -i FTD####.nii -subjid subject_1 -all |
2. with a folder of DICOM files
| Code Block |
|---|
recon-all -i /scratch/project/FTD#### -subjid subject_1 -all |
Pre-processing with manual corrections