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Pre-processing

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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):

  1. with a niftii file

recon-all -i FTD####.nii -subjid subject_1 -all

2. with a folder of DICOM files

recon-all -i /scratch/project/FTD#### -subjid subject_1 -all

Pre-processing with manual corrections

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