Preparing Data with FreesurferΒΆ
Running FreeSurfer
Make sure you’ve sourced your setupfreesurfer.sh file Make sure your environment variable for SUBJECTS_DIR is set to your desired location
$ export SUBJECTS_DIR=/Users/Viktoriya/Desktop/subjects
Next step will take input data and copy it into SUBJECTS_DIR
$ recon-all \
... -s example_data \
... -i /Users/Viktoriya/Desktop/subjects/example_MPRAGE.nii.gz \
... -T2 /Users/Viktoriya/Desktop/subjects/example_t2wspace.nii.gz
Now run the FreeSurfer reconstruction pipeline
$ recon-all -s example_data -all