Preparing Data with Freesurfer

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