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FreeSurfer Basic Reconstruction Work Flow
1. Source the correct version of FreeSurfer:
2. Set your SUBJECTS_DIR variable to your subjects directory:
setenv SUBJECTS_DIR your_subjects_dir
3. Make a subjects directory within your SUBJECTS_DIR:
4. Convert the DICOM files to .mgz files in the $SUBJECTS_DIR/your_subjects_name/mri/orig directory:
mri_convert your_dicom_file your_subject_name/mri/orig/001.mgz
If you have multiple scans from the same session, convert additional scans like:
mri_convert your_other_dicom_file your_subject_name/mri/orig/002.mgz
5. Start the script recon-all. See the BasicReconTable for individual steps that will be run.
recon-all -autorecon-all -subjid your_subject_name
6. Check your surfaces and talairach transform.
6.1 Make sure the talairach subject is linked to $SUBJECTS_DIR
if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.
6.2 tkregister2 --mgz --s your_subject_name --fstal 6.3 Check the white and pial surfaces:
tkmedit your_subject_name wm.mgz rh.white -aux brain.mgz
tkmedit your_subject_name wm.mgz lh.white -aux brain.mgz
For intructions on how to fix bad talairachs tranforms, refer to:
For examples of editing surfaces, refer to:
For instructions on how to fix poor normalizations or skull strips, refer to: