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FreeSurfer Basic Reconstruction Work Flow
1. Source the correct version of FreeSurfer:
source your_freesurfer_dir/SetUpFreeSurfer.csh
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:
mksubjdirs your_subject_name
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. For examples of editing surfaces and troubleshooting, refer to:
- ["FsTutorial/Talairach"]