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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:

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:

5. recon-all -autorecon-all -subjid your_subject_name

6. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to: