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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:

If you have multiple scans from the same session, convert additional scans like:

5. Start the script recon-all. See the BasicReconTable for individual steps that will be run.

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