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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 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:

6. Check the talairach transform:

  1. Check the skull strip:
  2. After you have an accurate brain volume, run the next step of recon-all:
    • recon-all -autorecon2 -subjid your_subject_name

  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

  4. After you have accurate pial and white surfaces run the final step of recon-all:
    • recon-all -autorecon3 -subjid your_subject_name