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This workflow completes the entire reconstruction process without stopping. See the BasicReconTable for a list of all the steps run by this command. After the process finishes the user should check the final surfaces and talairach transform. Any manual intervention needed to fix problems that occurred during the process are done at the end. Then the necessary steps are repeated, which can be both time-consuming and use a lot of compute power.

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 recon-all script:

• 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:

• ["FsTutorial/Talairach"]

For examples of editing surfaces, refer to:

• FsTutorial/FixingDefects

• FsTutorial/PialEdits

For instructions on how to fix poor normalizations or skull strips, refer to:

• FsTutorial/ControlPoints

• FsTutorial/SkullStripTutorial