• BasicReconstruction

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Using this workflow will perform all the steps of the entire volume and surface reconstruction stream without stopping. Upon completeion the user is able to check the final surfaces and if any manual intervention is needed to correct any of the steps those processes must be repeated.

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.

• 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