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This workflow uses the older version of FreeSurfer, in which manual editing of the wm volume was routinely required and subcortical segmentations were not a part of the regular processing stream.  See HistoricalReconTable for the steps run by this script.  Continue using this workflow if you've already begun processing your subjects this way.

= FreeSurfer Historical 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. If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:
    '''`mri_convert --conform `''your_subject_name''`/mri/orig/002.mgz `''your_subject_name''`/mri/orig.mgz`'''

 6. Start the recon-all script:
    '''`recon-all -stage1 -subjid `''your_subject_name'''''

 7. Check the talairach transform:
  7.1 Make sure the talairach subject is linked to `$SUBJECTS_DIR`
      if not: '''`ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.`'''
  7.2 '''`tkregister2 --mgz --s `''your_subject_name''` --fstal`'''

  For instructions on how to fix bad talairachs tranforms, refer to:
   * [[FsTutorial/Talairach]]

 8. Check the skull strip:
 '''`tkmedit `''your_subject_name''` brain.mgz -aux T1.mgz`'''

 For intructions on how to fix poor normalizations or skull strips, refer to:
  * FsTutorial/ControlPoints
  * FsTutorial/SkullStripFix

 9. Edit the wm.mgz volume

 For instructions on editing the wm.mgz, refer to:
  * FsTutorial/WhiteMatterEdits

 10. After you have made edits to your wm.mgz volume, run the next step of recon-all:
    '''`recon-all -stage2 -subjid `''your_subject_name'''''

 11. Check your inflated surfaces and wm.mgz volumes to make sure they are accurate.
  11.1 If more edits are needed, run the following command after making edits:
    '''`recon-all -stage2 -subjid `''your_subject_name'''''
  11.2 If no more edits are needed, continue on to the next step of recon-all:
    '''`recon-all -stage3 -stage4a -stage4b -subjid `''your_subject_name'''''

 13. 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 editing the final surfaces, refer to:
   * FsTutorial/PialEdits
   * FsTutorial/FinalSurfEx

 Note: these Tutorial sections show data processed using Basic workflow, so large defects were autofilled.