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   * ["FsTutorial/Talairach"]   * ["FsTutorial/Talairach"]
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6. Check the 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`'''
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  For intructions on how to fix bad talairachs tranforms, refer to:
   * ["FsTutorial/Talairach"]
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 7. Check the skull strip:
   '''`tkmedit `''your_subject_name''` brain.mgz -aux T1.mgz`'''

   * FsTutorial/ControlPoints
   * FsTutorial/SkullStripTutorial

 8. After you have an accurate brain volume, run the next step of recon-all:
    '''`recon-all -autorecon2 -subjid `''your_subject_name'''''

 9. 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/FixingDefects
   * FsTutorial/PialEdits
   * FsTutorial/FinalSurfEx

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

[wiki:FreeSurferWorkFlows top] | [wiki:FreeSurferWorkFlows previous] | [wiki:TroubleshootingReconstruction next]

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

For intructions on how to fix bad talairachs tranforms, refer to:

  • ["FsTutorial/Talairach"]
  • 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 examples of editing surfaces, refer to:

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

BasicReconstruction (last edited 2008-04-29 11:45:31 by localhost)