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:

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 For intructions on how to fix bad talairachs tranforms, refer to:
- ["FsTutorial/Talairach"]

Check the skull strip:
- tkmedit your_subject_name brain.mgz -aux T1.mgz
- FsTutorial/ControlPoints
- FsTutorial/SkullStripTutorial
After you have an accurate brain volume, run the next step of recon-all:
- recon-all -autorecon2 -subjid your_subject_name
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:
After you have accurate pial and white surfaces run the final step of recon-all:
- recon-all -autorecon3 -subjid your_subject_name

-Deletions are marked like this.
+Additions are marked like this.
 Line 24:
-. Check your surfaces and talairach transform. For examples of editing surfaces and troubleshooting, refer to:
+. 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:
-Line 27:
+Line 40:
-    * ["FsTutorial/Talairach"]
+For instructions on how to fix poor normalizations or skull strips, refer to:
-Line 31:
+Line 45:
+. 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`'''





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

   * ["FsTutorial/Talairach"]



 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'''''