• BasicReconstruction

[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:

• FsTutorial/FixingDefects

• FsTutorial/PialEdits

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

• FsTutorial/ControlPoints

• FsTutorial/SkullStripTutorial

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"]

1. Check the skull strip:

   • tkmedit your_subject_name brain.mgz -aux T1.mgz

   • FsTutorial/ControlPoints

   • FsTutorial/SkullStripTutorial

2. After you have an accurate brain volume, run the next step of recon-all:

   • recon-all -autorecon2 -subjid your_subject_name

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 editing the final surfaces, refer to:

     • FsTutorial/FixingDefects

     • FsTutorial/PialEdits

     • FsTutorial/FinalSurfEx

4. After you have accurate pial and white surfaces run the final step of recon-all:

   • recon-all -autorecon3 -subjid your_subject_name