• RecommendedReconstruction

[wiki:FreeSurferWorkFlows top] | [wiki:BasicReconstruction previous] | [wiki:HistoricalReconstruction next]

This workflow completes the reconstruction process in three different steps, allowing the user to check the outputs before proceeding. See the RecommendedReconTable for a list of the steps run with this command. Any manual intervention that is needed is done before moving on to the next step, which can save both time and use of computer power.

FreeSurfer Troubleshooting 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. Run the first step of recon-all. See the RecommendedReconTable for individual steps that will be run during the whole process.

   • recon-all -autorecon1 -subjid your_subject_name

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"]
7. Check the skull strip:

   • tkmedit your_subject_name brain.mgz -aux T1.mgz

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

     • 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