• HistoricalReconstruction

top | previous | next

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

12. 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.