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FreeSurfer Historical Reconstruction Work Flow
1. source your_freesurfer_dir/SetUpFreeSurfer.csh
2. setenv SUBJECTS_DIR your_subjects_dir
3. mksubjdirs your_subject_name`
4. 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. a.If you have multiple scans from the same session, motion correct and average them to produce the orig.mgz volume:
mri_motion_correct2 -i your_subject_name/mri/orig/001.mgz -i your_subject_name/mri/orig/002.mgz -o your_subject_name/mri/rawavg.mgz
mri_convert --conformyour_subject_name/mri/rawavg.mgz your_subject_name/mri/orig.mgz
- b.If you have a single scan, conform the volume to 1 mm^3 and 256x256x256:
mri_convert --conformyour_subject_name/mri/orig/002.mgz your_subject_name/mri/orig.mgz
6. recon-all -stage1 -subjid your_subject_name
7. Check the talairach transform:
Make sure the talairach subject is linked to $SUBJECTS_DIR
if not: ln -s $FREESURFER_HOME/subjects/talairach $SUBJECTS_DIR/.
b. tkregister2 --mgz --s your_subject_name --fstal --surf orig 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:
9. Edit the wm.mgz volume
- For instructions on editting the wm.mgz, refer to:
- FsTutorial/
10. recon-all -stage2 -subjid your_subject_name
11. (Possibly make more edits to wm.mgz volume)
12. recon-all -stage3 -stage4a -stage4b ?!!!!-avgtif -gcs!!!!? -subjid your_subject_name
13. 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: