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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

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

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:

  1. 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:

9. Edit the wm.mgz volume

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:

Note: these Tutorial sections show data processed using Basic workflow, so large defects were autofilled.