Deletions are marked like this. | Additions are marked like this. |
Line 5: | Line 5: |
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 --conform`''your_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 --conform`''your_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: a. 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: * FsTutorial/ControlPoints * FsTutorial/SkullStripTutorial 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 editting the final surfaces, refer to: * FsTutorial/FixingDefects * FsTutorial/PialEdits * FsTutorial/FinalSurfEx |
[wiki:FreeSurferWorkFlows top] | [wiki:IntermediateReconstruction previous] | [wiki:SubcorticalSegmentation next]
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 editting the final surfaces, refer to: