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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:

  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

  • 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:

HistoricalReconstruction (last edited 2021-09-22 11:45:30 by DevaniCordero)