Anatomical Analysis- Recon 1

Recon 1

  1. Create folder in freesurfer subjects directory (usr/local/freesurfer/subjects) titled [SUBJECT ID]_DICOMS
    1. Can be done in the files program or using terminal (instructions bellow)
      1. cd $SUBJECTS_DIR
      2. mkdir [SUBJECT ID]_DICOMS
  2. Move 1 set of MPRAGE files from hard drive into created folder from step 1
    1. Can be done in file program using ctrl+c or through terminal
    2. Example: cp -rv /media/ashleypresley/Seagate Expansion Drive/UCDMC/Cycle 2/22q Cycle 2/2RO3NC ~/usr/local/freesurfer/subjects/[SUBJECT ID]_DICOMS
      1. copy, recursive (all folders within folders), verbose (tell all that’s happening), file to be copied, location copied to
  3. Open terminal and change directory to created folder from step 1
    1. cd $SUBJECTS_DIR/[SUBJECT ID]_DICOMS
  4. Type command for recon1
    1. recon-all -autorecon1 -subjid [SUBJECT ID] -i 0001.dcm
  5. Allow recon1 to run in terminal (takes about 5 minutes on powerful computer, 30 minutes on okay computer)
  6. Once finished, change directory to freesurfer created one
    1. cd $SUBJECTS_DIR/[SUBJECT ID]
  7. Type command to view tal brain overlay
    1. tkregister2 —mgz —s [SUBJECT ID] —fstal
      1. Align moveable to target
      2. Click compare button to see align, use sliders to move brain and to resize
        1. Axial midline check
        2. Sagital and midline check
        3. Coreonal check
  8. When finished click save reg button
  9. Rerun Recon1
    1. Retype recon1 command
      1. recon-all -autorecon1 -s [SUBJECT ID]
  10. Type command to view brainmask
    1. (ensure that you’re in the new subject directory) $SUBJECTS_DIR/[SUBJECT ID]
    2. freeview -v T1.mgz brainmask.mgz
    3. If there is a lot of dura remaining, run gcut
      1. recon-all -skullstrip -clean-bm -gcut -subjid [SUBJECT ID]
        1. Gcut may cut off too much brain, open freeview to compare results
          1. type freeview into terminal, then select file -> load -> volume -> choose brainmask.gcuts.mgz
  11. When editing the skullstrip, you are editing the brainmask. Ensure that brainmask is checked and is above the T1 file in the volumes tab
    1. Right click + drag: enlarge or reduce brain
    2. Shift + left click + drag: change contrast
    3. To navigate the window:
      1. click navigate in the upper left (head with plus sign)
      2. Right click + drag: enlarge or reduce brain
      3. Shift + left click + drag: change contrast
    4. To edit:
      1. Click voxel edit in upper left corner (head with pencil)
      2. Change reference to T1 and keep brush size at 2
        1. Freehand icon allows you to delete