This process uses the command ["mri_fill"] to create a binarized volume. The input is the mri/wm volume and the output is the mri/filled volume. First, the cutting planes are determined to separate the hemispheres from each other and the pons. Then a seed point is located and used to fill each hemisphere. The rh will be filled with a value of 255, and the lh with a value of 127.

Occasionally, manual intervention is required to define the cutting planes and seed points. To do so, follow these steps:

  1. Open the subject's (subj) wm volume up in ["tkmedit"].
    • ["tkmedit"] subj wm
  2. View the MniTalairach coordinates: View->Information->MNI Coordinates

  3. Select the Corpus Callosum point, on the mid-posterior portion of it. Example: Corpus Callosum attachment:CCcor.jpg attachment:CChor.jpg attachment:CCsag.jpg
  4. Copy the MNI coordinates to the command line for either ["recon-all"] -cc-xyz .... or in ["mri_fill"] -C ....
  5. Do this for all of the other cutting plane points and seed points. Examples follow: Pons attachment:Pcor.jpg attachment:Phor.jpg attachment:Psag.jpg RH seed attachment:RHcor.jpg attachment:RHhor.jpg attachment:RHsag.jpg LH seed attachment:LHcor.jpg attachment:LHhor.jpg attachment:LHsag.jpg
  6. Not all points need to be defined, any range from none to all four may be defined. To inflate:

    BR BR ["mri_fill"] -C MNIcoords -P MNIcoords -rh MNIcoords -lh MNIcoords $SUBJECTS_DIR/subj/mri/wm $SUBJECTS_DIR/subj/mri/filled;inflate_subject-rh subj;inflate_subject-lh subj BR BR or, the equivalent in recon-all:

    BRBR ["recon-all"] -stage2 -cc-xyz MNIcoords -pons-xyz MNIcoords -rh-xyz MNIcoords -lh-xyz MNIcoords -subjid subj BRBR

    NOTE: These command line(s) need to be run EVERYTIME the subject's surfaces are reinflated