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.

  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

    CCcor.jpg CChor.jpg CCsag.jpg

  4. Copy the MNI coordinates to the command line for either

    recon-all -cc-xyz .... or in

    mri_fill -C ....

    Alternatively seed point can be given in voxel coordinates under the command line mri_fill :

    -CV <x> <y> <z> - the voxel coords of the seed for the corpus callosum

    -PV <x> <y> <z> - the voxel coords of the seed for the pons

  5. Do this for all of the other cutting plane points and seed points. Examples follow: Pons

    Pcor.jpg Phor.jpg Psag.jpg RH seed

    RHcor.jpg RHhor.jpg RHsag.jpg LH seed

    LHcor.jpg LHhor.jpg LHsag.jpg

  6. Not all points need to be defined, any range from none to all four may be defined. To inflate:

    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

    or, the equivalent in recon-all:

    recon-all -stage2 -cc-xyz MNIcoords -pons-xyz MNIcoords -rh-xyz MNIcoords -lh-xyz MNIcoords -subjid subj

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