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 seperate 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.

Occasionnally, 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 MNI talairach 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:


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:

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