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:
- Open the subject's (subj) wm volume up in ["tkmedit"].
- ["tkmedit"] subj wm
View the MniTalairach coordinates: View->Information->MNI Coordinates
- Select the Corpus Callosum point, on the mid-posterior portion of it. Example: Corpus Callosum attachment:CCcor.jpg attachment:CChor.jpg attachment:CCsag.jpg
- Copy the MNI coordinates to the command line for either ["recon-all"] -cc-xyz .... or in ["mri_fill"] -C ....
- 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
- 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:
NOTE: These command line(s) need to be run EVERYTIME the subject's surfaces are reinflated