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

 1. View the MniTalairach coordinates: '''View->Information->MNI Coordinates'''

 1. Select the Corpus Callosum point, on the mid-posterior portion of it. Example:

 Corpus Callosum

 {{attachment:CCcor.jpg}} {{attachment:CChor.jpg}} {{attachment:CCsag.jpg}}

 1. 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

 1. 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}}

 1. 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:
 <<BR>><<BR>>
 [[recon-all]] -stage2 -cc-xyz MNIcoords -pons-xyz MNIcoords -rh-xyz MNIcoords -lh-xyz MNIcoords -subjid subj
 <<BR>><<BR>>

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