• FreeSurferFill

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

   

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

   RH seed

   LH seed

   

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