| Deletions are marked like this. | Additions are marked like this. |
| Line 5: | Line 5: |
| 1.Open the subject's wm volume up in tkmedit. | 1.Open the subject's (subj) wm volume up in tkmedit. |
| Line 7: | Line 7: |
| '''tkmedit subject_name wm''' | {{{tkmedit subj wm}}} |
| Line 15: | Line 15: |
|
Corpus Callosum |
|
| Line 17: | Line 19: |
| 4.Copy the MNI coordinates to the command line for either '''recon-all -cc-xyz ....''' or in '''mri_fill -C ....''' | 4.Copy the MNI coordinates to the command line for either {{{recon-all -cc-xyz ....}}} or in {{{mri_fill -C ....}}} |
| Line 33: | Line 35: |
| 6.Not all points need to be defined, any range from none to all four may be defined. in mri_fill: | 6.Not all points need to be defined, any range from none to all four may be defined. To inflate: |
| Line 38: | Line 40: |
| or in the equivalent in recon-all: | or, the equivalent in recon-all: |
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:
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
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