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← Revision 9 as of 2008-04-29 11:46:03 ⇥
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| 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. | 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. |
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| Occasionnally, manual intervention is required to define the cutting planes and seed points. To do so, follow these steps: | Occasionally, manual intervention is required to define the cutting planes and seed points. To do so, follow these steps: |
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| 1.Open the subject's wm volume up in tkmedit. | 1. Open the subject's (subj) wm volume up in [[tkmedit]]. |
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| '''tkmedit subject_name wm''' | [[tkmedit]] subj wm |
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| 2.View the MNI talairach coordinates. | 1. View the MniTalairach coordinates: '''View->Information->MNI Coordinates''' |
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| '''View->Information->MNI Coordinates''' | 1. Select the Corpus Callosum point, on the mid-posterior portion of it. Example: |
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| 3.Select the Corpus Callosum point, on the mid-posterior portion of it. Example: | Corpus Callosum |
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| attachment:CCcor.jpg attachment:CChor.jpg attachment:CCsag.jpg | {{attachment:CCcor.jpg}} {{attachment:CChor.jpg}} {{attachment:CCsag.jpg}} |
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| 4.Copy the MNI coordinates to the command line for either '''recon-all -cc-xyz ....''' or in '''mri_fill -C ....''' | 1. Copy the MNI coordinates to the command line for either |
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| 5.Do this for all of the other cutting plane points and seed points. Examples follow: | [[recon-all]] -cc-xyz .... |
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| Pons | or in |
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| attachment:Pcor.jpg attachment:Phor.jpg attachment:Psag.jpg | [[mri_fill]] -C .... |
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| RH seed | 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 |
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| attachment:RHcor.jpg attachment:RHhor.jpg attachment:RHsag.jpg | 1. Do this for all of the other cutting plane points and seed points. Examples follow: |
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| LH seed | Pons |
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| attachment:LHcor.jpg attachment:LHhor.jpg attachment:LHsag.jpg | {{attachment:Pcor.jpg}} {{attachment:Phor.jpg}} {{attachment:Psag.jpg}} |
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| 6.Not all points need to be defined, any range from none to all four may be defined. in mri_fill: | RH seed |
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| {{{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}}} | {{attachment:RHcor.jpg}} {{attachment:RHhor.jpg}} {{attachment:RHsag.jpg}} |
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| LH seed | |
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| or in the equivalent in recon-all: | {{attachment:LHcor.jpg}} {{attachment:LHhor.jpg}} {{attachment:LHsag.jpg}} |
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| {{{recon-all -stage2 -cc-xyz MNIcoords -pons-xyz MNIcoords -rh-xyz MNIcoords -lh-xyz MNIcoords -subjid subj}}} | 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>> |
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| '''NOTE: these command line(s) need to be run EVERYTIME the subject's surfaces are reinflated''' | 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>> |
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| '''NOTE: These command line(s) need to be run EVERYTIME the subject's surfaces are reinflated''' |
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
- 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
- Do this for all of the other cutting plane points and seed points. Examples follow: Pons
RH seed 
LH seed 
- 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