| Deletions are marked like this. | Additions are marked like this. |
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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 (subj) wm volume up in tkmedit. | 1. Open the subject's (subj) wm volume up in ["tkmedit"]. |
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| {{{tkmedit subj 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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| Corpus Callosum | attachment:CCcor.jpg attachment:CChor.jpg attachment:CCsag.jpg |
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| attachment:CCcor.jpg attachment:CChor.jpg attachment:CCsag.jpg | 1. Copy the MNI coordinates to the command line for either |
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| 4.Copy the MNI coordinates to the command line for either {{{recon-all -cc-xyz ....}}} or in {{{mri_fill -C ....}}} | ["recon-all"] -cc-xyz .... |
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| 5.Do this for all of the other cutting plane points and seed points. Examples follow: | or in |
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| Pons | ["mri_fill"] -C .... |
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| attachment:Pcor.jpg attachment:Phor.jpg attachment:Psag.jpg | 1. Do this for all of the other cutting plane points and seed points. Examples follow: |
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| RH seed | Pons |
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| attachment:RHcor.jpg attachment:RHhor.jpg attachment:RHsag.jpg | attachment:Pcor.jpg attachment:Phor.jpg attachment:Psag.jpg |
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| LH seed | RH seed |
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| attachment:LHcor.jpg attachment:LHhor.jpg attachment:LHsag.jpg | attachment:RHcor.jpg attachment:RHhor.jpg attachment:RHsag.jpg |
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| 6.Not all points need to be defined, any range from none to all four may be defined. To inflate: | LH 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:LHcor.jpg attachment:LHhor.jpg attachment:LHsag.jpg |
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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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| or, the equivalent in recon-all: |
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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| {{{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''' |
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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 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:
BRBR ["recon-all"] -stage2 -cc-xyz MNIcoords -pons-xyz MNIcoords -rh-xyz MNIcoords -lh-xyz MNIcoords -subjid subj BRBR
NOTE: These command line(s) need to be run EVERYTIME the subject's surfaces are reinflated