Hi Thomas
you are probably better off getting it right out of the aseg.mgz. The cc
labels in it are:
#define CC_Posterior 251
#define CC_Mid_Posterior 252
#define CC_Central 253
#define CC_Mid_Anterior 254
#define CC_Anterior 255
so you should just be able to run mri_extrac_label directly
set mdir=$SUBJECTS_DIR/$s/mri
mri_extract_label $mdir/aseg.mgz 251 252 253 254 255 $mdir/cc.mgz
then go from there
cheers
Bruce
On Fri,
14 Mar 2014, Thomas PAUL wrote:
Dear FreeSurfer experts,
I've been using FreeSurfer for 2 months now, and I have a question on how to
proceed to do the following thing:
My goal is to obtain the CRS coordinates of the corpus callossum.
Here is what I was thinking to do, based on what I read:
1. Annotation to segmentation:
mri_annotation2label --seg --hemi ?? --subject bert volume_annot.mgh
=> I need to provide an hemisphere, which one should I use, should I do this
for both ?
2. Binarize the volume, keeping the label we want:
mri_binarize --i volume_annot.mgh --match 86 --o corpusCallossum.mgh
=> I use the number 86 based on the LUT table...
3. Execute:
mri_surfcluster --in corpusCallossum.mgh --thmin 0.5 --subject bert
--hemi ?? --o outputfile.mgh
Am I on the right path? I am not sure on how to use the outputfile.mgh
after. Did I miss any arguments in the command line?
Thank you in advance for your help
Thomas Paul.
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