yes

On Sat, 15 Mar 2014, Thomas PAUL wrote:

Thank you Bruce for your help, it works. I didn't noticed that
mri_extract_label existed. 
So just to be sure, the output volume is not a mask, right? If I want to
convert it to a mask, I use mri_binarize ?
Thomas Paul.


On Fri, Mar 14, 2014 at 2:51 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      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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