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.The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.