Use the --outmask option
On 10/07/2018 08:59 AM, N Saf wrote:
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Dear Douglos,
I did not understand how to use mri_label2label with the mask option(there is srcmask options not mask alone !). I extract my labels and as you explained I wanted to create i.e. binary mask of rh.fusiform.label with mri_label2label : mri_label2label --srcsubject case1 --srclabel rh.fusiform.label --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface --hemi rh
but it creats another label file not binary with mgh format I did not get how can I create mybinary.mgh mask in order to use in third command "mri_binarize --i lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh"
would you please help me with this, it would be a great favor.
Best regards, Nazanin
On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
Yes, that should work. You can create a mask by breaking the annotation into labels (mri_annotation2label), then converting the label into a binary mask (mri_label2label with --mask option), then mri_binarize --i lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh On 07/30/2018 01:47 AM, N Saf wrote: > > External Email - Use Caution > > Dear Freesurfer Experts, > > I wonder how can I show the cortical thickness surface on just one > region of my interest in Freeview. assume that I want to see the > thickness surface of one of the regions in DKTatlas. does it work if I > make a binary mask of that specific region on aparcDKTatlas.annot and > then multiply it to the ?h.thickness surface ?? any help will be > appreciated. > > Best Regards, > Nazanin > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
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