External Email - Use Caution 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 <dgr...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > 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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