Use the --outmask option On 10/07/2018 08:59 AM, N Saf wrote: > > 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 <mailto: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 > <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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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