if you want to mask the thickness, then use mri_mask On 10/10/2018 10:30 AM, N Saf wrote: > > External Email - Use Caution > > Dear Douglos, > > as you recommended, I used the --outmask and create the binary mask of > a label in mgh format. as I use the mri_binarize command with this > mask and ?h.thickness; the output is binary too or if I use --match > flag or --min --max flag the out put is 1 for those range, but I want > the thickness values on my mask, not 1 all over it , how should I do that? > > any detail information will be appreciated. > > BRG, > Nazanin > > > On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D. > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > 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> > <mailto: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> > > <mailto: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> > <mailto: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 > <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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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