You need to open the fsaverage surface using tksurfer or freeview, then find a vertex in the location where you want to create the label, then get the vertex number and replace "vertexno" in the command with that number
On 12/14/2016 02:54 PM, Leyton Moscoso, Cristian Eduardo wrote: > Hi Dou, > > I have had some issues with running /mri_volsynth/. > > It is not clear how to specify the coordinate for the selected vertex. > I tried it by adding the flag --c_ras x y z, but did not work? > > Thanks > > Cris > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > *Sent:* Tuesday, December 13, 2016 4:50 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Label creation > > Not that easy. I would do it by selecting a vertex that is close to > the coordinate you want, then > > > 1. Create a surface overlay with all vertices = 0 except your chosen > vertex > > mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness > --delta vertexno 0 0 0 --o delta.mgh > > > 2. Smooth the overlay to expand the non-0: > > mri_surf2surf --s fsaverage --hemi lh --sval delta.mgh --tval > delta.smoothed.mgh --nsmooth-in 10 > > This will expand out to a radius of 10 vertices > > > 3. Binarize it > > mri_binarize --i delta.smoothed.mgh --min .000000001 --o > delta.smoothed.bin.mgh > > > 4. Create the label: > > mri_cor2label --i delta.smoothed.bin.mgh --l delta.smoothed.bin.label > --surf fsaverage lh white > > > > > > On 12/13/16 12:53 PM, Leyton Moscoso, Cristian Eduardo wrote: >> Hi Freesurfer's experts >> >> Is there an easy way to create automatically a circular label with a >> radius centered on a vertex with predifined RAS/Tailarach coordinates >> on the fsaverage surface? >> >> Thanks >> >> Cris >> >> >> _______________________________________________ >> 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
