Hi Dorsa, ImageJ and the people on the ImageJ mailing list may be helpful in transforming one of the standard output formats provided by freeview, e.g. nii, to a standard input format provided by COMSOL. Here's a useful link. http://imagej.nih.gov/ij/list.html
HTH - Don > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, July 07, 2016 12:29 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] question about exporting volumes > > You can view it in freesurfer with > cd $SUBJECTS_DIR/subject/mri > freeview -v orig.mgz -v > aseg.mgz:lut=$FREESURFER_HOME/FreeSurferColorLUT.txt:opacity=.3:colormap > =lut > > I don't know anything about COMSOL > > > On 07/07/2016 12:25 PM, Dorsa Haji Ghaffari wrote: > > Thank you. I want to view the thalamus as a volume in freesurfer. Do > > you know how to do that? also by exporting I mean exporting it as a > > volume and then import it into COMSOL as a geometry. > > > > Thank you for your help! > > > > Dorsa > > > > > > On Wed, Jul 6, 2016 at 7:50 PM, Douglas N Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > what do you mean isolate? what do you mean export? You can create a > > binary mask in nifti format with mri_binarize --i aseg.mgz --match > > 10 49 > > --o thalamus.mask.nii.gz > > > > > > On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote: > > > > > > > > > > > > Hi, > > > > > > I was able to segment the MRI successfully, now I am trying to > > isolate > > > the thalamus and export it out of FS as a volume. Is there a way > > to do > > > that in FS? > > > > > > Thank you > > > > > > Dorsa > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://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 > <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 > > -- > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
