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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 greve@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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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.
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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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
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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer- bounces@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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.edumailto: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 greve@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@nmr.mgh.harvard.edu
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Dorsa Haji Ghaffari -
Douglas N Greve -
Krieger, Donald N.