you'll need to get the code associated with each lobe. You can do this by running tkmedit subject nu.mgz -seg lobeseg.mgz -aux lobeseg.mgz

This will show colors for the seg, but the names will be wrong. Click on a seg and see what number it gets in the aux. Then create a new color table to match, then run mri_segstats

doug

On 05/07/2014 04:51 PM, pfotiad@nmr.mgh.harvard.edu wrote:

Hi Doug,

Thanks for your help, the mri_aparc2aseg command worked fine. In addition, is there a way to get a binary volume for each of the lobes based on the result of the mri_aparc2aseg command? In other parcellation volumes, I would use mri_binarize and the FreeSurferColorLUT.txt table but here I coudn't think how this could be applicable.

Thanks again, Panos

...

Try using mri_aparc2aseg instead of label2vol. See the --help and/or look in the recon-all.log file to get the command line used to create the aparc+aseg.mgz file doug

On 05/07/2014 11:12 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi FS Community,

I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually?

Thank you in advance, Panos _______________________________________________ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Just use mri_binarize doug

On 05/07/2014 05:08 PM, pfotiad@nmr.mgh.harvard.edu wrote:

Hi Doug,

That sounds great! I'll go ahead and do that. I would just be interested in coming up with the binary maps of the lobes, not their associated stats. Should I still go ahead and use mri_segstats or should I use mri_binarize with the --match flag and the new color map instead? Thanks for all your help, Panos

...

you'll need to get the code associated with each lobe. You can do this by running tkmedit subject nu.mgz -seg lobeseg.mgz -aux lobeseg.mgz

This will show colors for the seg, but the names will be wrong. Click on a seg and see what number it gets in the aux. Then create a new color table to match, then run mri_segstats

doug

On 05/07/2014 04:51 PM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi Doug,

Thanks for your help, the mri_aparc2aseg command worked fine. In addition, is there a way to get a binary volume for each of the lobes based on the result of the mri_aparc2aseg command? In other parcellation volumes, I would use mri_binarize and the FreeSurferColorLUT.txt table but here I coudn't think how this could be applicable.

Thanks again, Panos

...

Try using mri_aparc2aseg instead of label2vol. See the --help and/or look in the recon-all.log file to get the command line used to create the aparc+aseg.mgz file doug

On 05/07/2014 11:12 AM, pfotiad@nmr.mgh.harvard.edu wrote:

...

Hi FS Community,

I created a lobes annotation file with the --lobesStrict flag of the mri_annotation2label and then converted it to a volume with the mri_label2vol command and the --annot flag. However, the resulting volume is just overlapping on top of the white surface, and not on the whole cortex. Is there a way to create a volume for the lobes that covers the whole cerebral cortex? That is a volume that shows you which part of the cerebral cortex belongs to each of the 6 lobes individually?

Thank you in advance, Panos _______________________________________________ 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer