no way to help without more info.
On 12/21/2015 01:10 PM, Sabrina Yu wrote:
When I try to load the overlay in freeview, it crashes immediately. Any thoughts on why this happens?
Thanks
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity
freeview or tksurfer. Load the relevant map as an overlay
On 12/21/2015 12:57 PM, Sabrina Yu wrote:
Hello,
Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
Thank you Sabrina
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N Greve greve@nmr.mgh.harvard.edu Sent: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity
On 12/15/2015 01:00 PM, Sabrina Yu wrote:
Hi,
Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?
If you want to view them on a volume instead of a surface, you can use mri_surf2vol
Thank you very much.
*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity
Hello,
I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.
- Does the wmparc.stats contain mean white matter intensity values
for each ROI?
Yes
- Is it possible to extract these same mean intensity values for gray
matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.
There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)
Thank you,
Sabrina Yu
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.
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