Hi Sabrina
you need to tell us what you did the caused the crash. What was the command line? How did you try to load it?
cheers Bruce On Mon, 21 Dec 2015, 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
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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/
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