Hi Doug,
Thank you for taking the time to answer, I really appreciate it! I have completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh files. What should be the next step for creating those maps? Unsure on how to overlay the mgh files.
Thanks, Sabrina
On Feb 4, 2016, at 4:48 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Sabrina, sorry, I was working on a grant, and now I'm out of town until Monday. I can try to push you forward on this now, but I have to be brief. Those images where made from data created with the pctsurfcon scriopt. If you run it with --help, you will get some docs on it. This is already run by default with output {lr}h.w-g.pct.mgh which is the GM/WM intensity in Figure 1. This script will also create the GM and WM intensity files but deletes them by default. You can re-run it and specify the temporary folder with --tmp, and those files will be in there. I don't know what they will be called but hopefully it will be obvious.
doug
On 2/4/16 2:14 PM, Sabrina Yu wrote:
Hi sorry, haven't heard back yet from Freesurfers. Just following up on how to generate gray matter & white matter intensity maps overlaid onto brain like in Salat paper.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
Figure 1 (c). The mean maps of signal intensity.
Thanks! ________________________________________ From: Sabrina Yu Sent: Thursday, January 28, 2016 10:51 AM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: Gray matter intensity
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57
Figure 1 (c). The mean maps of signal intensity.
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: Thursday, January 28, 2016 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity
which figure(s) in particular?
On 01/28/2016 01:41 PM, Sabrina Yu wrote:
Hi,
Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?
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: 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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