External Email - Use Caution
Thank you for your reply! It was very helpful.
I was able to successfully create the difference mask according to your instruction.
As far as the sum.dat output from mri_segstats, I'm uncertain as to what columns to look at to find the percent of each ROI that had edits; all I get is information regarding the number of voxels, and the mean, stdDev, min, max, and range of intensity for each structure.
To provide some more context, the goal of this endeavor is to essentially create a sort of "log" of edits, to know the regions where voxels were erased or added (and to which volume). In terms of identifying only edited regions, would it be better to create a mask which extracts only voxels with a value of 1 or 255?
Also, I had a question regarding a different topic with regards to to aparc+aseg.mgz after rerunning recon-all: although the pial surface changed after rerunning recon-all, the aparc+aseg.mgz didn't seem to change. I've attached a screenshot where you can see the aparc+aseg extending significantly beyond the pial surface, so I'm wondering why that might be, and whether it's a problem? In the troubleshooting slides it does mention that it's okay if the cortical ribbon extends beyond the surface, since the ribbon isn't used for anything, but why would it not change to reflect changes in the pial surface?
Thank you very much again for your assistance.
-Jee Won ________________________________________
Date: Fri, 8 Oct 2021 12:48:03 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Comparing volumes before and after editing To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8558ace1-9ef4-a75c-984b-1b53cc87e2ea@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
If you subtract them, eg, fscalc vol1.mgz sub vol2.mgz abs gte 0.5 -o diff.mgz This command will subtract the two, take the absolute values, then threshold (binarize) the differences. I'm not sure what you are looking for in terms of aparc+aseg, but you can do something like mri_segstats --ctab-default --seg aparc+aseg.mgz --excludeid 0 --i diff.mgz --sum sum.dat and sum.dat will tell you the percent of each ROI that had edits
On 10/1/2021 4:01 PM, Kang, Jee Won wrote:
????????External Email - Use Caution
Hello all,
I'm very new to Freesurfer and have?started with quality-checking recons. I wanted to know if there is a way to compare volumes before and after edits were made before recon-all has been re-run.
For example, if we have brainmask.mgz that has been edited and brainmask_ORIG.mgz before any edits were made, is there a way to create?a volume overlay and extract the areas where edits were made (perhaps parsed from aparc+aseg)?
Thank you for your assistance on this!
-Jee Won
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1tDN495Zmz69_tS_DgP3uRxsUNUoW4dfYipN6gNbM54T8su...
