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Hi,
Thanks for this. Using mri_surf2vol as a QC hadn't occured to me and is a nice
solution. I feel again using --fillribbon is the best way to project the
surface to the volume for my case?
There is one other issue I had seen, but didn't know if it would affect my
procedure. As I am examining the entorhinal cortex, it seems like part of my
mask expands past the surfaces created by recon-all. I attach a screenshot of
what I mean (the entorhinal mask is in yellow). When I then run mri_surf2vol,
the output I get covers very well the part of my original mask that IS within
the pial surfaces, but doesn't extend to include the rest of the mask. So it
seems this is affecting the process.
Do you have any suggestions as to how I can solve this issue? Would it be worth
trying to reconstruct the surfaces- although they are in line with the bert
subject template of freesurfer.
Thanks,
Marianna
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: 27 May 2021 9:39 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Choosing projfrac/projdist and checking mri_vol2surf
output
If I understand you correctly, you have an ROI defined in the volume and you
want to transfer it to the surface. Is that right? First you should look at the
ROI in the volume along with the surfaces and make sure that they pass through
the ROI. I would generally use the projfrac-max option for something like this.
After you get a surface overlay, you can map it back to the volume
(mri_surf2vol) and see if it looks right relative to the full volume ROI.
On 5/21/2021 6:41 AM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
Hi all,
I have a question regarding checking the output of mri_vol2surf. I am
converting a manually segmented volume ROI into a surface label in order to
gain information such as cortical thickness.
What is the best practice for quality control and checking the surface
rendering of the ROI? Are there any protocols or suggestions? As slight changes
in projfrac change the output by a large degree, it's difficult to assess what
is the closest to the original volume ROI. The suggestions also vary (others
say projfrac 0.5, others to use projfrac-max or projdist). The main output
statistic I'm interested in cortical thickness of the region (if this
influences the options).
How do you choose and establish what is the best option?
Thanks
Marianna
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