On 5/28/2021 9:25 AM, M Pope wrote:
External Email - Use Caution
External Email - Use Caution
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?
Probably does not matter since this is just QC.
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.
Often the surface is inaccurate in that part of EC because there is no
gray/white contrast. You can edit the wm.mgz to add WM voxels there.
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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://secure-web.cisco.com/1crndCNiNtoGVMPUhoNnIxDSbZaX5xv97bIlJ1N0pCUII7EcUVI4slR0gbGN3F62lLnTmj7wr-dJaeO9AKmBNBMeRzatolyfg2XS1XoFHeDuVU1n5eI0HQGrT2PoZZ_VYiryY1YhhJbsD-EUTUlMW_2tw6yWS3nTlcCuYS6XJUtsKSnQimsZ_ul5RXOMaKs2vYbC7LZ7Y20VR6b01z1Akn0G73LdPu-zgYWeS1aWy8RoC9O8ATX7WyQMimsPJ-iBV5-5ynzL01HECR1yfmCIn5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
<https://secure-web.cisco.com/1crndCNiNtoGVMPUhoNnIxDSbZaX5xv97bIlJ1N0pCUII7EcUVI4slR0gbGN3F62lLnTmj7wr-dJaeO9AKmBNBMeRzatolyfg2XS1XoFHeDuVU1n5eI0HQGrT2PoZZ_VYiryY1YhhJbsD-EUTUlMW_2tw6yWS3nTlcCuYS6XJUtsKSnQimsZ_ul5RXOMaKs2vYbC7LZ7Y20VR6b01z1Akn0G73LdPu-zgYWeS1aWy8RoC9O8ATX7WyQMimsPJ-iBV5-5ynzL01HECR1yfmCIn5Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1F8p448890AiMz2gjAtcXle9Q065AgONKG4pWEFQ4nsRvkDjwC_V70dvnOS1W3EwEE6PnkLT3MnaPVjAvCPt0tpdR69VvCYuI6bXPD7Y4h7bPH7sXsQuXD7LjmsS6GM20b4YeXLO13IMmxzuPdjiZQKvFHKZdZ3KFCE40Ls6snKUwh0BTrHyrmrraXF4vE6eup2g-egJ967H0Wb3_1rHyp3pu67ubozubbgFa6sDHhzTjwrUawNXVP8cHFEvKUrCqiaRraipIAlUEAL0gWd4gzA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________
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 Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
