[Simnibs-discuss] Charm Segmentation Issues in Simnibs 4 Beta

Joel Upston jupston at unm.edu
Fri Aug 5 18:12:27 CEST 2022


Thank you for the quick response. Yes the template alignment seems to be a bit better from the affine from headreco, than that of what is given through the charm optimization. I tried the noneck which didn’t change it but just tried the “atlas” init_type parameter and that worked. How exactly is it different?

Thank you,

Joel Upston

On Aug 5, 2022, at 5:18 AM, Oula <oulap at drcmr.dk> wrote:


Hi Joel,

Did you check the template alignment after forcing the affine from headreco? You can also try switching the init_type from "mni" to "atlas" in the [samseg] section of the settings file. It also looks like the scans don't have neck so please include the --noneck flag if that's the case.

If you've tried all these things already, I'm happy to have a look if you're allowed to share a scan or two from the data set.


On 8/5/22 12:32, Joel Upston wrote:

Hi there,

I have worked with the Simnibs 3.2.6 headreco to do segmentation and now trying out the charm segmentation routine in the Simnibs 4 Beta release. I have multiple subjects (about 10 subjects tried so far) that have looked good in the headreco segmentation in terms of the brain segmentation especially using the T1 and T2 but when I try this with the charm segmentation, I run into a problem about 50% of the time. The problem is that the cortical surface is smooth and pushed up right next to the csf boundary layer, but the wm surface looks good. I have attached an image of what is happening to show a better description. I have made sure that the template is aligned by forcing in the code to use the Simnibs 3 warp from MNI2Conform 12 parameter alignment, where the previous headmodel seemed to be  accurate. I also try to change some of the settings in the settings.ini file such as all parameters in the segment section and th_initial in the surface section with no avail. As I run the same subject in the Simnibs 3.2.6 the headmodel looks good, I have tried to edit via switching out the brain+csf segmentation from simnibs3 to simnibs 4 and reran the mesh after editing. This works reasonably well but the some of the external to brain structures are affected, plus requires double the runtime to run versions 3 and 4. Have you noticed a problem similar to this and do you have any recommendations to try? Thank you for all your work and I appreciate the research to keep improving this modeling.

Thank you,

Joel Upston


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220805/352290fc/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Correct_GM_surface_from_headreco.png
Type: image/png
Size: 128092 bytes
Desc: Correct_GM_surface_from_headreco.png
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220805/352290fc/attachment-0003.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Incorrect_GM_surface_from_charm.png
Type: image/png
Size: 104518 bytes
Desc: Incorrect_GM_surface_from_charm.png
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220805/352290fc/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot%20from%202022-08-04%2012-51-01.png
Type: image/png
Size: 370088 bytes
Desc: Screenshot%20from%202022-08-04%2012-51-01.png
URL: <https://mailman.drcmr.dk/pipermail/simnibs-discuss/attachments/20220805/352290fc/attachment-0005.png>

More information about the Simnibs-discuss mailing list