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

Oula oulap at drcmr.dk
Fri Aug 5 13:18:50 CEST 2022

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 

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
> Correct_GM_surface_from_headreco.png
> Incorrect_GM_surface_from_charm.png
> Screenshot from 2022-08-04 12-51-01.png
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