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

Oula oulap at drcmr.dk
Mon Aug 8 08:30:00 CEST 2022

Hi Joel,

The standard init_type ("mni") does a registration between the T1w MNI 
template and the input scan using a correlation metric. This assumes 
that the tissue intensities of the input scan and the MNI template are 
more or less the same, and it can sometimes fail if that's not the case 
(even if the input is a T1w scan).

Init_type="atlas" does a registration between the input and a 
probabilistic atlas using a mutual information-based metric (similar to 
what SPM12 does). This metric doesn't care about the specific tissue 
intensities of the input, so you could, for example, feed in a T2w scan 
and it should still work.

The reason I set "mni" as default is that it's faster and seemed to work 
well on the cases I tested it. I'll try to do more testing on different 
T1w scans to see if we should set the "atlas"-option as default.



On 8/5/22 18:12, Joel Upston wrote:
>  Oula,
> 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:
>> *  [EXTERNAL]*
>> 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.
>> Best,
>> Oula
>> 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%20from%202022-08-04%2012-51-01.png
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