[Simnibs-discuss] charm head modelling problems

Oula Puonti oulap at drcmr.dk
Mon Dec 5 12:58:06 CET 2022

Hi Vincent,

Could you maybe send the charm_report.html file to: support at simnibs.org

Happy to look at the data as well if you're allowed to share it.



On 12/5/22 12:11, Vincent Rochas wrote:
> Dear simNIBS users and programmers
> I have used simNIBS previous versions with very good results and 
> reasonable simulations for tCS. I was using /headreco/ function with 
> two MRIs T1 and T2, converted from Dicom to Nifti using SPM12.
> I am now trying the new version of simNIBS (4.0) using the /charm/ 
> function and experiencing some troubles.
> - The MRIs I was previously using are apparently not compliant with 
> the needed standard in term of orientation (?) and there was a 
> complain about sform and qform annotation, so I was advised to use 
> –forceqform by the /charm/ function which I did.
> - After using the –forceqform option it runs the segmentation. However 
> the resulting .msh file in the m2m folder corresponds to another face 
> and head than my patient MRI!
> I tried to re-run the ernie segmentation (without needing the 
> –forceqform option). The command line was like: charm ernie 
> ernie_T1.nii.gz ernie_T2.nii.gz The results is again this same face 
> wrapped on ernie’s shape I guess. Or Ernie’s head wrapped differently 
> I don’t know. In the case of the patient it is surely not the head and 
> face of the patient at all, and this same head though. Also the 
> segmentation of the cortex doesn’t look very precise, sulci are not 
> well delineated.
> I then checked the log.html and I noticed a difference with the 
> examples provided by simNIBS (the prototypic ernie segmentation). On 
> the DEBUG line I have 'init_type': 'atlas' instead of 'init_type': 
> mni' in the example segmentation.
> I don’t know if it is the problem but might explain why it is 
> differently sticking the atlas maybe on the patient’s T1 as a result.
> That might be a trivial problem or an option that I missed. I would be 
> happy to have your opinion.
> Best,
> Vincent
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