[Simnibs-discuss] Charm Issue

[Oula Puonti]

Hi Mags,

I haven't seen this before. The terminal output looks alright to me.

How does the mesh (.msh file) look if you open it in gmsh?

Also if you open charm_report.html (inside the m2m_folder) does the
segmentation look okay?

Best,
Oula

On Fri, 2023-02-10 at 14:54 +0000, Mags McAllister wrote:
> I’ve attached the terminal output here in case it helps uncover
> what’s happening here.
>  
> Thanks!
> Mags
>  
> From:Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of
> Mags McAllister <margaret.mcallister at duke.edu>
> Date: Thursday, February 9, 2023 at 3:54 PM
> To: discuss at simnibs.org <discuss at simnibs.org>
> Subject: [Simnibs-discuss] Charm Issue
> Hello, 
>  
> I have come across a very strange issue creating the reconstruction
> with charm. I input a T1 with full coverage of the skull, but the
> model it created looks like this. The T1_upsampled,
> T1_bias_corrected, and T1 nifti files in the m2m folder all show the
> full scan. The surface files however reflect only the bottom half of
> the brain like what I view in the simnibs gui.
>  
> I’m re-running this now with the same issue and can share the
> terminal output when it concludes. The command I used was ‘charm
> subID T1.nii.gz’.
>  
> I appreciate any advice or thoughts others have!
> Mags M. 
>  
> A picture containing colorful
> 
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