[Simnibs-discuss] Charm Issue

[Mags McAllister]

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.

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