[Simnibs-discuss] manual correction

Oula Puonti oupu at dtu.dk
Wed Aug 19 13:36:32 CEST 2020

Hi Witold,

1) When using CAT the cortical and white matter surfaces are not generated from the volume files (.nii.gz), but rather the surface files stored in the mask_prerp folder. Thus editing the volume files

will have no effect on the cortical or white matter surfaces in the final headmodel. You can, however, edit the CSF, skull, and scalp masks and these edits are propagated to the final head model.

If you want to edit the GM and WM masks, please disable CAT12 (--no-cat flag). After that the edits on the WM and GM masks will also change the final headmodel.

2) We have not studied this systematically, but in my experience CAT12 does a good job even if the grade it assigns is B. That being said, you should still inspect the resulting segmentation for large errors using the

headreco check call.

3 & 4) I'm not that experienced with manual edits and the little experience I have is limited to freeview. I've heard people succesfully using ITK snap, but if you find it too difficult, I would consider using freeview through the windows subsystem for linux. It's a bit trickier, but the instructions here are quite clear:



From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of w.tomasz at sensusmed.pl <w.tomasz at sensusmed.pl>
Sent: Tuesday, August 18, 2020 5:37:11 PM
To: Guilherme B Saturnino
Cc: discuss at simnibs.org
Subject: [Simnibs-discuss] manual correction


I had the pleasure of talking to you for a while at the April webinar on brain modeling after stroke.
I am currently researching the use of stimulation in a person with tinnitus with personalized stimulation.
I have a question about the manual correction of the brain model (the model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2 images) in the automatic model creation in the CAT report gets results on the B and B + levels.
I'm a beginner when it comes to modeling (I am more concerned with NIBS in clinical applications), sorry if my questions are trivial :

1. on the SIMNIBS website, it says that it is not possible to do CAT cuttings, whether in such a system we use "m2m_ernie \ mask_prep \ MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing. Does a manual correction make sense in such a situation?

2. From your and your team's experience, how big are the differences in electric field distributions between the B / B + and A-level models?

3.I wanted to use ITK-SNAP for the correction proposed on one of your toutorials but I am a beginner I have a hard time figuring out how to check if (how exactly) the surface contours follow the tissue shapes in the T1w image, with more masks than one .

4. Could you suggest a program other than FS to evaluate the created model? Since I'm a Windows 10 and FS user, it's more complicated here.

Thank you very much for your help and your time!
Best regards,
Witold Tomasz
psycholog, psychoterapeuta, terapeuta tDCS

Ośrodek psychoterapii i neurorehabilitacji
Sensusmed Witold Tomasz
p:      504288040  m: 789335047
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        ul.Madalińskiego 3/1
w:      www.sensusmed.pl<http://www.sensusmed.pl>  e: w.tomasz at sensusmed.pl<mailto:w.tomasz at sensusmed.pl>

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