[Simnibs-discuss] About the usage of custom CAT12 segmentation

Oula Puonti oupu at dtu.dk
Wed Dec 2 10:33:46 CET 2020

Hi Ti Chun Hang Eden,

I haven't tried the stroke tool, so not sure what it outputs, but if the stroke lesion is segmented out separately you could assign that to CSF in the mask_prep folder (after binarization).

In the final mesh the lesioned area would then be CSF, but you can afterwards relabel it back to stroke lesion using the segmentation mask if you want.


From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of TI, Chun Hang Eden <1155138422 at link.cuhk.edu.hk>
Sent: Thursday, November 26, 2020 2:14:14 AM
To: simnibs-discuss at drcmr.dk
Subject: [Simnibs-discuss] About the usage of custom CAT12 segmentation

Dear Sir/Madam,

I have been using SIMNIBS headreco segmentation to generate cortical surface reconstruction for stroke patients, knowing CAT12 is not optimized for these types of brains.

The newest version of CAT12 includes a function (Stroke Lesion Correction), which produces a better segmentation result after my inspection. Is there a way to incorporate these segmentation results directly, to proceed to the next stage?

 I tried to use the segmentation results from that, to replace the results in /segments/cat directories, and binarized the segmentation mask. However, when I run the preparecat function, I encounter the following errors.

I suspect that the error results from the difference of the number of vertices of the mesh generated from the initial preparevol command and the custom segmentation results from new CAT12.
Is there any way to generate a .off file based on the new CAT12 features?

I have been using Simnibs for a long time and really appreciate your team's effort in maintaining and updating the software for better progression of this research field. Look forward to your reply

Best regards,

Ti Chun Hang Eden
PhD, Department of Biomedical Engineering
The Chinese University of Hong Kong
Email: 1155138422 at link.cuhk.edu.hk
Mobile: +852 91339153
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