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Hi there,</div>
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I have worked with the Simnibs 3.2.6 headreco to do segmentation and now trying out the charm segmentation routine in the Simnibs 4 Beta release. I have multiple subjects (about 10 subjects tried so far) that have looked good in the headreco segmentation in
terms of the brain segmentation <span style="background-color:rgb(255, 255, 255);display:inline !important">
especially </span>using the T1 and T2 but when I try this with the charm segmentation, I run into a problem about 50% of the time. The problem is that the cortical surface is smooth and pushed up right next to the csf boundary layer, but the wm surface looks
good. I have attached an image of what is happening to show a better description. I have made sure that the template is aligned by forcing in the code to use the Simnibs 3 warp from MNI2Conform 12 parameter alignment, where the previous headmodel seemed to
be accurate. I also try to change some of the settings in the settings.ini file such as all parameters in the segment section and th_initial in the surface section with no avail. As I run the same subject in the Simnibs 3.2.6 the headmodel looks good, I have
tried to edit via switching out the brain+csf segmentation from simnibs3 to simnibs 4 and reran the mesh after editing. This works reasonably well but the some of the external to brain structures are affected, plus requires double the runtime to run versions
3 and 4. Have you noticed a problem similar to this and do you have any recommendations to try? Thank you for all your work and I appreciate the research to keep improving this modeling.</div>
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Thank you,</div>
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Joel Upston</div>
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<img alt="Correct_GM_surface_from_headreco.png" src="cid:C7DF49F3-A23D-4633-9D12-01F5DCAFAF34"><br>
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<img alt="Incorrect_GM_surface_from_charm.png" src="cid:3CC60956-EB29-4D2C-8358-94A16EFA6751"><br>
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<img id="32A1A34F-43FD-42CA-9990-D08828BD128B" alt="Screenshot from 2022-08-04 12-51-01.png" src="cid:32A1A34F-43FD-42CA-9990-D08828BD128B"></div>
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