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<p>Hi Joel,</p>
<p>Did you check the template alignment after forcing the affine
from headreco? You can also try switching the init_type from "mni"
to "atlas" in the [samseg] section of the settings file. It also
looks like the scans don't have neck so please include the
--noneck flag if that's the case.</p>
<p>If you've tried all these things already, I'm happy to have a
look if you're allowed to share a scan or two from the data set.</p>
<p>Best,<br>
Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 8/5/22 12:32, Joel Upston wrote:<br>
</div>
<blockquote type="cite"
cite="mid:222E2ED5-F642-4E69-84BB-1131664D4FE8@unm.edu">
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
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Hi there,</div>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
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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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
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Thank you,</div>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
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Joel Upston</div>
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<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<img alt="Correct_GM_surface_from_headreco.png"
src="cid:part1.GhNwKxfv.ghhYpiCM@drcmr.dk" class=""><br>
</div>
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font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<img alt="Incorrect_GM_surface_from_charm.png"
src="cid:part2.JFMftLlX.UUqLQqer@drcmr.dk" class=""><br>
</div>
<img id="32A1A34F-43FD-42CA-9990-D08828BD128B" alt="Screenshot
from 2022-08-04 12-51-01.png"
src="cid:part3.evZGGuF1.00P53ADF@drcmr.dk" class=""></div>
</blockquote>
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