<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body dir="auto">
<div dir="ltr"> Oula,
<div><br>
</div>
<div>Thank you for the quick response. Yes the template alignment seems to be a bit better from the affine from headreco, than that of what is given through the charm optimization. I tried the noneck which didn’t change it but just tried the “atlas” init_type
parameter and that worked. How exactly is it different? <br>
<div><br>
<div dir="ltr">Thank you,
<div><br>
</div>
<div>Joel Upston</div>
</div>
<div dir="ltr"><br>
<blockquote type="cite">On Aug 5, 2022, at 5:18 AM, Oula <oulap@drcmr.dk> wrote:<br>
<br>
</blockquote>
</div>
<blockquote type="cite">
<div dir="ltr">
<p class="MsoNormal" style="line-height:12.0pt;background:#FF6666"><b><span style="font-size:10.0pt;color:white"> [EXTERNAL]</span></b></p>
<b></b>
<div>
<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">
<div dir="ltr">
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Hi there,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Thank you,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Joel Upston</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<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"><br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
<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"><br>
</div>
<img id="32A1A34F-43FD-42CA-9990-D08828BD128B" alt="Screenshot%20from%202022-08-04%2012-51-01.png" src="cid:part3.evZGGuF1.00P53ADF@drcmr.dk"></div>
</blockquote>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</body>
</html>