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<p>Hi Joel,</p>
<p>The standard init_type ("mni") does a registration between the
T1w MNI template and the input scan using a correlation metric.
This assumes that the tissue intensities of the input scan and the
MNI template are more or less the same, and it can sometimes fail
if that's not the case (even if the input is a T1w scan). <br>
</p>
<p>Init_type="atlas" does a registration between the input and a
probabilistic atlas using a mutual information-based metric
(similar to what SPM12 does). This metric doesn't care about the
specific tissue intensities of the input, so you could, for
example, feed in a T2w scan and it should still work.</p>
<p>The reason I set "mni" as default is that it's faster and seemed
to work well on the cases I tested it. I'll try to do more testing
on different T1w scans to see if we should set the "atlas"-option
as default.</p>
<p>Best,</p>
<p>Oula</p>
<p> <br>
</p>
<div class="moz-cite-prefix">On 8/5/22 18:12, Joel Upston wrote:<br>
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cite="mid:194A1B83-E82B-4B57-AE1A-00517C2FF857@unm.edu">
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<div dir="ltr"> Oula,
<div><br>
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<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
<a class="moz-txt-link-rfc2396E" href="mailto:oulap@drcmr.dk"><oulap@drcmr.dk></a> wrote:<br>
<br>
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style="line-height:12.0pt;background:#FF6666"><b><span
style="font-size:10.0pt;color:white"> [EXTERNAL]</span></b></p>
<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>
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<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; font-size: 12pt; color:
rgb(0, 0, 0);" class="elementToProof">
Hi there,</div>
<div style="font-family: Calibri, Arial,
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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>
<div style="font-family: Calibri, Arial,
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<br>
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<div style="font-family: Calibri, Arial,
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Thank you,</div>
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<br>
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<div style="font-family: Calibri, Arial,
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rgb(0, 0, 0);" class="elementToProof">
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.QCAOTP2r.o28mgR4v@drcmr.dk"
class=""><br>
</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="Incorrect_GM_surface_from_charm.png"
src="cid:part2.FIFgPlnA.f8JbtZmv@drcmr.dk"
class=""><br>
</div>
<img id="32A1A34F-43FD-42CA-9990-D08828BD128B"
alt="Screenshot%20from%202022-08-04%2012-51-01.png"
src="cid:part3.1MdYObP0.TFcjq0Pc@drcmr.dk"
class=""></div>
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