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<p>Hi Joel,</p>
<p>I'd be interested to look at cases 1) and 2). I didn't have any
subjects with severe atrophy to test on so I think these can
certainly be improved. Also having the cortical GM pushed all the
way up to the CSF surface sounds strange.</p>
<p>W.r.t. fixing the affine: there are examples on how to do this in
the documentation. If you click through tutorial -> Creating
Head Models and then go all the way down on that page and click on
"Fixing the Affine Registration". This should give you some
pointers on how to do that. I'll also implement a flag for passing
a registration matrix and skipping the optimization. <br>
</p>
<p>Best,</p>
<p>Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 8/10/22 17:56, Joel Upston wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6883EDE5-361C-4697-A1CA-430194520691@unm.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
Oula,
<div><br>
</div>
<div>Thank you for the explanation and I found as you said that
“mni” is faster but does seem to fail more than “atlas”. However
after more testing with these settings it looks like it is
still having issues about 40% of the time, this is over about 20
subjects I have tested some with T1 and T2 others with just T1.
Some of the issues are summarized as follows:</div>
<div><br>
</div>
<div>1) The template appears to be registered correctly and the
tissue types are correctly segmented except the gray matter
which as I mentioned before is “pushed” right to the edge of the
csf inner layer. In these cases running the same scan through
headreco with cat12 seems to generate the correct gm surface but
then have to use outside programs to combine the two
segmentations via editing, use the add_tissues_to_upsampling and
then rerun the meshing. </div>
<div><br>
</div>
<div>2) Some of the population of this dataset is above 50, with
some atrophy and large ventricles. The ventricles that are often
large, fail in the charm segmentation. My solution is to again
use the headreco segmentation ventricles in the charm
segmentation.</div>
<div><br>
</div>
<div>3) The probabilistic atlas is still not in registration with
the T1, or could be improved. Would it be possible to add in a
12 parameter registration matrix (similar to the init transform)
that it is forced to used, that way if another outside program
such as AFNI or spm gets a better registration I can use that? I
have noticed that using the init transform with the proper
alignment ends up finding the same incorrect minimum in the
registration optimization. </div>
<div><br>
</div>
<div>Overall I am happy to share some of this data as well to help
with some of these issues. Thank you for all your help and all
your contributions to automate a more accurate head model for
the field. </div>
<div><br>
<br>
<div dir="ltr">Thank you,
<div><br>
</div>
<div>Joel Upston</div>
</div>
<div dir="ltr"><br>
<blockquote type="cite">On Aug 8, 2022, at 12:30 AM, Oula
<a class="moz-txt-link-rfc2396E" href="mailto:oulap@drcmr.dk"><oulap@drcmr.dk></a> 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>
<div>
<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>
</div>
<blockquote type="cite"
cite="mid:194A1B83-E82B-4B57-AE1A-00517C2FF857@unm.edu">
<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 <a class="moz-txt-link-rfc2396E"
href="mailto:oulap@drcmr.dk"
moz-do-not-send="true">
<oulap@drcmr.dk></a> 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>
<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:
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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>
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<div style="font-family: Calibri, Arial,
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Thank you,</div>
<div style="font-family: Calibri, Arial,
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<br>
</div>
<div style="font-family: Calibri, Arial,
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class="elementToProof">
Joel Upston</div>
<div style="font-family: Calibri, Arial,
Helvetica, sans-serif; font-size:
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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.XvOmVQvv.gVzaZAQF@drcmr.dk" class=""><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.KlSnrDQY.WcKZL0Y9@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.WIlROTAi.IeMi9QgU@drcmr.dk"
class=""></div>
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