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<p><font size="2"><font face="Victor Mono">Hi Daniela</font></font></p>
<p><font size="2"><font face="Victor Mono">Yes, try to delete the
msh file, rerun the meshing steps, and then the check again
(you can add -f flag when running the check command to force
remaking of the fsmesh files). Then let's see.<br>
</font></font></p>
<p><font size="2"><font face="Victor Mono">Best,</font></font></p>
<p><font size="2"><font face="Victor Mono">Jesper <br>
</font></font></p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/29/2022 18:19, Rodriguez
Manrique, Daniela wrote:<br>
</div>
<blockquote type="cite"
cite="mid:a3b355949f5b475299af8243cd0dac1d@tum.de">
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<p>Dear Jesper,</p>
<p><br>
</p>
<p>thank you for your reply. We have tried deleting the two
fsmesh files (brain_contr.fsmesh and head_contr.fsmesh) before
running headreco surfacemesh, headreco volumemesh and headreco
check. However, this led to even more disappointing results of
no changes in SubID_final_contr.nii. <br>
</p>
<p><br>
</p>
<p>Do you suggest we also delete the .msh files?</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Daniela Rodriguez<br>
</p>
<p><br>
</p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b> Jesper
Duemose Nielsen <a class="moz-txt-link-rfc2396E" href="mailto:jesperdn@drcmr.dk"><jesperdn@drcmr.dk></a><br>
<b>Sent:</b> 29 December 2022 08:48:16<br>
<b>To:</b> Rodriguez Manrique, Daniela; Oula;
<a class="moz-txt-link-abbreviated" href="mailto:support@simnibs.org">support@simnibs.org</a><br>
<b>Subject:</b> Re: Issues with FreeView related to SimNIBS</font>
<div> </div>
</div>
<div>
<p><font size="2"><font face="Victor Mono">Hi Daniela</font></font></p>
<p><font size="2"><font face="Victor Mono"><br>
</font></font></p>
<p><font size="2"><font face="Victor Mono">As I believe Axel
(and perhaps also Oula) is on vacation at the moment, let
me try to send a few comments your way.</font></font></p>
<p><font size="2"><font face="Victor Mono"><br>
</font></font></p>
<p><font size="2"><font face="Victor Mono">What is used in
simulations is the .msh file (SubID.msh I suppose) of
which SubID_final_contr.nii is just a voxelized version I
believe. The fsmesh files are only used for visualization
with FreeView. What might be happening here is that
headreco just uses the fsmesh files that are already there
(from checking your previous run). Perhaps try to delete
the fsmesh files and run headreco check again. (unless of
course you already did that in which case I am not sure
what is causing this behavior.) I don't have the code
right now so I cannot really check.</font></font></p>
<p><font size="2"><font face="Victor Mono"><br>
</font></font></p>
<p><font size="2"><font face="Victor Mono">Also, you could view
the .msh file directly in gmsh.</font></font></p>
<p><font size="2"><font face="Victor Mono"><br>
</font></font></p>
<p><font size="2"><font face="Victor Mono">Best,</font></font></p>
<p><font size="2"><font face="Victor Mono">Jesper<br>
</font></font></p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/28/2022 16:40, Rodriguez
Manrique, Daniela wrote:<br>
</div>
<blockquote type="cite"
cite="mid:a8048556799c4b2f89e22dee3e0366e2@tum.de">
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dir="ltr">
<div id="divtagdefaultwrapper" dir="ltr" style="font-size:
12pt; color: rgb(0, 0, 0); font-family: Calibri,
Helvetica, sans-serif, "EmojiFont", "Apple
Color Emoji", "Segoe UI Emoji",
NotoColorEmoji, "Segoe UI Symbol", "Android
Emoji", EmojiSymbols;">
<p>Dear Oula and SimNIBS Support,</p>
<p><br>
</p>
<p>I hope you had wholesome holidays. I regret to have to
bother you with another SimNIBS question.</p>
<p><br>
</p>
<p>When we have noticed issues with headreco segmentation
in the different tissue masks, we've used free view to
edit the respective binary mask located in /mask_prep
e.g. MASK_CSF.nii.gz. Upon changing the mask we rerun
"headreco surfacemesh S<span>ubID" and "headreco </span>volumemesh
SubID". Then look at "headreco check SubID" to check the
changes in the segmentation.</p>
<p><br>
</p>
<p>We find that neither head_contr.fmesh nor
brain_contr.fsmesh have changed, but that only
SubID_final_contr.nii gets changed. Is this file the one
that gets used during electrical field modelling? We are
unsure whether we have corrected the segmentation errors
sufficiently for it to improce the electrical field
modelling doen by SimNIBS.<br>
</p>
<p><br>
</p>
<p>(These steps are illustrated here: <a
href="https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html?highlight=headreco+surfacemesh"
class="OWAAutoLink moz-txt-link-freetext"
id="LPlnk74307" previewremoved="true"
moz-do-not-send="true">
https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html?highlight=headreco+surfacemesh</a>)</p>
<p><br>
</p>
<p>Thank you very much for your assistance once again <span>😊</span></p>
<p><br>
</p>
<p>Best Regards,<br>
Daniela Rodriguez<br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Rodriguez Manrique, Daniela<br>
<b>Sent:</b> 31 August 2022 10:55:33<br>
<b>To:</b> Oula; <a class="moz-txt-link-abbreviated
moz-txt-link-freetext"
href="mailto:support@simnibs.org"
moz-do-not-send="true">
support@simnibs.org</a><br>
<b>Subject:</b> Re: Issues with FreeView related to
SimNIBS</font>
<div> </div>
</div>
<div>
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{margin-top:0;
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12pt; color: rgb(0, 0, 0); font-family: Calibri,
Helvetica, sans-serif, "EmojiFont",
"Apple Color Emoji", "Segoe UI
Emoji", NotoColorEmoji, "Segoe UI
Symbol", "Android Emoji", EmojiSymbols;">
<p>Hi Oula,</p>
<p><br>
</p>
<p>that in deed was the solution! Thanks so much for
hekping us out.</p>
<p><br>
</p>
<p>Best Regards,</p>
<p><br>
</p>
<p>Daniela Rodriguez M.<br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Oula
<a class="moz-txt-link-rfc2396E"
href="mailto:oulap@drcmr.dk" moz-do-not-send="true"><oulap@drcmr.dk></a><br>
<b>Sent:</b> 30 August 2022 07:55:53<br>
<b>To:</b> Rodriguez Manrique, Daniela; <a
class="moz-txt-link-abbreviated
moz-txt-link-freetext"
href="mailto:support@simnibs.org"
moz-do-not-send="true">
support@simnibs.org</a><br>
<b>Subject:</b> Re: Issues with FreeView related to
SimNIBS</font>
<div> </div>
</div>
<div>
<p>Hi Daniela,</p>
<p><br>
</p>
<p>Sorry for the late reply. It seems that freeview in
fs v7.1.1 does not work as it used to and closes down
immediately after opening.</p>
<p><br>
</p>
<p>If you use freeview from fs v6.0.0 that should work.</p>
<p><br>
</p>
<p>Best,<br>
Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 8/17/22 14:42, Rodriguez
Manrique, Daniela wrote:<br>
</div>
<blockquote type="cite">
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style="font-size: 12pt; color: rgb(0, 0, 0);
font-family: Calibri, Helvetica, sans-serif,
"EmojiFont", "Apple Color
Emoji", "Segoe UI Emoji",
NotoColorEmoji, "Segoe UI Symbol",
"Android Emoji", EmojiSymbols;">
<p>Dear Oula,</p>
<p>Indeed, I do not see these files. What could the
reason for them missing? Freesurfer home is set to
the version 7.1.1.</p>
<p>I see the files wm_fromMesh.nii.gz
gm_fromMesh.nii.gz unsure whether these are
realted.</p>
<p><br>
</p>
<p>Thank you for your help,</p>
<p>Daniela Rodriguez<br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block;
width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Oula
<a class="moz-txt-link-rfc2396E"
href="mailto:oulap@drcmr.dk"
moz-do-not-send="true">
<oulap@drcmr.dk></a><br>
<b>Sent:</b> 15 August 2022 08:29:55<br>
<b>To:</b> Rodriguez Manrique, Daniela; <a
class="moz-txt-link-abbreviated
moz-txt-link-freetext"
href="mailto:support@simnibs.org"
moz-do-not-send="true">
support@simnibs.org</a><br>
<b>Subject:</b> Re: Issues with FreeView related
to SimNIBS</font>
<div> </div>
</div>
<div>
<p>Hi Daniela,</p>
<p><br>
</p>
<p>Do you see these files in the m2m-folder:
brain_contr.fsmesh head_contr.fsmesh?</p>
<p><br>
</p>
<p>-Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 8/13/22 17:23,
Rodriguez Manrique, Daniela wrote:<br>
</div>
<blockquote type="cite">
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{margin-top:0;
margin-bottom:0}</style>
<div id="divtagdefaultwrapper" dir="ltr"
style="font-size: 12pt; color: rgb(0, 0, 0);
font-family: Calibri, Helvetica, sans-serif,
"EmojiFont", "Apple Color
Emoji", "Segoe UI Emoji",
NotoColorEmoji, "Segoe UI Symbol",
"Android Emoji", EmojiSymbols;">
<p>Hi Oula,</p>
<p><br>
</p>
<p>no worries.</p>
<p><br>
</p>
<p>I do not see any errors in the terminal when
I run the check command. However, it only
opens one of the windows and I am unsure where
to change this setting as the terminal gives
me no information about this or error message.</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Daniela<br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block;
width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri,
sans-serif" color="#000000"><b>From:</b> Oula
<a class="moz-txt-link-rfc2396E"
href="mailto:oulap@drcmr.dk"
moz-do-not-send="true">
<oulap@drcmr.dk></a><br>
<b>Sent:</b> 25 July 2022 09:38:09<br>
<b>To:</b> Rodriguez Manrique, Daniela; <a
class="moz-txt-link-abbreviated
moz-txt-link-freetext"
href="mailto:support@simnibs.org"
moz-do-not-send="true">
support@simnibs.org</a><br>
<b>Subject:</b> Re: Issues with FreeView
related to SimNIBS</font>
<div> </div>
</div>
<div>
<p>Hi Daniela,</p>
<p><br>
</p>
<p>Sorry for the late reply, the SimNIBS team
was on vacation.</p>
<p><br>
</p>
<p>When you run the check command do you see any
errors in the terminal? The check command
actually should open two windows: one showing
the colored segmentation results and the other
one showing the MNI transformation. The
screenshot you sent is showing the MNI
transformation results. It seems for some
reason the first window did not open or was
closed. The terminal output will likely give
some clues to why this might be.</p>
<p><br>
</p>
<p>Best,<br>
Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 7/5/22 15:43,
Rodriguez Manrique, Daniela wrote:<br>
</div>
<blockquote type="cite">
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<div>
<p>Dear SimNIBS support,</p>
<p><br>
</p>
<p>first of all apologies for emailing
developers of SimNIBS seperately, I was
not aware of this email address.</p>
<p><br>
</p>
<p>I have some questions regarding
FreeView in the SimNiBS Pipeline. <br>
</p>
<p><br>
</p>
<p>To check the segmentation we use the
command "headreco check <subject
ID>" as instructed below. This would
open up the FreeView window and show us
the different matrixes for different
materials in different colours (also as
seen below). </p>
<p><img naturalheight="736"
naturalwidth="838" size="0"
id="img605241" tabindex="0" class=""
style="max-width:99.9%"
src="cid:part1.pbX0BouK.cQZO4MF3@drcmr.dk"></p>
<p><br>
</p>
<p>This was the case for a long time with
my previous intern. She was able to edit
the segmentation and re-run it when
finding errors. Now for some reason,
however, when using the same command, a
different window opens where no coloured
matrixes are shown (see second picture
below). I have noted that both versions
of FreeView are the same (FreeView 3.0).
Additionally previous subjects where it
once was possible to edit the
segmentation, no longer show the
coloured matrixes.</p>
<p><img naturalheight="635"
naturalwidth="856" size="0"
id="img197872" tabindex="0" class=""
style="max-width:99.9%"
src="cid:part2.IX9Pp2wX.ZzUHCSMx@drcmr.dk"><br>
</p>
<p>Have you encountered this problem
before? Or do you have any pointers on
what might be happening here? Even upon
re-installation of FreeSurfer I am not
able to obtain the coloured matrixes and
have not found much information online.</p>
<p><br>
</p>
<p>Thank you for taking the time to read
my email.</p>
<p><br>
</p>
<p>Best Regards,</p>
Daniela Rodriguez</div>
<br>
</div>
</blockquote>
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