<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Witold,</p>
<p>regarding your question 1: correct<br>
</p>
<p>regarding your question 2: You cannot use SimNIBS to
automatically optimize electrode position for TI. However, I added
a matlab function and an example on how to calculate and
visualize the TI envelop amplitude, so that you can manually test
and optimize the montages:</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/simnibs/simnibs/blob/master/simnibs/matlab/get_maxTI.m">https://github.com/simnibs/simnibs/blob/master/simnibs/matlab/get_maxTI.m</a>
<br>
</p>
<p><a class="moz-txt-link-freetext" href="https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TI.m">https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TI.m</a><br>
</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Axel</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 8/28/2020 10:20 PM,
<a class="moz-txt-link-abbreviated" href="mailto:w.tomasz@sensusmed.pl">w.tomasz@sensusmed.pl</a> wrote:<br>
</div>
<blockquote type="cite"
cite="mid:fb9fa16250136c43ff5c6339b16aa571@sensusmed.pl">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div class="v1pre">Hi Oula,<br>
<br>
<span class="v1tlid-translation v1translation"><span>Thanks for
your answers and suggestions.<br>
<span class="tlid-translation translation"><span class="">1)If
I understand correctly, the final headform in the B and
B + ranges will be sufficient to calculate the optimal
stimulation if I first check with Freesurfer for large
deviations in bone and skin mapping ?</span></span></span></span><br>
<br>
2)<span class="tlid-translation translation"><span>Is it
possible to use software to calculate appropriate electrode
placement for transcranial temporal interference
stimulation?</span><br>
<span>Of course also to visualize the distribution of the
electric field.</span><br>
<span class="">For example, for fields with a frequency of 200
and 210 Hz.</span><br>
<span class="">The area of interest is the L-amygdala.</span></span><br>
<br>
Best regards,<br>
Witold<br>
W dniu 2020-08-19 13:36, Oula Puonti napisał(a):
<blockquote type="cite" style="padding: 0 0.4em; border-left:
#1010ff 2px solid; margin: 0">Hi Witold, <br>
<br>
1) When using CAT the cortical and white matter surfaces are
not<br>
generated from the volume files (.nii.gz), but rather the
surface<br>
files stored in the mask_prerp folder. Thus editing the volume
files <br>
<br>
will have no effect on the cortical or white matter surfaces
in the<br>
final headmodel. You can, however, edit the CSF, skull, and
scalp<br>
masks and these edits are propagated to the final head model.
<br>
<br>
If you want to edit the GM and WM masks, please disable CAT12<br>
(--no-cat flag). After that the edits on the WM and GM masks
will also<br>
change the final headmodel. <br>
<br>
2) We have not studied this systematically, but in my
experience CAT12<br>
does a good job even if the grade it assigns is B. That being
said,<br>
you should still inspect the resulting segmentation for large
errors<br>
using the <br>
<br>
headreco check call. <br>
<br>
3 & 4) I'm not that experienced with manual edits and the
little<br>
experience I have is limited to freeview. I've heard people<br>
succesfully using ITK snap, but if you find it too difficult,
I would<br>
consider using freeview through the windows subsystem for
linux. It's<br>
a bit trickier, but the instructions here are quite clear: <br>
<br>
<a
href="https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport"
target="_blank" rel="noopener noreferrer"
moz-do-not-send="true">https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport</a><br>
<br>
Best,<br>
Oula <br>
-------------------------<br>
<br>
From: Simnibs-discuss <<a
href="mailto:simnibs-discuss-bounces@drcmr.dk"
rel="noreferrer" moz-do-not-send="true">simnibs-discuss-bounces@drcmr.dk</a>>
on behalf of<br>
<a href="mailto:w.tomasz@sensusmed.pl" rel="noreferrer"
moz-do-not-send="true">w.tomasz@sensusmed.pl</a> <<a
href="mailto:w.tomasz@sensusmed.pl" rel="noreferrer"
moz-do-not-send="true">w.tomasz@sensusmed.pl</a>><br>
Sent: Tuesday, August 18, 2020 5:37:11 PM<br>
To: Guilherme B Saturnino<br>
Cc: <a href="mailto:discuss@simnibs.org" rel="noreferrer"
moz-do-not-send="true">discuss@simnibs.org</a><br>
Subject: [Simnibs-discuss] manual correction <br>
<br>
Hello,<br>
<br>
I had the pleasure of talking to you for a while at the April
webinar<br>
on brain modeling after stroke.<br>
I am currently researching the use of stimulation in a person
with<br>
tinnitus with personalized stimulation. <br>
I have a question about the manual correction of the brain
model (the<br>
model created from the t1_mprage_sag and
t2_space_dark_fluid_sag_p2<br>
images) in the automatic model creation in the CAT report gets
results<br>
on the B and B + levels.<br>
I'm a beginner when it comes to modeling (I am more concerned
with<br>
NIBS in clinical applications), sorry if my questions are
trivial : <br>
<br>
1. on the SIMNIBS website, it says that it is not possible to
do CAT<br>
cuttings, whether in such a system we use "m2m_ernie \
mask_prep \<br>
MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual
editing.<br>
Does a manual correction make sense in such a situation? <br>
<br>
2. From your and your team's experience, how big are the
differences<br>
in electric field distributions between the B / B + and
A-level<br>
models?<br>
<br>
3.I wanted to use ITK-SNAP for the correction proposed on one
of your<br>
toutorials but I am a beginner I have a hard time figuring out
how to<br>
check if (how exactly) the surface contours follow the tissue
shapes<br>
in the T1w image, with more masks than one .<br>
<br>
4. Could you suggest a program other than FS to evaluate the
created<br>
model? Since I'm a Windows 10 and FS user, it's more
complicated here.<br>
<br>
Thank you very much for your help and your time!<br>
Best regards,<br>
-- <br>
<br>
Witold Tomasz<br>
<br>
psycholog, psychoterapeuta, terapeuta tDCS<br>
<br>
Ośrodek psychoterapii i neurorehabilitacji<br>
<br>
Sensusmed Witold Tomasz<br>
<br>
p:<br>
504288040 m: 789335047<br>
<br>
a:<br>
Kraków 30-303<br>
<br>
ul.Madalińskiego 3/1<br>
<br>
w:<br>
<a href="http://www.sensusmed.pl" target="_blank"
rel="noopener noreferrer" moz-do-not-send="true">www.sensusmed.pl</a>
[<a href="http://www.sensusmed.pl" target="_blank"
rel="noopener noreferrer" moz-do-not-send="true">1</a>] e:
<a href="mailto:w.tomasz@sensusmed.pl" rel="noreferrer"
moz-do-not-send="true">w.tomasz@sensusmed.pl</a><br>
<br>
<br>
<br>
Links:<br>
------<br>
[1] <a href="http://www.sensusmed.pl" target="_blank"
rel="noopener noreferrer" moz-do-not-send="true">http://www.sensusmed.pl</a></blockquote>
<br>
<div id="v1_rc_sig">-- <br>
<table style="border-collapse: collapse; border-width: 0px;
border: 0px; margin: 0; padding: 0;" cellspacing="0"
cellpadding="0" border="0">
<tbody>
<tr>
<td style="border-top: 0; border-bottom: 0;
border-right: solid 3px #FF94A3; padding: 0 7px 0 0;"
valign="top"><img id="v1preview-image-url"
src="https://drive.google.com/uc?id=0B_hgtJUYICqhM3dUUE1PSlpjQTQ"
moz-do-not-send="true"></td>
<td style="padding: 0 0 0 12px;">
<table style="border-collapse: collapse; border-width:
0px; border: 0px; margin: 0; padding: 0;"
cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<td style="padding-bottom: 5px; color: #ff94a3;
font-size: 18px; font-family: Arial,
Helvetica, sans-serif;" colspan="2">Witold
Tomasz</td>
</tr>
<tr>
<td style="padding: 0px; color: #333333;
font-size: 14px; font-family: Arial,
Helvetica, sans-serif;" colspan="2"><em>psycholog,
psychoterapeuta, terapeuta tDCS<br>
</em></td>
</tr>
<tr>
<td style="padding: 0px; color: #333333;
font-size: 14px; font-family: Arial,
Helvetica, sans-serif;" colspan="2">Ośrodek
psychoterapii i neurorehabilitacji</td>
</tr>
<tr>
<td style="padding: 0px; color: #333333;
font-size: 14px; font-family: Arial,
Helvetica, sans-serif;" colspan="2"><strong>Sensusmed
Witold Tomasz</strong></td>
</tr>
<tr>
<td style="padding: 0px; vertical-align: top;
width: 20px; color: #ff94a3; font-size: 14px;
font-family: Arial, Helvetica, sans-serif;"
width="20" valign="top">p:</td>
<td style="padding: 0px; vertical-align: top;
color: #333333; font-size: 14px; font-family:
Arial, Helvetica, sans-serif;" valign="top">504288040 <span
style="color: #ff94a3;">m: </span>789335047</td>
</tr>
<tr>
<td style="padding: 0px; vertical-align: top;
width: 20px; color: #ff94a3; font-size: 14px;
font-family: Arial, Helvetica, sans-serif;"
width="20" valign="top">a:</td>
<td style="padding: 0px; vertical-align: top;
color: #333333; font-size: 14px; font-family:
Arial, Helvetica, sans-serif;" valign="top">Kraków
30-303</td>
</tr>
<tr>
<td style="padding: 0px; vertical-align: top;
width: 20px; color: #ff94a3; font-size: 14px;
font-family: Arial, Helvetica, sans-serif;"
width="20" valign="top"> </td>
<td style="padding: 0px; vertical-align: top;
color: #333333; font-size: 14px; font-family:
Arial, Helvetica, sans-serif;" valign="top">ul.Madalińskiego
3/1</td>
</tr>
<tr>
<td style="padding: 0px; vertical-align: top;
width: 20px; color: #ff94a3; font-size: 14px;
font-family: Arial, Helvetica, sans-serif;"
width="20" valign="top">w:</td>
<td style="padding: 0px; vertical-align: top;
color: #333333; font-size: 14px; font-family:
Arial, Helvetica, sans-serif;" valign="top"><a
style="color: #1da1db; text-decoration:
none; font-weight: normal; font-size: 14px;"
href="http://www.sensusmed.pl"
target="_blank" rel="noopener noreferrer"
moz-do-not-send="true">www.sensusmed.pl</a> <span
style="color: #ff94a3;">e: </span><a
style="color: #1da1db; text-decoration:
none; font-weight: normal; font-size: 14px;"
href="mailto:w.tomasz@sensusmed.pl"
rel="noreferrer" moz-do-not-send="true">w.tomasz@sensusmed.pl</a></td>
</tr>
</tbody>
</table>
</td>
</tr>
</tbody>
</table>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Simnibs-discuss mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Simnibs-discuss@drcmr.dk">Simnibs-discuss@drcmr.dk</a>
<a class="moz-txt-link-freetext" href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
<a class="moz-txt-link-abbreviated" href="http://www.drcmr.dk">www.drcmr.dk</a>
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
<a class="moz-txt-link-freetext" href="http://www.healthtech.dtu.dk/">http://www.healthtech.dtu.dk/</a></pre>
</body>
</html>