<div dir="ltr">Hi Axel,<div><br></div><div>Wonderful!! Thank you so very much for confirming this. We are working on setting up a protocol and instructions for younger lab members on how to use simnibs and I can now include a note about this. We thank you immensely for not only answering the above q, but for all of the work you and the team have put in to bring simnibs to the world. <br><br>Cheers!</div><div><br></div><div>Grace </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 26, 2022 at 4:11 AM Axel Thielscher <<a href="mailto:axelt@drcmr.dk" target="_blank">axelt@drcmr.dk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Grace,</p>
<p>the two files are indeed identical, unless you specify something
else using the -d option. <br>
</p>
<p>The qform and sform of the T1fs_conform just are set to the same,
which then likely causes AFNI to select TLRC. <br>
</p>
<p>Best regards,</p>
<p>Axel<br>
</p>
<p><br>
</p>
<div>On 25-04-2022 21:37, Grace Hallenbeck
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Annalisa,<br>
<br>
</div>
<div>Thanks for your reply. We have made progress on the
translation matrix cited above, but currently we have a more
pressing question.<br>
<br>
The file output from a successful headreco, T1fs_conform.nii,
appears to be identical to our input T1, though from the
simnibs website, "<font color="#000000"><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures">The
head meshing procedures create a NifTI file called </span><code style="box-sizing:inherit;padding:2px 0px 1px 3px;border-right:0px;border-radius:3px 0px 0px 3px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;font-family:Monaco,Menlo,Consolas,"Courier New",monospace">m2m_</code><code style="box-sizing:inherit;padding:2px 0px 1px;border-right:0px;border-left:0px;border-radius:0px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;font-family:Monaco,Menlo,Consolas,"Courier New",monospace"><i style="box-sizing:inherit">subID</i></code><code style="box-sizing:inherit;padding:2px 3px 1px 0px;border-left:0px;border-radius:0px 3px 3px 0px;font-size:12px;line-height:1.50001;font-variant-ligatures:none;white-space:pre-wrap;word-break:normal;font-family:Monaco,Menlo,Consolas,"Courier New",monospace">/T1fs_conform.nii.gz</code><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures">.
This file contains a transformed T1 image of the subject,
with the world coordinates used by SimNIBS."<br>
<br>
However, the voxel orientations and resolutions are
identical (per 3dinfo from afni), with one exception: the
template space of the conform file is TLRC while that of
the original T1 is ORIG. So, my questions are the
following:<br>
<br>
1. Should these files be identical?<br>
2. Why is the template space of the conform file TLRC? <br>
<br>
copy/pasting header info here for clarity:<br>
<br>
INPUT T1<br>
</span></font>
<p><span style="font-variant-ligatures:no-common-ligatures">(base)
darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes grace>
3dinfo T1.nii</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">++
3dinfo: AFNI version=AFNI_16.2.09 (Aug<span> </span>6 2016)
[64-bit]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p><span style="font-variant-ligatures:no-common-ligatures">Dataset
File:<span> </span>T1.nii</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Identifier
Code: NII_Hd_qtnnMonBYdt6jsb2XWw<span> </span>Creation
Date: Fri Aug 31 11:14:18 2018</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Template
Space:<span> </span>ORIG</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Dataset
Type:<span> </span>Anat
Bucket (-abuc)</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Byte
Order:<span> </span>LSB_FIRST
{assumed} [this CPU native = LSB_FIRST]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Storage
Mode:<span> </span>NIFTI</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Storage
Space: <span> </span>32,768,000
(33 million [mega]) bytes</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Geometry
String:
"MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Data
Axes Tilt:<span> </span>Plumb</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Data
Axes Orientation:</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>first<span> </span>(x) =
Right-to-Left</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>second (y)
= Superior-to-Inferior</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>third<span> </span>(z) =
Posterior-to-Anterior <span> </span>[-orient
RSP]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">R-to-L
extent:<span> </span>-128.100
[R] -to- <span> </span>127.100
[L] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">A-to-P
extent:<span> </span>-127.100
[A] -to- <span> </span>128.100
[P] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">I-to-S
extent:<span> </span>-127.100
[I] -to- <span> </span>128.100
[S] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Number
of values stored at each pixel = 1</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>-- At
sub-brick #0 '?' datum type is byte:<span> </span>0
to <span> </span>255</span></p>
<font color="#000000"><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures"><br>
T1fs_conform<br>
</span></font>
<p><span style="font-variant-ligatures:no-common-ligatures">(base)
darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes grace>
3dinfo T1fs_conform.nii</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">++
3dinfo: AFNI version=AFNI_16.2.09 (Aug<span> </span>6 2016)
[64-bit]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">** AFNI
converts NIFTI_datatype=512 (UINT16) in file
T1fs_conform.nii to FLOAT32</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>Warnings
of this type will be muted for this session.</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>Set
AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see
none.</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"></span><br>
</p>
<p><span style="font-variant-ligatures:no-common-ligatures">Dataset
File:<span> </span>T1fs_conform.nii</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Identifier
Code: NII_BDbiP8aLlBK7bpodSIpPwA<span> </span>Creation
Date: Mon Apr 25 15:30:40 2022</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Template
Space:<span> </span>TLRC</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Dataset
Type:<span> </span>Anat
Bucket (-abuc)</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Byte
Order:<span> </span>LSB_FIRST
{assumed} [this CPU native = LSB_FIRST]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Storage
Mode:<span> </span>NIFTI</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Storage
Space: <span> </span>131,072,000
(131 million [mega]) bytes</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Geometry
String:
"MATRIX(0.8,0,0,-128.1,0,0,-0.8,128.1,0,-0.8,0,128.1):320,320,320"</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Data
Axes Tilt:<span> </span>Plumb</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Data
Axes Orientation:</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>first<span> </span>(x) =
Right-to-Left</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>second (y)
= Superior-to-Inferior</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>third<span> </span>(z) =
Posterior-to-Anterior <span> </span>[-orient
RSP]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">R-to-L
extent:<span> </span>-128.100
[R] -to- <span> </span>127.100
[L] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">A-to-P
extent:<span> </span>-127.100
[A] -to- <span> </span>128.100
[P] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">I-to-S
extent:<span> </span>-127.100
[I] -to- <span> </span>128.100
[S] -step- <span>
</span>0.800 mm [320 voxels]</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures">Number
of values stored at each pixel = 1</span></p>
<p><span style="font-variant-ligatures:no-common-ligatures"><span> </span>-- At
sub-brick #0 '?' datum type is float</span></p>
<font color="#000000"><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures"><br>
Thanks very much for your help!<br>
<br>
Sincerely,</span></font></div>
<div><font color="#000000"><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures"><br>
</span></font></div>
<div><font color="#000000"><span style="font-family:Slack-Lato,Slack-Fractions,appleLogo,sans-serif;font-size:15px;font-variant-ligatures:common-ligatures">Grace </span></font></div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Apr 19, 2022 at 6:16
AM Annalisa Schuler <<a href="mailto:annalisa.schuler@hsancamillo.it" target="_blank">annalisa.schuler@hsancamillo.it</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div style="font-family:arial,helvetica,sans-serif;font-size:11pt;color:rgb(0,0,0)">
<div>Dear all,</div>
<div><br>
</div>
<div>are you using neuronavigation for your project, if
yes you should get a matrix including coil position,
translation and orientation from your stimulation
session, which allows you to calculate exact positions
using matsimnibs (<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__simnibs.github.io_simnibs_build_html_documentation_sim-5Fstruct_position.html&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=hlYoGF-M-jRATsmPq_apB2jsYCrtnhaxmOo1DPoxuno&e=" target="_blank">https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html</a>).</div>
<div><br>
</div>
<div>All the best,</div>
<div><br>
</div>
<div>AL</div>
<div><br>
</div>
<div><strong>Annalisa Schuler</strong><br>
Ricercatrice Psicologa<br>
_______________________________________________<br>
<strong>SAN CAMILLO IRCCS S.R.L. società unipersonale</strong><br>
soggetta a direzione e coordinamento da parte della<br>
Fondazione Villa Salus<br>
Via Alberoni, 70 - 30126 Venezia - Lido<br>
P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3<br>
<br>
<div> <strong>Certificazione UNI EN ISO 9001:2015<br>
</strong> Certificato SGQ 5010016444 emesso da TUV SUD
Italia<br>
<br>
<strong>Laboratorio di Imaging Clinico e Stimolazione</strong><br>
</div>
<br>
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<div><br>
</div>
<hr id="gmail-m_-468203938329023598gmail-m_-3765000359133313044gmail-m_-4969986970453937481zwchr">
<div><b>Da: </b>"Clayton E Curtis" <<a href="mailto:clayton.curtis@nyu.edu" target="_blank">clayton.curtis@nyu.edu</a>><br>
<b>A: </b>"Grace Hallenbeck" <<a href="mailto:geh261@nyu.edu" target="_blank">geh261@nyu.edu</a>><br>
<b>Cc: </b>"<a href="mailto:discuss@simnibs.org" target="_blank">discuss@simnibs.org</a>"
<<a href="mailto:discuss@simnibs.org" target="_blank">discuss@simnibs.org</a>><br>
<b>Inviato: </b>Venerdì, 15 aprile 2022 19:12:59<br>
<b>Oggetto: </b>Re: [Simnibs-discuss] coil positioning
in simnibs 3.2.6<br>
</div>
<div><br>
</div>
<div>
<div dir="ltr">Hi,<br>
<div>I just wanted to add a couple of details here.
We are using Brainsight to acquire the Coil
Position, and that looks spot on. But we are
interested in correctly orienting the coil before
running the model. The documentation was rather
sparse here. </div>
<br>
<div>Also, Grace is alluding the fact that when we
make changes to the Reference Coordinates, it makes
changes to the Coil Position. Not sure what this is
about?</div>
<br>
<div>Thanks for your help!</div>
<br>
<div>/cc</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Apr 15, 2022
at 12:48 PM Grace Hallenbeck <<a href="mailto:geh261@nyu.edu" target="_blank">geh261@nyu.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear simnibs crew,<br>
<div>Hello! My name is Grace Hallenbeck and I'm a
post-doc working with Clay Curtis (cc'ed here)
at NYU. We're interested in using simnibs to
model the effects of TMS and today we've been
trying to correctly position the coil
orientation in the simnibs gui but are having
some difficulty. <br>
<br>
We have a coordinate of interest that we're
plugging in for the x,y,z 'Position' fields. But
we're unclear on the best way to work with the
'Direction Reference' coordinates, which is what
we think controls the coil orientation. In the
screenshot below, I've plugged in the same x,y,z
coords as in 'Position', but this has the coil
handle (as I understand, 180 deg opposite the
green line) pointing slightly off the coil
orientation we actually applied TMS at with this
subject (what we are attempting to model). <br>
<br>
So our question is: how can we finely
modulate the coil orientation, keeping the
'Position' x,y,z coords constant? We would
greatly appreciate any help on this as we're
getting a publication ready and hope to include
some modeling results. </div>
<img src="cid:1806618c90ec44801151" alt="Screen Shot 2022-04-15 at 12.32.29 PM.png" style="margin-right: 0px;" width="406" height="348"><br>
<br>
All the best & thanks for your work,<br>
<div>Grace Hallenbeck</div>
</div>
</blockquote>
</div>
<br>
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</blockquote>
</div>
<br>
<fieldset></fieldset>
<pre>_______________________________________________
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</pre>
</blockquote>
<pre cols="72">--
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.drcmr.dk&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=y-8OqGfp5QNYyd4Z-vICXp4-YKY5U5G0nPHvB2FWBdc&e=" target="_blank">www.drcmr.dk</a>
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Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.healthtech.dtu.dk_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=TilFEc3dmbkVu85iQtGYtRln6F-wp_0E42GGp3pyMAsoDDJV8Iki3W6sDdqGiQZk&s=0__DQITmG8VYJwqHpTIbjBxmsjxxXgoPyEWPfVlWG6s&e=" target="_blank">http://www.healthtech.dtu.dk/</a></pre>
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