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<p>Hi Dan,</p>
<p><br>
</p>
<p>This transformation is embedded inside the NifTi files. It's
often called the "affine". Normally the X axis corresponds to
left/right, Y to posterior/anterior and Z to bottom/top, but it
can vary depending on how the image was acquired and how the
subject was positioned inside the scanner, so it is not so
reliable. However, the co-register images, located in the
m2m_{subID}/toMNI folder, are sure to follow this convention, if
the co-registration worked (it generally does). We also use the
co-registrations to calculate the 10-10 EEG positions, including
FP1, which are stored in
m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv. <br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Guilherme</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 14/07/2020 23.12, Mccalley, Daniel
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BN6PR11MB4004AF857174ED030B20A8E9A5610@BN6PR11MB4004.namprd11.prod.outlook.com">
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Hi all,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thanks again for the help! </div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Oula, would you be able to point me toward the header file that
may have information on the voxel-to-world transformation? It
would be useful to know which direction is up/down, left/right,
forward/backward if X Y and Z aren't always accurate</div>
<div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Best,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div id="Signature">
<div>
<div style="font-family:Tahoma; font-size:13px">Dan McCalley
<div>Medical University of South Carolina</div>
<div>College of Graduate Studies, Neuroscience</div>
<div><br>
</div>
</div>
</div>
</div>
</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> Oula
Puonti <a class="moz-txt-link-rfc2396E" href="mailto:oupu@dtu.dk"><oupu@dtu.dk></a><br>
<b>Sent:</b> Monday, July 13, 2020 2:44 AM<br>
<b>To:</b> Mccalley, Daniel <a class="moz-txt-link-rfc2396E" href="mailto:mccalled@musc.edu"><mccalled@musc.edu></a>;
Guilherme B Saturnino <a class="moz-txt-link-rfc2396E" href="mailto:guilhermebs@drcmr.dk"><guilhermebs@drcmr.dk></a>;
<a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a> <a class="moz-txt-link-rfc2396E" href="mailto:discuss@simnibs.org"><discuss@simnibs.org></a><br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting subject
specific locations on the scalp</font>
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<p>Hi Daniel,</p>
<p><br>
</p>
<p>Thanks for the clarification. </p>
<p><br>
</p>
<p>I could see two problems: </p>
<p><br>
</p>
<p>1) The Nz coordinate from SimNIBS is not correctly
placed. This can happen due to segmentation/registration
errors. You should open the MRI scan in a viewer, for
example freeview, and check that the Nz coordinate that
SimNIBS outputs matches the nasion location on the scan.</p>
<p><br>
</p>
<p>2) The header, i.e., voxel-to-world transformation, of
the MRIs is different between subjects. If you always
substract the X and Y distances you might end up moving in
a different direction than intended.</p>
<p><br>
</p>
<p>Best,</p>
<p>Oula </p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Mccalley, Daniel
<a class="moz-txt-link-rfc2396E" href="mailto:mccalled@musc.edu"><mccalled@musc.edu></a><br>
<b>Sent:</b> Friday, July 10, 2020 6:43:03 PM<br>
<b>To:</b> Oula Puonti; Guilherme B Saturnino;
<a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a><br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting subject
specific locations on the scalp</font>
<div> </div>
</div>
<div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Hi all, </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Thank you so much for the fast replies! </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Let me clear up a few things about our experiment -- </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
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<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
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When our participants come in, the experimenter measures
the individual's head (nasion to inion, tragus to tragus,
circumference). Each person's measurements are of course
different and there is some amount of error/rounding made
by the experimenter in each measurement. <b>Our
participants are never fitted with an EEG cap</b> to
locate our cortical target (FP1).</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Instead, starting at Nz, we take 10% of the distance for
Nz to Inion (generally ranges from 2-4 cm, I referred to
this as Y in my initial example) and move up and we take
5% of the total head circumference and move that distance
left (towards FP1, I referred to this as X in my initial
example). The experimenter makes a mark on the persons
head with sharpie, but <b>unfortunately we did not use a
fiducial for this study</b>.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Given that the FP1 location is determined in a
patient-tailored manner and we expect some degree of
experimenter error in making these measurements, I'd like
to as closely as possible recreate an e-field at the site
of stimulation for each person using these measurements.
Thus far, I have used the coordinates for Nz that SIMNIBs
produces and made adjustments from there based on X and Y
displacement for each subject. This almost always produces
a result close to FP1, but in some instances it seems the
result remains near the eye or in entirely unexpected head
locations</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Does that information help? </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Thank you all again for your help! </div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Best,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div id="x_Signature">
<div>
<div style="font-family:Tahoma; font-size:13px">Dan
McCalley
<div>Medical University of South Carolina</div>
<div>College of Graduate Studies, Neuroscience</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Oula Puonti
<a class="moz-txt-link-rfc2396E" href="mailto:oupu@dtu.dk"><oupu@dtu.dk></a><br>
<b>Sent:</b> Friday, July 10, 2020 3:35 AM<br>
<b>To:</b> Guilherme B Saturnino
<a class="moz-txt-link-rfc2396E" href="mailto:guilhermebs@drcmr.dk"><guilhermebs@drcmr.dk></a>; Mccalley, Daniel
<a class="moz-txt-link-rfc2396E" href="mailto:mccalled@musc.edu"><mccalled@musc.edu></a>; <a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a>
<a class="moz-txt-link-rfc2396E" href="mailto:discuss@simnibs.org"><discuss@simnibs.org></a><br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting subject
specific locations on the scalp</font>
<div> </div>
</div>
<div><b>
<p style="color:#ee7600; font-size:13pt;
text-align:center; background-color:#FFFFFF;
text-decoration:underline">
CAUTION: External</p>
</b>
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<p>Hi,</p>
<p><br>
</p>
<p>Just to add to what Guilherme said: Are you
locating the nasion manually or using coordinates
that SimNIBS outputs automatically? If the latter,
please check that the fiducial placements look
correct.</p>
<p><br>
</p>
<p>Best,</p>
<p>Oula</p>
<p><br>
</p>
<p><br>
</p>
</div>
<hr tabindex="-1" style="display:inline-block;
width:98%">
<div id="x_x_divRplyFwdMsg" dir="ltr"><font
style="font-size:11pt" face="Calibri, sans-serif"
color="#000000"><b>From:</b> Simnibs-discuss
<a class="moz-txt-link-rfc2396E" href="mailto:simnibs-discuss-bounces@drcmr.dk"><simnibs-discuss-bounces@drcmr.dk></a> on behalf
of Guilherme B Saturnino
<a class="moz-txt-link-rfc2396E" href="mailto:guilhermebs@drcmr.dk"><guilhermebs@drcmr.dk></a><br>
<b>Sent:</b> Friday, July 10, 2020 9:31:07 AM<br>
<b>To:</b> Mccalley, Daniel; <a class="moz-txt-link-abbreviated" href="mailto:discuss@simnibs.org">discuss@simnibs.org</a><br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting
subject specific locations on the scalp</font>
<div> </div>
</div>
<div>
<p>Hello,</p>
<p><br>
</p>
<p>SimNIBS 3 offers two ways of getting 10/10 EEG
positions out of the box.</p>
<p><br>
</p>
<p>1) Use the eeg positions calculated using MNI
transformations, which are stored in
m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv.
Those can also be accessed in the
<a
href="https://urldefense.com/v3/__https://simnibs.github.io/simnibs/build/html/tutorial/gui.html__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBSlfQpNA$"
moz-do-not-send="true">
GUI</a>, which loads it automatically, or in
scripts (<a
href="https://urldefense.com/v3/__https://github.com/simnibs/simnibs/blob/v3.1.2/simnibs/examples/simulations/TMS.m__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBXnVXhnJ$"
moz-do-not-send="true">MATLAB example</a>)</p>
<p><br>
</p>
<p>2) Using the <a
href="https://urldefense.com/v3/__https://simnibs.github.io/simnibs/build/html/documentation/command_line/eeg_positions.html__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBd53sE1Z$"
moz-do-not-send="true">
eeg_positions</a> command line tool with the Nz,
LPA, RPA and Iz as an input</p>
<p><br>
</p>
<p>Those two were compared and validated <a
href="https://urldefense.com/v3/__https://link.springer.com/chapter/10.1007/978-3-030-21293-3_1__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBSy4FP92$"
moz-do-not-send="true">
here</a>.</p>
<p> <br>
</p>
<p>I'm not sure why it is not working in your case
though, might be due to head size, as you are moving
by constant amounts?</p>
<p><br>
</p>
<p>Best Regards,</p>
<p>Guilherme<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="x_x_moz-cite-prefix">On 09/07/2020 19.48,
Mccalley, Daniel wrote:<br>
</div>
<blockquote type="cite">
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Hi all, </div>
<div
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<br>
</div>
<div
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Our lab targets the FP1 with TMS. We use a simple
measurement system (<a
href="https://urldefense.com/v3/__http://clinicalresearcher.org/F3/__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBcP0FOvN$"
moz-do-not-send="true">http://clinicalresearcher.org/F3/</a>)
to locate exactly where we want to place the coil
for each subject. Typically, we measure the
subject's head, and then, starting from nasion,
we'll move up Y mm and left X mm (where X and Y
are determined from each subject's given head
size).</div>
<div
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<br>
</div>
<div
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font-size:12pt; color:rgb(0,0,0)">
Ideally, we'd like to create an electric field
model for each subject that accounts for the TMS
parameters as well as the exact location used. To
implement this in SIMNIBS, I've tried the
following: </div>
<div
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<br>
</div>
<div
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1) Open a subjects m2m file and find the
coordinates for nasion (say, for example, that
these coordinates are X= -2.78, Y= 117.59, Z=
-20.63).</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
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<br>
</div>
<div
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font-size:12pt; color:rgb(0,0,0)">
2) Determine Y and X used to locate FP1 for the
given subject (say, for example, that starting
from nasion, we moved 37 mm in the Y direction,
and over 32 mm in the X direction). </div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
3) Subtract the displacements in the Y and X
directions from the original nasion coordinates,
resulting in X= -34.78 and Y=80.69</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
4) Add a new position wherein the reference
coordinates match the original nasion coordinates
(and the Define Reference Coordinates box is
checked) and the coordinates calculated in step 3
are input in the position fields (Z is left blank
for SIMNIBs to calculate) </div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
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<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
5) Adjust for coil orientation and TMS parameters</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
This seems to have worked well for 90-95% of our
subjects, however there are a few subjects in
which the resulting coil placement appears to be
over the eye (Note: Ordinarily I'd attach examples
of the working and not-working subjects, but I'm
not sure if the skin reconstruction of our
participants falls under PHI). <br>
<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Am I going about this the wrong way? Could this
reflect a problem with segmentation/meshing? Or
maybe a problem with the experimenter measurements
of the subjects head? Any advice would be greatly
appreciated. Thank you all so much!</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
Best,</div>
<div>
<div
style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div id="x_x_Signature">
<div>
<div style="font-family:Tahoma;
font-size:13px">Dan McCalley
<div>Medical University of South Carolina</div>
<div>College of Graduate Studies,
Neuroscience</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
<br>
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