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<p>Also adding to Oula's response: The SimNIBS eeg positions are
also adapted to each patient, using either non-linear MNI
transformations (the positions in
m2m_{SubID}/eeg_positions/EEG10-10_UI_Jurak_2007.csv) or by
measuring distances (in %) with respect to the fiducials
(eeg_positions) script.</p>
<p><br>
</p>
<p>Best,</p>
<p>Guilherme<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 13/07/2020 08.44, Oula Puonti wrote:<br>
</div>
<blockquote type="cite"
cite="mid:6c2d5d4ae0cb4dbe923df0f188f1a641@dtu.dk">
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dir="ltr">
<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 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>
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>
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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="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> 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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font-family:Calibri,Helvetica,sans-serif">
<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_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_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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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>
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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
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<br>
</div>
<div
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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;
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<br>
</div>
<div
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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;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div
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5) Adjust for coil orientation and TMS parameters</div>
<div
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<br>
</div>
<div
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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_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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<pre class="x_moz-quote-pre">_______________________________________________
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