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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>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Mccalley, Daniel <mccalled@musc.edu><br>
<b>Sent:</b> Friday, July 10, 2020 6:43:03 PM<br>
<b>To:</b> Oula Puonti; Guilherme B Saturnino; discuss@simnibs.org<br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting subject specific locations on the scalp</font>
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Hi all, </div>
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Thank you so much for the fast replies! </div>
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<br>
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Let me clear up a few things about our experiment -- </div>
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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>
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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>
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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>
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Does that information help? </div>
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<br>
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Thank you all again for your help! </div>
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Best,</div>
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<div style="font-family:Tahoma; font-size:13px">Dan McCalley
<div>Medical University of South Carolina</div>
<div>College of Graduate Studies, Neuroscience</div>
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</div>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Oula Puonti <oupu@dtu.dk><br>
<b>Sent:</b> Friday, July 10, 2020 3:35 AM<br>
<b>To:</b> Guilherme B Saturnino <guilhermebs@drcmr.dk>; Mccalley, Daniel <mccalled@musc.edu>; discuss@simnibs.org <discuss@simnibs.org><br>
<b>Subject:</b> Re: [Simnibs-discuss] Targeting subject specific locations on the scalp</font>
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CAUTION: External</p>
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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>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Simnibs-discuss <simnibs-discuss-bounces@drcmr.dk> on behalf of Guilherme B Saturnino <guilhermebs@drcmr.dk><br>
<b>Sent:</b> Friday, July 10, 2020 9:31:07 AM<br>
<b>To:</b> Mccalley, Daniel; discuss@simnibs.org<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$">
GUI</a>, which loads it automatically, or in scripts (<a href="https://urldefense.com/v3/__https://github.com/simnibs/simnibs/blob/v3.1.2/simnibs/examples/simulations/TMS.m__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBXnVXhnJ$">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$">
eeg_positions</a> command line tool with the Nz, LPA, RPA and Iz as an input</p>
<p><br>
</p>
<p>Those two were compared and validated <a href="https://urldefense.com/v3/__https://link.springer.com/chapter/10.1007/978-3-030-21293-3_1__;!!Ab1_Rw!VmHiKnZCbukEHQmiiCDWTKL0HVw7v3spr5BG5nz_3hj_QfY9egavym9kBSy4FP92$">
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>
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Hi all, </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$">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>
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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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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>
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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>
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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>
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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>
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5) Adjust for coil orientation and TMS parameters</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>
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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>
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Best,</div>
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<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>
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