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    <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>
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              <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>
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      <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>
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