<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body>
    <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 class="moz-cite-prefix">On 25-04-2022 21:37, Grace Hallenbeck
      wrote:<br>
    </div>
    <blockquote type="cite"
cite="mid:CAB2vMnG6mVr93DD1S6xxZS+Vr6TZ40MF0jOcDq1bk0D+jxvxXA@mail.gmail.com">
      <meta http-equiv="content-type" content="text/html; charset=UTF-8">
      <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 class="gmail-c-mrkdwn__code gmail-c-mrkdwn__code--no_right_cap" 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 class="gmail-c-mrkdwn__code gmail-c-mrkdwn__code--no_left_cap gmail-c-mrkdwn__code--no_right_cap" 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 class="gmail-c-mrkdwn__code gmail-c-mrkdwn__code--no_left_cap" 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 class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">(base)
darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes grace>
              3dinfo T1.nii</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">++
              3dinfo: AFNI version=AFNI_16.2.09 (Aug<span
                class="gmail-Apple-converted-space">  </span>6 2016)
              [64-bit]</span></p>
          <p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9);min-height:14px"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"></span><br>
          </p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Dataset
              File:<span class="gmail-Apple-converted-space">    </span>T1.nii</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Identifier
              Code: NII_Hd_qtnnMonBYdt6jsb2XWw<span
                class="gmail-Apple-converted-space">  </span>Creation
              Date: Fri Aug 31 11:14:18 2018</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Template
              Space:<span class="gmail-Apple-converted-space">  </span>ORIG</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Dataset
              Type:<span class="gmail-Apple-converted-space">    </span>Anat
              Bucket (-abuc)</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Byte
              Order:<span class="gmail-Apple-converted-space">      </span>LSB_FIRST
              {assumed} [this CPU native = LSB_FIRST]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Storage
              Mode:<span class="gmail-Apple-converted-space">    </span>NIFTI</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Storage
              Space: <span class="gmail-Apple-converted-space">  </span>32,768,000
              (33 million [mega]) bytes</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              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 class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Data
              Axes Tilt:<span class="gmail-Apple-converted-space">  </span>Plumb</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Data
              Axes Orientation:</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>first<span
                class="gmail-Apple-converted-space">  </span>(x) =
              Right-to-Left</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>second (y)
              = Superior-to-Inferior</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>third<span
                class="gmail-Apple-converted-space">  </span>(z) =
              Posterior-to-Anterior <span
                class="gmail-Apple-converted-space">  </span>[-orient
              RSP]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">R-to-L
              extent:<span class="gmail-Apple-converted-space">  </span>-128.100
              [R] -to- <span class="gmail-Apple-converted-space">  </span>127.100
              [L] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">A-to-P
              extent:<span class="gmail-Apple-converted-space">  </span>-127.100
              [A] -to- <span class="gmail-Apple-converted-space">  </span>128.100
              [P] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">I-to-S
              extent:<span class="gmail-Apple-converted-space">  </span>-127.100
              [I] -to- <span class="gmail-Apple-converted-space">  </span>128.100
              [S] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Number
              of values stored at each pixel = 1</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>-- At
              sub-brick #0 '?' datum type is byte:<span
                class="gmail-Apple-converted-space">            </span>0
              to <span class="gmail-Apple-converted-space">          </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 class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">(base)
darkphoenix:/home/grace/simnibs_simulation_GH5/subject_volumes grace>
              3dinfo T1fs_conform.nii</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">++
              3dinfo: AFNI version=AFNI_16.2.09 (Aug<span
                class="gmail-Apple-converted-space">  </span>6 2016)
              [64-bit]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">** AFNI
              converts NIFTI_datatype=512 (UINT16) in file
              T1fs_conform.nii to FLOAT32</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">     </span>Warnings
              of this type will be muted for this session.</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">     </span>Set
              AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see
              none.</span></p>
          <p class="gmail-p2"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9);min-height:14px"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"></span><br>
          </p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Dataset
              File:<span class="gmail-Apple-converted-space">    </span>T1fs_conform.nii</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Identifier
              Code: NII_BDbiP8aLlBK7bpodSIpPwA<span
                class="gmail-Apple-converted-space">  </span>Creation
              Date: Mon Apr 25 15:30:40 2022</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Template
              Space:<span class="gmail-Apple-converted-space">  </span>TLRC</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Dataset
              Type:<span class="gmail-Apple-converted-space">    </span>Anat
              Bucket (-abuc)</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Byte
              Order:<span class="gmail-Apple-converted-space">      </span>LSB_FIRST
              {assumed} [this CPU native = LSB_FIRST]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Storage
              Mode:<span class="gmail-Apple-converted-space">    </span>NIFTI</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Storage
              Space: <span class="gmail-Apple-converted-space">  </span>131,072,000
              (131 million [mega]) bytes</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              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 class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Data
              Axes Tilt:<span class="gmail-Apple-converted-space">  </span>Plumb</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Data
              Axes Orientation:</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>first<span
                class="gmail-Apple-converted-space">  </span>(x) =
              Right-to-Left</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>second (y)
              = Superior-to-Inferior</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </span>third<span
                class="gmail-Apple-converted-space">  </span>(z) =
              Posterior-to-Anterior <span
                class="gmail-Apple-converted-space">  </span>[-orient
              RSP]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">R-to-L
              extent:<span class="gmail-Apple-converted-space">  </span>-128.100
              [R] -to- <span class="gmail-Apple-converted-space">  </span>127.100
              [L] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">A-to-P
              extent:<span class="gmail-Apple-converted-space">  </span>-127.100
              [A] -to- <span class="gmail-Apple-converted-space">  </span>128.100
              [P] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">I-to-S
              extent:<span class="gmail-Apple-converted-space">  </span>-127.100
              [I] -to- <span class="gmail-Apple-converted-space">  </span>128.100
              [S] -step- <span class="gmail-Apple-converted-space">   
              </span>0.800 mm [320 voxels]</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures">Number
              of values stored at each pixel = 1</span></p>
          <p class="gmail-p1"
style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:12px;line-height:normal;font-family:"Andale
Mono";color:rgb(47,255,18);background-color:rgba(0,0,0,0.9)"><span
              class="gmail-s1"
              style="font-variant-ligatures:no-common-ligatures"><span
                class="gmail-Apple-converted-space">  </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"
            moz-do-not-send="true" class="moz-txt-link-freetext">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" moz-do-not-send="true">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>
                <div> <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=n7WrKbPtiB6T0x_y37Fmp6LflxWHPketwsV8lhgBvnc&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true">Sito web</a> | <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.facebook.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=8yayA4Zr6-zDVlz5EXiQU6dbWv8kwh2opI5qhf6nQ4A&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true">Facebook</a> | <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_company_san-2Dcamillo-2Dirccs&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZSfKGfVvtq97KLPP2EEhBcCTZI3HlBavqLi2mkM0Zw&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true">Linkedin</a> | <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_SanCamilloIRCCS&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=81zmg2aVNdMorLXTwO7exfqWC_MIwZiGlqWOBdx40c0&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true">Twitter</a> | <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.instagram.com_irccssancamillo_&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=MZqznf8r5k9Gxtz2IU0Cc0DEBhVgeKeGiE6B4SO2p_0&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true">Instagram</a>
                </div>
                <div> <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=CIYDpmlDD17OMI-6_fbAAXJJrT1lO7mpXWEoum-BN8I&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true"><img
                      src="https://hsancamillo.it/public/LogoIRCCS.png"
                      alt="San Camillo IRCCS" moz-do-not-send="true"
                      width="180" height="85"></a>
                </div>
                <br>
                <div> <a
href="https://urldefense.proofpoint.com/v2/url?u=https-3A__hsancamillo.it_5x1000&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=zDVq1TXIa5etg45xOryPQg&m=Z9O7rUy3DGkKjwU4-wmN8faqHOffD2o3LlKHDNVgOJszwoWIFS3BC9Cx8fu_3TfY&s=wBw6kgoykSkkYXdHiOIBs_hvP1kQL0rnA1sqinrb5oQ&e="
                    rel="noopener noreferrer" target="_blank"
                    moz-do-not-send="true"><img
                      src="https://hsancamillo.it/public/Immagine5x000Firma.png"
                      alt="5x1000 al San Camillo Onlus"
                      moz-do-not-send="true" width="640" height="160"></a>
                </div>
              </div>
              <div><br>
              </div>
              <hr id="gmail-m_-4969986970453937481zwchr">
              <div><b>Da: </b>"Clayton E Curtis" <<a
                  href="mailto:clayton.curtis@nyu.edu" target="_blank"
                  moz-do-not-send="true" class="moz-txt-link-freetext">clayton.curtis@nyu.edu</a>><br>
                <b>A: </b>"Grace Hallenbeck" <<a
                  href="mailto:geh261@nyu.edu" target="_blank"
                  moz-do-not-send="true" class="moz-txt-link-freetext">geh261@nyu.edu</a>><br>
                <b>Cc: </b>"<a href="mailto:discuss@simnibs.org"
                  target="_blank" moz-do-not-send="true"
                  class="moz-txt-link-freetext">discuss@simnibs.org</a>"
                <<a href="mailto:discuss@simnibs.org" target="_blank"
                  moz-do-not-send="true" class="moz-txt-link-freetext">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"
                      moz-do-not-send="true"
                      class="moz-txt-link-freetext">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:part1.g3vQomFe.gpaJ0Igi@drcmr.dk"
                        alt="Screen Shot 2022-04-15 at 12.32.29 PM.png"
                        style="margin-right: 0px;" class="" width="406"
                        height="348"><br>
                      <br>
                      All the best & thanks for your work,<br>
                      <div>Grace Hallenbeck</div>
                    </div>
                  </blockquote>
                </div>
                <br>
                _______________________________________________<br>
                Simnibs-discuss mailing list<br>
                <a href="mailto:Simnibs-discuss@drcmr.dk"
                  target="_blank" moz-do-not-send="true"
                  class="moz-txt-link-freetext">Simnibs-discuss@drcmr.dk</a><br>
                <a
                  href="https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss"
                  target="_blank" moz-do-not-send="true"
                  class="moz-txt-link-freetext">https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss</a><br>
              </div>
            </div>
          </div>
        </blockquote>
      </div>
      <br>
      <fieldset class="moz-mime-attachment-header"></fieldset>
      <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
Professor of Neurophysics and Neuroimaging
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>
  </body>
</html>