<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">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">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>
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</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">clayton.curtis@nyu.edu</a>><br><b>A: </b>"Grace Hallenbeck" <<a href="mailto:geh261@nyu.edu" target="_blank">geh261@nyu.edu</a>><br><b>Cc: </b>"<a href="mailto:discuss@simnibs.org" target="_blank">discuss@simnibs.org</a>" <<a href="mailto:discuss@simnibs.org" target="_blank">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">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:1806236dc66842a5e921" alt="Screen Shot 2022-04-15 at 12.32.29 PM.png" width="406" height="348" style="margin-right: 0px;"><br><br>All the best & thanks for your work,<br><div>Grace Hallenbeck</div></div>
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