<div class="markdown-here-wrapper" id="markdown-here-wrapper-684946" style><p style="margin:1.2em 0px!important">I was wondering how to get the voxel positions (or origin and voxel size) for a fieltrip mri structure.</p>
<p style="margin:1.2em 0px!important">I have an anatomical scan which I have normalised to the T1 brain:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;overflow:auto;margin:1.2em 0px"><code class="language-matlab" style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:nowrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;white-space:pre;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block;padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);background-repeat:initial initial">>> mrin

mrin = 

      anatomy: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">181</span>x217x181 double]</span>
    transform: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">4</span>x4 double]</span>
          dim: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">181</span> <span class="number" style="color:rgb(0,153,153)">217</span> <span class="number" style="color:rgb(0,153,153)">181</span>]</span>
       params: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">1</span>x1 struct]</span>
      initial: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">4</span>x4 double]</span>
     coordsys: <span class="string" style="color:rgb(221,17,68)">'spm'</span>
          cfg: <span class="matrix">[<span class="number" style="color:rgb(0,153,153)">1</span>x1 struct]</span></code></pre>
<p style="margin:1.2em 0px!important">I can I obtain the location of any voxel in MNI coordinates (mm or cm)? When loading a Nifti file (with load_nii) I can find origin and voxel_size with:</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;overflow:auto;margin:1.2em 0px"><code class="language-matlab" style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:nowrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline;white-space:pre;border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block;padding:0.5em;color:rgb(51,51,51);background-color:rgb(248,248,255);background-repeat:initial initial">voxel_size = <span class="built_in" style="color:rgb(0,134,179)">abs</span>(<span class="transposed_variable">nii.</span><span class="transposed_variable">hdr.</span><span class="transposed_variable">dime.</span>pixdim(<span class="number" style="color:rgb(0,153,153)">2</span>:<span class="number" style="color:rgb(0,153,153)">4</span>));        <span class="comment" style="color:rgb(153,153,136);font-style:italic">% vol in mm</span>
origin = <span class="built_in" style="color:rgb(0,134,179)">round</span>(<span class="built_in" style="color:rgb(0,134,179)">abs</span>(<span class="transposed_variable">nii.</span><span class="transposed_variable">hdr.</span><span class="transposed_variable">hist.</span>originator(<span class="number" style="color:rgb(0,153,153)">1</span>:<span class="number" style="color:rgb(0,153,153)">3</span>)));</code></pre>

<p style="margin:1.2em 0px!important">and then <code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;padding:0px 0.3em;white-space:nowrap;border:1px solid rgb(234,234,234);background-color:rgb(248,248,248);border-top-left-radius:3px;border-top-right-radius:3px;border-bottom-right-radius:3px;border-bottom-left-radius:3px;display:inline">posmm = (vox-origin) .* voxel_size</code>. Is there any way to do the same from the fieldtrip structure? I can't find the corresponding header information. </p>

<p style="margin:1.2em 0px!important">Thanks</p>
<p style="margin:1.2em 0px!important">Robin</p>
</div>