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<p style="margin:1em 0px">Running the full Freesurfer reconstruction pipeline (without the hybrid skull stripping and Talaraich alignment on the fieldtrip side) appears to have been successful.</p>
<p style="margin:1em 0px">However, when I try to continue with the tutorial I find that my volume and source grid don't line up (even before any issues converting to sensor space):</p>
<p style="margin:1em 0px">Figure: <a style="color:rgb(51,51,238);text-decoration:none" href="http://imgur.com/uo9uPUc">http://imgur.com/uo9uPUc</a> (code below)</p>
<p style="margin:1em 0px">Does anyone have any idea what could be wrong?</p>
<p style="margin:1em 0px">What coordinate system is the sub-oct-6-src.fif file in (created by MNE suite)?<br>If it is in talairach coordinates, how do I load the Talairach aligned image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)</p>
<p style="margin:1em 0px">Do I need to manually include the transform from transform/talairach.xfm? To include that can I use it directly as mri.transform in fieldtrip or do I need to multiply it by the existing mri.transform which is there when loading the raw anatomy scan (.img)? Come to think of it what does that transform represent?</p>
<p style="margin:1em 0px">Sorry if these are not fieldtrip questions but I am trying to follow the fieldtrip MNE tutorial so I was hoping someone might know. </p>
<p style="margin:1em 0px">Thanks</p>
<p style="margin:1em 0px">Robin</p>
<pre style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;overflow:auto;margin:1em 0px"><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-radius:3px 3px 3px 3px;display:inline;white-space:pre;border-radius:3px 3px 3px 3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block;padding:0.5em;color:rgb(51,51,51);background:none repeat scroll 0% 0% rgb(248,248,255)" class="language-matlab"><span style="color:rgb(153,153,136);font-style:italic" class="comment">% load freesurfer image</span>
mri_fs_tal = ft_read_mri(fullfile(fs_dir, <span class="transposed_variable">sub.</span>code, <span style="color:rgb(221,17,68)" class="string">'mri'</span>, <span style="color:rgb(221,17,68)" class="string">'orig.mgz'</span>));
mri_fs_tal = ft_convert_units(mri_fs_tal, <span style="color:rgb(221,17,68)" class="string">'cm'</span>);
<span style="color:rgb(153,153,136);font-style:italic" class="comment">% load MNE grid</span>
<span style="color:rgb(153,153,136);font-style:italic" class="comment">% computed with mne_setup_source_space --ico -6</span>
bnd = ft_read_headshape(fullfile(fs_dir, <span class="transposed_variable">sub.</span>code, <span style="color:rgb(221,17,68)" class="string">'bem'</span>, <span class="matrix">[sub.code <span style="color:rgb(221,17,68)" class="string">'-oct-6-src.fif'</span>]</span>), <span style="color:rgb(221,17,68)" class="string">'format'</span>, <span style="color:rgb(221,17,68)" class="string">'mne_source'</span>);
sourcespace = ft_convert_units(bnd, <span style="color:rgb(221,17,68)" class="string">'cm'</span>);
<span style="color:rgb(153,153,136);font-style:italic" class="comment">% Volume conduction model</span>
cfg = <span class="matrix">[]</span>;
<span class="transposed_variable">cfg.</span>coordsys = <span style="color:rgb(221,17,68)" class="string">'spm'</span>;
<span class="transposed_variable">cfg.</span>output = <span class="cell">{<span style="color:rgb(221,17,68)" class="string">'brain'</span>}</span>;
seg = ft_volumesegment(cfg, mri_fs_tal);
cfg = <span class="matrix">[]</span>;
<span class="transposed_variable">cfg.</span>method = <span style="color:rgb(221,17,68)" class="string">'singleshell'</span>;
vol = ft_prepare_headmodel(cfg, seg);
<span style="color:rgb(153,153,136);font-style:italic" class="comment">% Check volume conduction</span>
figure; hold on
ft_plot_vol(vol, <span style="color:rgb(221,17,68)" class="string">'facecolor'</span>, <span style="color:rgb(221,17,68)" class="string">'none'</span>); alpha <span style="color:rgb(0,153,153)" class="number">0.5</span>;
ft_plot_mesh(sourcespace, <span style="color:rgb(221,17,68)" class="string">'edgecolor'</span>, <span style="color:rgb(221,17,68)" class="string">'none'</span>); camlight</code></pre>
<p style="margin:1em 0px">On Wed, May 1, 2013 at 5:41 PM, Robin <a style="color:rgb(51,51,238);text-decoration:none" href="mailto:robince@gmail.com">robince@gmail.com</a> wrote:</p>
<blockquote style="margin:1em 0px;border-left:4px solid rgb(221,221,221);padding:0px 1em;color:rgb(119,119,119);quotes:none">
<p style="margin:1em 0px">I am trying to run through the MNE tutorial here:</p>
<p style="margin:1em 0px"><a style="color:rgb(51,51,238);text-decoration:none" href="http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate">http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate</a></p>
<p style="margin:1em 0px">Unfortunately after the volumetric processing in freesurfer my<br>intermediate result looks wrong.</p>
<p style="margin:1em 0px">I have followed the steps (including interactive alignment to<br>Talairach) according to the tutorial. I wondered if anyone has any<br>idea what could be wrong, or could point to some more possible<br>
diagnostic commands to run?</p>
<p style="margin:1em 0px">The original Subject01.mgz file seems to have been saved correctly.<br>But if I load the orig.mgz created with:<br>mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz<br>and plot it with ft_sourceplot it has the same offset and upside down<br>
position as the final incorrectly segments freesurfer image. Could<br>this indicate a problem?</p>
<p style="margin:1em 0px">Thanks for any help,</p>
<p style="margin:1em 0px">Cheers</p>
<p style="margin:1em 0px">Robin</p>
</blockquote>
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