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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It certainly works with the unit conversions in the version I’m currently using, which is from 2/5/2013 - - thanks so much!! As soon as I have a chance, I’ll
download the latest version to test.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks again!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Allison Nugent, PhD<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MRI Physicist<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Experimental Therapeutics and Pathophysiology Branch<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NIMH/NIH/DHHS<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ph. 301-451-8863<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">nugenta@mail.nih.gov</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> "Jörn M. Horschig" [mailto:jm.horschig@donders.ru.nl]
<br>
<b>Sent:</b> Friday, February 15, 2013 11:56 AM<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] headmodels<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear Allison,<br>
<br>
I was encountering similar issues the last two days and hope to have fixed some unit conversion bugs. Thus it might be that with the newest FT version, you don't need to manually convert the units anymore as JM suggested. Could you give it a try for me and
see whether it works without JMs manual approach in the newest FT version?<br>
<br>
Best,<br>
Jörn<br>
<br>
On 2/15/2013 3:51 PM, Nugent, Allison C. (NIH/NIMH) [E] wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello, I’m very sorry to repost this, but I’m hoping that someone might be able to give me advice.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have an MRI in nifti format. It has already been re-aligned with the fiducial markers. I’ve scoured the tutorials, but most seem to deal with MRIs that
are already in the ctf coordinate system. </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I’ve imported the MRI like so:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">mri=ft_read_mri(‘ABC_ortho_anat.nii’);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">mri=ft_determine_coordsys(mri)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I re-label the coordinate axes, and set the origin – when it’s done, it has “Neuromag” as the coordsys, although that’s not how it was created. Next:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">cfg=[]; cfg.method=’interactive’</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">mri_realigned=ft_volumerealign(cfg,mri) % to set the fiducial points</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">cfg=[];</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">[segmentedmri]=ft_volumesegment(cfg, mri_realigned)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">During execution I get this warning:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Warning: could not open /tmp/tpe3eb8b07_40e0_49bf_88d2_e0c227c3d7af.img
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Even though the file appears to exist – and the program completes and produces a segmented MRI that looks fine. Finally:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">hdr=ft_read_header(‘ACN.ds’);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">cfg=[]; cfg.method=’singleshell’;</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">vol_realistic=ft_prepare_headmodel(cfg,segmentedmri);</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">figure</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">ft_plot_vol(vol_realistic);hold on</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">ft_plot_sens(hdr.grad)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The plot has the sensor array and the headmodel on different scales – like it didn’t properly adjust for the difference in mm and cm, even though the units
are specified in the data structures. I’d ultimately also like to be able to use the localspheres model, and compare results, but since I can’t figure out how to plot that headmodel to check it, I thought I’d start with one that I can plot.
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank you!</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Allison Nugent, PhD</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MRI Physicist</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Experimental Therapeutics and Pathophysiology Branch</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">NIMH/NIH/DHHS</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ph. 301-451-8863</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="mailto:nugenta@mail.nih.gov">nugenta@mail.nih.gov</a></span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>fieldtrip mailing list<o:p></o:p></pre>
<pre><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><o:p></o:p></pre>
<pre><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Jörn M. Horschig<o:p></o:p></pre>
<pre>PhD Student<o:p></o:p></pre>
<pre>Donders Institute for Brain, Cognition and Behaviour <o:p></o:p></pre>
<pre>Centre for Cognitive Neuroimaging<o:p></o:p></pre>
<pre>Radboud University Nijmegen <o:p></o:p></pre>
<pre>Neuronal Oscillations Group<o:p></o:p></pre>
<pre>FieldTrip Development Team<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>P.O. Box 9101<o:p></o:p></pre>
<pre>NL-6500 HB Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Contact:<o:p></o:p></pre>
<pre>E-Mail: <a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><o:p></o:p></pre>
<pre>Tel: +31-(0)24-36-68493<o:p></o:p></pre>
<pre>Web: <a href="http://www.ru.nl/donders">http://www.ru.nl/donders</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Visiting address:<o:p></o:p></pre>
<pre>Trigon, room 2.30<o:p></o:p></pre>
<pre>Kapittelweg 29<o:p></o:p></pre>
<pre>NL-6525 EN Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
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