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Hi Nick,
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<div class="">You need to use the anatomical MRI that you used to create your headmodel etc., register it to ctf-space using ft_volumerealign (in the interactive mode, it seems), and then use some magical matrix multiplications to get the appropriate transformation
matrix that can be applied to the headmodel (to get it in ctf space), or (when taking the inverse of this transformation matrix) to the grad structure (to get it in spm space).</div>
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<div class="">The solution is embedded here: <a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate" class="">http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate</a></div>
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<div class="">look for the transform_vox2spm and transform_vox2ctf, and the magical variable T.</div>
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<div class="">Best,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 24 Sep 2016, at 06:24, Nicholas A. Peatfield <<a href="mailto:nick.peatfield@gmail.com" class="">nick.peatfield@gmail.com</a>> wrote:</div>
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<p dir="ltr" class="">Hi Arjen,</p>
<p dir="ltr" class="">Yeah I looked into that but spm to ctf is not supported. And changing the grads to spm seems also not possible. Unless I use ft realignsens but the behaviour of that seems a little weird in my experience, and seems more suited to electrodes.</p>
<p dir="ltr" class="">Cheers</p>
<p dir="ltr" class="">Nick </p>
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<div class="gmail_quote">On Sep 23, 2016 7:35 PM, "Arjen Stolk" <<a href="mailto:a.stolk8@gmail.com" class="">a.stolk8@gmail.com</a>> wrote:<br type="attribution" class="">
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<div style="direction:inherit" class="">Hi Nick,</div>
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<div style="direction:inherit" class="">You may want to have a look at ft_convert_coordsys which can switch volumes between different coordinate systems. </div>
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<div style="direction:inherit" class="">Best,</div>
<div style="direction:inherit" class="">Arjen</div>
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On Sep 23, 2016, at 4:55 PM, Nicholas A. Peatfield <<a href="mailto:nick.peatfield@gmail.com" target="_blank" class="">nick.peatfield@gmail.com</a>> wrote:<br class="">
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<div dir="ltr" class="">Hi all,
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<div class="">I'm getting into a problem wherein I have headmodel that are in SPM space and the grads are in CTF space. I would usually keep all the headmodels in CTF space and align based on that but for this dataset and the format of the MRIs,POS etc... there
seems to be some problems (could take longer to explain but lets keep this brief).</div>
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<div class="">So this of course leads to the issue that the grad and the headmodel within beamformer_lcmv is misaligned by 90 degrees, which is of course not good. Is there a quick solution that I have not come across to either convert the headmodel to ctf
or convert the grad structure to spm coordsys? When I specify in the ft_prepare_sourcemodel I explicitly say (cfg.coordsys = 'ctf') but the outputted sourcemodel is still misaligned between the headmodel and the grads (see attached image - oh and the lf is
also misaligned of course).</div>
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<div class="">Any help would be greatly appreciated. And I hope that this question hasn't come up before as I did quite a bit of google searching before sending this email.</div>
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<div class="">With Regards,</div>
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<div class="">Nick</div>
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<div class=""><font face="arial, helvetica, sans-serif" size="2" class="">Nicholas Peatfield, PhD</font></div>
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