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<p class="MsoNormal"><span style="font-size:11.0pt">Hi!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have checked the archives without finding an answer or seeing a discussion of this problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">We are trying to use ft_volumewrite() to export functional and anatomical data for visualization outside FieldTrip, for example with Freeview. The problem is that the orientation of the axes is wrong, AP and
RL have been swapped. But when checking the axes with ft_determine_coordsys() they are fine.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Using either MGZ or NIFTI file formats does not matter. I get the same problem when opening the files in either Freeview or MRIcron.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">ft_volumewrite() has a cfg.coordsys option that includes a ‘ctf’, but it does not help (and the documentation says that this will only matter for Analyze, vmp, and vmr file formats anyway).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Here is a screen copy from FreeView:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-GB"><img width="610" height="417" id="Picture_x0020_1" src="cid:image001.png@01D28858.28D2D110"></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">And here is the figure from ft_determine_coordys() (the yellow labels are hard to read, but they are correct)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-GB"><img width="541" height="406" id="Picture_x0020_2" src="cid:image002.png@01D28858.28D2D110"></span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The functional data have been acquired with the CTF MEG in Nottingham, and the MRI data have been co-registered in CTF coordinates for functional analysis. All source analyses and plots are fine inside FT,
my problem is only to export the data correctly using ft_volumewrite(). <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Has anyone had the same problem?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Johan Wessberg<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Inst. of Neuroscience and Physiology<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">University of Gothenburg, Sweden<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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