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Hi Johan,
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<div class="">ft_volumewrite does not write any information with respect to how the axes in the coordinate system need to be interpreted to the output file. In other words, it only writes the anatomical image, along with some transformation matrix that typically
maps voxels to head coordinates. If the external software ‘expects’ some specific coordinate system, or if it defaults to interpreting the coordinate system along to some convention, if it cannot find the required information in the file, the mapping may or
may not be correct.</div>
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<div class="">In your case it seems that freeview interprets the x/y/z axes in the coordinate system (attached with the MRI-file) as RAS, whereas you expected it to be correctly interpreted as ALS (CTF-convention). You could write the volume with a RAS transformation
matrix.</div>
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<div class="">Best,</div>
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<div class="">Jan-Mathijs</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
J.M.Schoffelen, MD PhD<br class="">
Senior Researcher, VIDI-fellow<br class="">
Telephone: +31-24-3614793</div>
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Physical location: room 00.028</div>
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Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br class="">
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<blockquote type="cite" class="">
<div class="">On 16 Feb 2017, at 13:25, Johan Wessberg <<a href="mailto:johan.wessberg@gu.se" class="">johan.wessberg@gu.se</a>> wrote:</div>
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<span style="font-size: 11pt;" class="">Hi!<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">I have checked the archives without finding an answer or seeing a discussion of this problem.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class="">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 class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">Here is a screen copy from FreeView:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><span id="cid:image001.png@01D28858.28D2D110"><image001.png></span></span><span style="font-size: 11pt;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">And here is the figure from ft_determine_coordys() (the yellow labels are hard to read, but they are correct)<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><span id="cid:image002.png@01D28858.28D2D110"><image002.png></span></span><span style="font-size: 11pt;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">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().<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Calibri;" class="">
<span style="font-size: 11pt;" class="">Has anyone had the same problem?<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">Johan Wessberg<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">Inst. of Neuroscience and Physiology<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class="">University of Gothenburg, Sweden<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">fieldtrip
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:fieldtrip@donders.ru.nl" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">fieldtrip@donders.ru.nl</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
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