[FieldTrip] Problem with ft_volumewrite and axis labels

Johan Wessberg johan.wessberg at gu.se
Thu Feb 16 13:25:37 CET 2017


I have checked the archives without finding an answer or seeing a discussion of this problem.

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.

Using either MGZ or NIFTI file formats does not matter. I get the same problem when opening the files in either Freeview or MRIcron.
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).

Here is a screen copy from FreeView:

[cid:image001.png at 01D28858.28D2D110]

And here is the figure from ft_determine_coordys()  (the yellow labels are hard to read, but they are correct)

[cid:image002.png at 01D28858.28D2D110]

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().

Has anyone had the same problem?

Johan Wessberg

Inst. of Neuroscience and Physiology
University of Gothenburg, Sweden

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