[FieldTrip] ft_volumereslice shifts the brain

"Jens Klinzing, Universität Tübingen" jens.klinzing at uni-tuebingen.de
Wed Mar 23 23:52:47 CET 2016

Hi everyone,
I have a problem with ft_volumereslice, applied to Nifti MRIs (haven't 
tested it on other formats). The function shifts the image to bring the 
brain in the center, as announced in the documentation.

However, this is done
a) in a way that the nose of my MRI is cut off (s. below), which is 
suboptimal since I register EEG electrodes and fiducials in relation to 
the MRI and the cut is done close to the nasion,
b) in contrast to the documentation it shifts the brain whether or not a 
coordinate system (.coordsys) is given. I guess this happens during 
ft_sourceinterpolate which is called inside ft_volumereslice (line 180). 
The shift that could be done in ft_volumereslice (line 103ff) is not 
performed if there is no .coordsys, but the shift in the returned MRI is 
still there.

Before and After (without an mri.coordsys):

Sure I can just increase the dimensions of the MRI, then I get the nose 
back, but I was wondering if anyone can explain this behavior of 
ft_volumereslice and whether it is a genuine bug or not.

Thanks and greetings,

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