[FieldTrip] Volume Reslice Question

[Schoffelen, J.M. (Jan Mathijs)]

Hi JT,

You’d first need to ensure that ‘mri_realigned’ is correctly realigned. Since the resliced MRI image is upside down, this suggests that the coordinate system information that is used by FieldTrip (i.e. the mri_realigned.coordsys -> it looks like ‘ctf’ ) is not compatible with what’s in the data.

If you search the documentation for coordinate systems I think there should be plenty of information that will get you on the road.

Best wishes,
JM


On 30 Mar 2022, at 05:45, JT Galla via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello!

I am trying to reslice my MRI image for the purposes of EEG Source Reconstruction using the following code:


cfg          = [];
mri_resliced = ft_volumereslice(cfg, mri_realigned);

However, when I go to view the output of this command I see that the reslice method has completely removed axial slices and has inverted coronal and sagittal slices. This is, of course, ruining subsequent head model generations so any guidance that could be provided on why this might be happening and how to fix it would be greatly appreciated. Attached is a screenshot of what my replaced image looks like.

<Screen Shot 2022-03-29 at 11.38.25 PM.png>


Thank you for your time!

JT Galla
Duke University c/o ’23
Neuroscience Major, Chemistry & Computational Biology Minor
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