[Neuroimaging] Fmriprep fails during nibabel after manual realignment to LPI

Papale, Andrew E papalea at pitt.edu
Wed Aug 24 11:37:57 EDT 2022

Hi Neuroimaging Python Community,

(This is my first post, so let me know if I’m doing this right)

I had to manually reorient an image for this subject where the phase encoding direction was incorrect due to an overly steep obliquity to the bounding box.

I used the following commands on the BIDS-converted nifti files (both sbref, BOLD) and also the field maps.

fslorient -deleteorient fix_lpi.nii
3drefit -orient LPI fix_lpi.nii
But I am getting this error when trying to run fmriprep like usual:

[Graphical user interface, text, application  Description automatically generated]

Any advice?


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