[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?
Thanks,
Andrew
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