Problem with imaging dimensions in fMRIPrep

Hi NeuroStars,
I had to re-process some task-fMRI with a newer version of fMRIPrep (v20.2.0) and ran into some issues. The registration to standard space in the report looks fine. However, when I try to overlay the bold image on the MNI template in any other software (FSLeyes, mricron, nilearn), the registration looks completely off.


The background image is the ICBM152 2009c non-linear asymmetric template. The overlay is the brain mask generated by fMRIPrep, i.e. sub-…/func/sub-…_task-…_space-MNI152NLin2009cAsym_desc-brain_mask

I find this quite puzzling because I processed the same BIDS dataset with fMRIPrep v.1.2.1 and did not have any issues.

Any pointers for what I could try to fix this are massively appreciated!

Here is the image showing correct alignment for the older version of fMRIPrep with the same dataset:

This seems related to a new improvement in the latest fix of fmriprep: v20.2.2. Could you try with this new version?

The changes are listed there: What’s new — fmriprep version documentation

And what I think could be related to your problem here:

Thank you for the speedy reply. I re-ran one of the participants with v20.2.2 and that has resolved the issue around the MNI alignment. Thank you!

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