Wrong registration between fMRI data and fieldmap

[Liu_Ruobing]

Hi every one, recently I am working on a fMRIPrep for

this example dataset for subeject 33 session Y01: original -containning two imaginary and two real fieldmaps apart from two magnetitude fieldmaps under fmap folder; and processed – I merged imaginary and real fieldmaps into two phase fieldmaps first using Python Nib.arctan function.

Here is the command that I use for fmriprep:apptainer exec docker://nipreps/fmriprep fmriprep $inPath $outPath participant --participant-label sub-NCANDA00033 --output-spaces MNI152NLin2009cAsym MNI152NLin6Asym:res-2 anat -w $cachePath --fs-license-file $licFile --skip_bids_validation --nthreads 5 --low-mem --cifti-output --ignore slicetiming

The fmriprep-output shows that there is something wrong with registration.

(upload://mzpqtzDAT62EGsh88AvzMiNxbAL.jpeg)

Can you help me on this please? How can I fix the registration problem. I am stuck on this for a long while. Thank you! Appreciate it if you could help!

[Liu_Ruobing]

I used ANTs registration for func and fmap registration myself, the results looks okay. So probably it’s fmriprep pipeline error. Has anyone concurred such problem before?