Fmriprep:anat_epi not alignment

Hi experts,
I intend to analyze the data in AFNI at the individual level:

fmriprep-docker /media/work21/BIDS/Nifti /media/work21/ BIDS_T1 participant --participant-label 1 --output-spaces T1w --skull-strip-t1w force --fs-license-file /home/Downloads/freesurfer/license.txt --fs-no-reconall --n_cpus 32


However, after preprocessed by fmriprep and GLM, I found that epi image became deviated from anat. Could you please tell me know how can I fix this? Is there a command that might work for me?

Thanks for the helping!


I notice that you said you wanted to process the data with AFNI, so I will suggest an AFNI-based processing solution, using “” for your preprocessing (which in includes alignment, motion correction, blurring, etc. as well as GLM regression modeling).

I am not sure how the slignment ended up as such here, because I don’t know about the processing tool you used, the options used, nor its internal details. You can see the help here:
… which has examples to try, e.g., Ex. 9 or Ex. 11 for rest. If you have task here, you might want to check out the AFNI Bootcamp example here (the demo data is downloadable, so you can follow along with the tutorial):