Fmriprep error using spm-coregister: Estimate & Reslice processed files

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Hi @Steven

thank you very much for your reply.

  1. I will change the structure of my root bids directory.

  2. originally, I did fmriprep with raw data, but all subs have this issue ( a mismatch of alignment in this part: Alignment between the anatomical reference of the fieldmap and the target EPI, which I also posted in neurostars:Anatomical reference of the fieldmap and the target EPI alignment issue , you can check it for detail).

but I got no reply, and I figure maybe I can align the fmap with func files before fmriprep to solve the issue.

at first, I tried to use fslreorient2std and fslorient -setsform, but it didn’t work well,
so I tried spm and the alignment turned out really well, but followed by the issue I posted here.

  1. I also tried with fmriprep 24.1.0 , got the same problem (same crash report). so I figure it might not be the version’s problem.