Error in fmriprep processing : operands could not be broadcast together with shapes (3,3) (4,)

Hi experts,

I am running fmriprep on the HBN SSI dataset (The Healthy Brain Network Serial Scanning Initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions - PMC) using the following command line.

“singularity run –cleanenv /ocean/projects/soc220002p/shared/images/fmriprep_latest.sif /ocean/projects/soc220002p/shared/HNU_AWS2 /ocean/projects/soc220002p/shared/fmri_prep_process/ participant –participant-label sub-0025427ses1 –fs-license-file /ocean/projects/soc220002p/shared/sandbox_fmriprep/license.txt –force-bbr -v -v --n_cpus 1”

I am getting outputs which look fine but fmriprep says that I am getting this crash file ending by : operands could not be broadcast together with shapes (3,3) (44), see the crash file attached to this mail

Any idea of what might be the problem ?

Thank you very much for your help,



Hi Charles. Please provide the following information to help us diagnose the issue:

  1. What version of fMRIPrep are you using?
  2. Are your data BIDS valid?
  3. Can you provide the output of tree on a raw subject data directory?

What I am guessing is maybe there are BOLD files with different dimensions, and fMRIPrep is having trouble applying the fieldmaps to all files.


1 Like

Hi Steven,

Thanks a lot. I am using fMRIPrep v21.0.1
My data have been BIDS-validated. Here is the tree attached to this message, and also the beginning of the terminal when I am launching fmriprep.

Thanks again,


are the voxel dimensions of all fmri the same?

Yes I think that they are. I just checked (see attached) the voxel size of each image for a given a subject.

Thanks for your help,


It looks like the fieldmaps are not being associated to the BOLD images becasue there are not accompanying json files.