IntendedFor Error while running bids-fmriprep

1

Hi!

While running bids-fmriprep on my data, I get this error message:

[ERR] ‘IntendedFor’ field needs to point to an existing file. (code: 37 - INTENDED_FOR)
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: anat/sub-103_T1w.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-MEMORY_run-01_bold.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-MEMORY_run-02_bold.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-IAPS_run-01_bold.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-IAPS_run-02_bold.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-IAPS_run-03_bold.nii.gz
./sub-103/fmap/sub-103_phasediff.nii.gz
Evidence: func/sub-103_task-IAPS_run-04_bold.nii.gz

There’s a discussion about this error here, but their solution doesn’t seem to apply to my case. I am running the bids-fmriprep gear on Flywheel across sessions and subjects. Could anyone enlighten me on what the problem is and how to resolve it?

Thank you!

2

Hi,

A few things that can help us answer:
What version of fMRIPrep are you running? Are your data otherwise BIDS valid? Is this error subject-specific? What is your full fMRIPrep command?

You should not be associating fmaps with T1 files. fMRIPrep only does susceptibility distortion correction on EPI/BOLD files.

Can you confirm these files exist?

Best,
Steven

3

Hi Steven,

Thanks for following up. I am using the bids-fmriprep gear version 20.2.6 on Flywheel. My data is BIDS valid and the error is not subject-specific. I did not run a fMRIPrep command; I clicked the run bids-fmriprep gear on Flywheel which automates the process for me.

I did not know that I could not associate fmaps with T1 files, so thank you for that. I also do not have the func/sub-103_task-IAPS_run-01_bold.nii.gz file.

Best,
Jo

4

If you want to use the most up-to-date container, I would recommend switching to Docker/Singularity.

You should make sure the IntendedFor fields in the JSONS point to files (only to the *bold.nii.gz files) that exist.

Best,
Steven

5

Thanks Steven. I have a follow-up question.

func/sub-103_task-IAPS_run-01_bold.nii.gz

Do you know of possible reasons why this file doesn’t exist? I think the right file name should be ses-xxx/func/sub-sub103_ses-xxx_task-IAPS_run-01_bold.nii.gz. I don’t know how the file name ‘func/sub-103_task-IAPS_run-01_bold.nii.gz’ was created.

Thank you, I appreciate your help!

Best,
Jo

6

How did you get your data and create the JSONs?