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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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Failed to generate the boilerplate #3305

Open LueHa opened 3 weeks ago

LueHa commented 3 weeks ago

What happened?

In the HTML output file, the methods say: Failed to generate the boilerplate

What command did you use?

RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=26.1.1 -it \
    -v /Users/XY/BIDS_tutorial/derivatives/license.txt:/opt/freesurfer/license.txt:ro \
    -v /Users/hannah 1/Documents/XY:/data:ro \
    -v /Users/XY/Documents/XYZ:/out nipreps/fmriprep:23.2.3 \
    /data /out participant \
    --skip_bids_validation \
    --participant-label 30171

What version of fMRIPrep are you running?

23.2.3

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Methods
Failed to generate the boilerplate

Errors
No errors to report!

Additional information / screenshots

The online BIDS validator only indicates that I have a valid BIDS format if I click on "ignore NIFTI Headers". Otherwise it says: Error 1: [Code 12] REPETITION_TIME_MISMATCH Reason: Repetition time defined in the JSON (2.000 sec.) did not match the one defined in the NIFTI header (0.000 sec.)

tsalo commented 3 weeks ago

Can you share the full logs?