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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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fMRIprep did not generate multi echo outputs. #3362

Open TamerGezici opened 2 months ago

TamerGezici commented 2 months ago

What happened?

I ran fmriprep on multi echo data, but the outputs did not create any of the multi echo files

Input BIDS: image

Output of prep: image

What command did you use?

docker run -ti --rm \
    -v /f/Tamer/prep/bids_data:/data:ro \
    -v /f/Tamer/prep/output:/out \
    -v /f/Tamer/prep/freesurfer.txt:/license.txt:ro \
    nipreps/fmriprep /data /out participant \
    --fs-license-file /license.txt \
    --me-output-echos \
    --ignore slicetiming

What version of fMRIPrep are you running?

Latest

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.

No response

Additional information / screenshots

No response

tsalo commented 2 months ago

Can you share the full stdout and stderr log files?

effigies commented 2 months ago

Do you have at least three echos? If not, fMRIPrep does not have anything useful to do with the echos. The log should make clear what decisions were made near the very beginning.