BIDS Validation failing on naming error, '_echo'

I’m getting an error from the BIDS validator in fmriprep for files with this naming convention

1: [ERR] Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a “.bidsignore” file in your dataset (see for details). Please note that derived (processed) data should be placed in /derivative
s folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder. (code: 1 - NOT_INCLUDED)

When I remove the ‘_echo-1’ (or whichever instance of ‘echo’) from the name of the files the validator doesn’t fail. Looking at the BIDS specification, I’m not sure why including the echo in the name would cause this issue - is there something I’m missing? Do I need to include the echo information in the name for fmriprep to work?

echo is not currently a supported entity for files with the T1w suffix. There is an open issue about possibly supporting it though:

In terms of inferring this from the specification, there are two places within the specification to check for these things: the MRI entity table and the anatomical MRI section’s filename templates.

In the MRI entity table, the first row includes the T1w suffix, and the corresponding cell under the echo column does not contain “OPTIONAL” or “REQUIRED”: Entity table - Brain Imaging Data Structure v1.6.1-dev

The filename templates in the anatomical MRI section of the specification are less clear (Magnetic Resonance Imaging - Brain Imaging Data Structure v1.6.1-dev). There are so many anatomical MRI suffixes with equivalent rules that the templates combine them under “<suffix>”. It wouldn’t be clear which suffixes fall under each group. However, for the two patterns that use this suffix consolidation, neither supports echo.

I don’t believe fMRIPrep supports multi-echo T1w scans. However, I do remember seeing a similar question about MEMPRAGEs at MEMPRAGE RMS (not echoes) for recon-all with fMRIprep. The recommendation was to (1) calculate the RMS image (which I think is what Freesurfer wants) and (2) name that file as if it was a normal T1w so that fMRIPrep would use it.

I hope that helps.

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Thanks so much @tsalo! I was able to get fmriprep running using the RMS images. Will see if the issue for multi-echo closes and could re-run at that point.