fmriprep bids output not fully covered by bids-validator

[miltoncamacho]

I have come across an issue when trying to run the bits validator on the bids output from fmriprep. It is clear that the files that fmriprep produces are not fully compliant (perhaps they do not need to be).

Here are some error examples.

	Please visit https://neurostars.org/search?q=SIDECAR_KEY_REQUIRED for existing conversations about this issue.
	[ERROR] NOT_INCLUDED 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 https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.
		/containers/
		/sub-2532/figures/
		16 more files with the same issue
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	[ERROR] SIDECAR_KEY_REQUIRED A data file's JSON sidecar is missing a key listed as required.
		SpatialReference
		/sub-2532/ses-1a/anat/sub-2532_ses-1a_rec-filtered_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz - Field description: For images with a single reference, the value MUST be a single string.
For images with multiple references, such as surface and volume references,
a JSON object MUST be used.
		/sub-2532/ses-1a/anat/sub-2532_ses-1a_rec-filtered_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz - Field description: For images with a single reference, the value MUST be a single string.
For images with multiple references, such as surface and volume references,
a JSON object MUST be used.
		10 more files with the same issue
		SkullStripped
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-coeff_fieldmap.nii.gz - Field description: Whether the volume was skull stripped (non-brain voxels set to zero) or not.
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-epi_fieldmap.nii.gz - Field description: Whether the volume was skull stripped (non-brain voxels set to zero) or not.
		3 more files with the same issue
	Please visit https://neurostars.org/search?q=SIDECAR_KEY_REQUIRED for existing conversations about this issue.
	[ERROR] ALL_FILENAME_RULES_HAVE_ISSUES Multiple filename rules were found as potential matches. All of them had at least one issue during filename validation.
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-coeff_fieldmap.nii.gz - Rules that matched with issues: rules.files.deriv.preprocessed_data.fmap_fieldmaps_common, rules.files.raw.fmap.fieldmaps
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-epi_fieldmap.nii.gz - Rules that matched with issues: rules.files.deriv.preprocessed_data.fmap_fieldmaps_common, rules.files.raw.fmap.fieldmaps
		7 more files with the same issue
	Please visit https://neurostars.org/search?q=ALL_FILENAME_RULES_HAVE_ISSUES for existing conversations about this issue.
	[ERROR] FILENAME_MISMATCH The filename is not formatted correctly. This could result from entity duplication or reordering.
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-coeff_fieldmap.nii.gz - Expected filename: sub-2532_ses-1a_desc-coeff_fieldmap.nii.gz
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-epi_fieldmap.nii.gz - Expected filename: sub-2532_ses-1a_desc-epi_fieldmap.nii.gz
		2 more files with the same issue
	Please visit https://neurostars.org/search?q=FILENAME_MISMATCH for existing conversations about this issue.
	[ERROR] FIELDMAP_WITHOUT_MAGNITUDE_FILE 'fieldmap.nii[.gz]' file does not have an associated 'magnitude.nii[.gz]' file.
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-coeff_fieldmap.nii.gz
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-epi_fieldmap.nii.gz
		1 more files with the same issue
	Please visit https://neurostars.org/search?q=FIELDMAP_WITHOUT_MAGNITUDE_FILE for existing conversations about this issue.
	[ERROR] INTENDED_FOR 'IntendedFor' field needs to point to an existing file.
Files must be subject-relative paths or BIDS URIs.
		/sub-2532/ses-1a/fmap/sub-2532_ses-1a_fmapid-sub2532ses1ataskpartlycloudy_desc-preproc_fieldmap.nii.gz
	Please visit https://neurostars.org/search?q=INTENDED_FOR for existing conversations about this issue.
	[ERROR] SIDECAR_WITHOUT_DATAFILE A json sidecar file was found without a corresponding data file
		/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_desc-confounds_timeseries.json
		/sub-2532/ses-1a/func/sub-2532_ses-1a_task-partlycloudy_desc-coreg_boldref.json
		3 more files with the same issue
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          Summary:                         Available Tasks:        Available Modalities:
          65 Files, 2.34 MB                partlycloudy            MRI                  
          1 - Subjects 1 - Sessions                        

What should be the next steps to include the coverage of bids-validator? Is the best option still ignoring the problem files?

@bpinsard