Can't run mriqc group analysis on a subset of the sample (separate echos)

[caaam3]

What happened?

I have multiecho data and I have ran mriqc on the participant level for all participants for each echo separately using bids-filter-file. Now I want to run a group analysis for each echo separately as I don't want all echos in the same group report. I have specified that in the bids-filter-file and when I run the code it identifies it as a filter and later on in the config file in logs it also only selects the first echo as intended. However, the generated reports are of all echos together.

What command did you use?

docker run -it --rm -v <bids_root_dir>:/data:ro -v <output_dir>:/out \
-v <bids-filter-file_dir>:<bids-filter-file_dir> \
nipreps/mriqc:24.0.2 /data /out group \
--task-id nf \
--bids-filter-file <dir> \
--verbose-reports \
--no-sub \
-w <output_dir>/group/echo1

What version of the software are you running?

24.1.0 and in the latest try 24.0.2 (see above) although it still shows 24.1.0. in logs

How are you running this software?

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

[Remi-Gau]

I may be wrong but I think bids-filter are not yet supported at the group level, no?

Or more specifically you can pass a bids filter file but it won't affect the output.

[caaam3]

Yeah, that seems to be the case since it recognizes the filter file but it doesn't get used. I ended up having to separate the different echos into different folders in order to get separate group reports.

[Shotgunosine]

If I'm reading the code correctly, the bids filter would need to be applied in this step, where the json's are collected to construct a TSV:

mriqc/mriqc/utils/misc.py

Line 199 in d7f9c89

jsonfiles = list(output_dir.glob(f'sub-*/**/{IMTYPES[mod]}/sub-*_{mod}.json'))

Does that seem correct to folks more familiar with MRIQC?