Using mriqc on multiecho data


My lab recently acquired some multiecho scans (some with 3 echoes, some with 4) and wants to compare these scans for quality while we prepare to launch a new scanning project (post-COVID-19).

I ran the scans through mriqc, and to my surprise, mriqc treated each echo as an individual scan. I may have been mistaken in assuming that it would be able to combine the echoes into a sharper image - but is it possible? Is there some flag or something to indicate to mriqc that there is multiecho data present? I couldn’t find any guidance in the mriqc docs.

Any guidance on this would be greatly appreciated.

Henry Jones

Hi Henry

I’m not an MRIQC expert but from searching their documentation and Github issues it seems like you are right. See for instance issue #773.

If you’re specifically looking to combine your multi-echo into a single-echo time series, I would suggest using the tedana package, specifically the function t2smap. The tedana documentation recommends applying slice time correction and 3D volume realignment before doing multi-echo combination.

Hope this helps somewhat.


Hi Stephan,

Thank you for this informative answer! I will continue on with my processing of the data and will try tedana and t2smap.


Hi Stephan,

So, to execute that, would you suggesting running fmriprep and then taking the slice timed / 3d volume re-aligned output of that and running it through t2smap?


Hi McKenzie

Sorry this is probably too late (2020 happened…) but in case it’s still useful, yes that would be my suggestion. You could of course also use whatever tools or pipelines you prefer to run 3D realignment and slice timing correction first.