My neuroimaging lab is interested in using the MRIQC package However, the majority of our data is not stored in the BIDS format, and we would like to run MRIQC ​​​​​using our current data infrastructure. Are there any leads on ourselves engineering MRIQC to work outside of BIDS?

The main issues we have with converting to BIDS are (1) It isn’t practical to convert our naming system (2) Changing the internal file structure will disrupt scripts which are already designed to work upon our current system.