Would you ever consider setting parameterize_dirs to false as a default in nipype? We are working on integrating MRIQC into CBRAIN (http://www.cbrain.ca/), and have run into an issue with file name lengths. While the solution posted above should hopefully work for this version of MRIQC, having this changed in nipype's defaults would make it so we don't have to implement this change in future containerized versions of MRIQC + limit the likelihood of this happening for other pipelines we work with. I would understand if there are negative repercussions of this change that would outweigh the potential utility. Thanks!

Originally posted by @erikglee in #2061 (comment)

I think the main repercussion is that working directories could stop being reusable with an upgrade in nipype. If there's general sentiment in this direction, I think we could do it in a minor release.