Pertains to some thoughts #12, but opening a specific issue for BIDS. Unlike #12, I don't think niimasker should be specific to fmriprep.
Currently, BIDS input is not required. However this limits what we can provide in reports (i.e. having one report per subject, rather than per input file--which is wayyyy too many).
As well, niimasker puts all the timeseries files in one output directory, which can be messy with many subjects. Following BIDS would mean that this output could also be in BIDS format (whenever I use niimasker, I always end up writing a script that does this anyways).
I've found pybids to be a bit flakey in the past, but if niimasker requires BIDS, inputs should be validated.
Pertains to some thoughts #12, but opening a specific issue for BIDS. Unlike #12, I don't think niimasker should be specific to fmriprep.
Currently, BIDS input is not required. However this limits what we can provide in reports (i.e. having one report per subject, rather than per input file--which is wayyyy too many).
As well, niimasker puts all the timeseries files in one output directory, which can be messy with many subjects. Following BIDS would mean that this output could also be in BIDS format (whenever I use niimasker, I always end up writing a script that does this anyways).
I've found pybids to be a bit flakey in the past, but if niimasker requires BIDS, inputs should be validated.