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Until now we have discussed pros and cons of different concepts and features in BEP028. The few use cases implemented as sidecar .jsonld files corresponding to standard examples. To go a little bit deeper and foster a broader range of users we would like to formulate real-life examples and discuss their implementation with the current standard
First set of user stories
As a researcher I'd like to found out which realignment algorithm was applied in order to understand how it affects my final results
As an SPM developper implementing the BIDS-PROv export I'd like to get a list of all activities in order to verify that it is consistent with my matlabbatch script.
As an SPM user I'd like to visualize the BIDSProv graph corresponding to my matlabbtach file in order to get a visual representation of my pipeline (for example to be shared in a paper).
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Could you share with us (in a comment below), what would be your favorite way(s) of using the info available in BIDS-Prov (i.e. a description of the pipeline that was applied to a given dataset)? Thank you!
For investigation of megaverse analysies, a comprensive representation of all the options in all the different packages. This is both for the 'recording keeping' aspect, and also to have a formal structure to 'parameterise' the possible differences for prospective investigations (i.e. choosing which elements of a pipeline to manipulate).
Echoing @tiborauer, conducting meta-analystic reviews of methods used, and then (for a set of studies all investigating the same task) proping the systematic differences in the results as explained by methodological differences extracted from BIDS-Prov.
@cmaumet - thanks for starting this. after we settle on a list it may be useful to cast them into a priority survey.
even the starting bids dataset is a derivative and has provenance. so this would at least tell us how a bids dataset was generated and could identify issues with scanners, dicom conversion, datalad, heudiconv/other converters.
more practical issues
link entities to other entities they were derived from. right now this doesn't exist in BIDS.
Find software used. Make methods searchable and visualizable
Find transformers that generated a given file. (right now this is at the whole derivatives level, bids-prov could potentially give us more granularity)
visualize analyses steps
Generate COBIDAS compliant report
Query parameters of any pipeline
more advanced use cases:
Determine impact of different parameters and environment on results (this is related to the meta analysis issue)
determine what pipelines can produce entity X and what inputs are required for that pipeline.
Discover related transforms/pipelines/analyses
Generate diffs between two pipelines
Regenerate analyses from prov record
ps. i'm leaning towards using the term transform instead of pipeline, but in my head they are synonymous.