Could not create report with --group-by desc

[htwangtw]

The only valid option seems to be --group-by seg desc

If this is the case the CLI input can perhaps be simplified!

[HippocampusGirl]

I think my idea was to have support for custom BIDS tags as well, like is used in HALFpipe for multiverse pipelines (but that is maybe a very niche use case). I agree that it would be nice to simplify this

[htwangtw]

That would make sense actually!

If that's the case, it might be useful to allow any generic tag.
I am setting my Tuesday mornings to work on this for the summer so can have a look at it then

[htwangtw]

Looking into this further and played around with the configurations, I learned that the metrics can be grouped by any entities but seg. For reproducing the PLOS compbio paper, I would inclined to make desc (where giga connectome dumps the denoising strategy name), along with seg as the default groups regardless of the user inputs. Hence group-by would take optional entities only, such as task, session, subject, etc.

The --seg-to-atlas argument is big and error prone. The current workflow will need all the seg name and file path for things to work. As for now I would implement something that raise warning and skip when the seg-path pair is not provided. Later I can think of how to simplify the CLI.