UX-fMRIPrep (Options)

[Najmahan]

fMRI prep uses two prefixes for optional parameters:

--

Usually (for example in fsl tools) --parameter should be followed by a = to set teh value of a variable; while -parameter is an argument. In fmriprep this is not very consistent, and a lot of the parametrization depends on what is available in the BIDS folder. Therefore, it would be very helpful if the user can click on where they need to fill the field, and be given a list of the files in the BIDS directory, from which to select.

[prioux]

I don't understand. You've got a bullet point and a double dash? Do you mean - and -- ?

The options in the CBRAIN form are EXACTLY the same as the FMRIPrep tool itself, we're not going to change that. An experience FMRIPrep user will want ot see the options in CBRAIN with the same convention as the command-line tool.

I am not sure what you mean by 'depends on what is available in the BIDS folder'. But that being said it is not possible for the form to show any part of the input files, it doesn't have access to them (imagine that the BIDS data is a remote dataset in antoher province for instance, it's not possible to list the content live without synchronizing it all, which defeats the point of having distributed data)