Subject-specific parameters

[glatard]

Users should be able to enter subject-specific parameters to a pipeline execution. After discussion with @pbellec and @poquirion, this will be implemented by:

• [ ] extending PSOM so that it can load a "fine-tuning" parameter configuration file that contains all the subject-specific params.
• [ ] adding this parameter file as an input of the pipelines in CBRAIN.
• [ ] add a validation tool to check parameter files before pipelines are launched. This validation tool could be integrated in the same way as the BIDS validator. It would allow users to tag invalid parameter files.

[poquirion]

The easiest thing would be to directly have a .m file that can control subjects parameters. But I don't know how we will validate the code. Another possibilité is to have a csv (or tsv) that that has the following structure:

sub_number, option_name, value 
sub_number, option_name, value 
[...]

This would be easier to validate.

In any case there will be a version of the input file saved every time the pipeline is ran with that file.

[poquirion]

I have a made a yaml parser for that purpose it exist in the niak bids-app branch:

there is two config type: group and subject:

group
  option1: x
  option2
    type1: y
    type3: x
1-3
  option3: z
5
  option4: xx

is equivalent to

opt.option1 = x 
opt.option2.type1 = y
opt.option2.type2 = z
opt.tune(1).subject = 'subject_0001'
opt.tune(1).option3 = z
opt.tune(2).subject = 'subject_0002'
opt.tune(2).option3 = z
opt.tune(3).subject = 'subject_0003'
opt.tune(3).option3 = z
opt.tune(5).subject = 'subject_0005'
opt.tune(5).option4 = xx