Make hMRI toolbox compatible with BIDS

[nbeliy]

Dear developers, can you make the toolbox compatible with datasets folowing BIDS?

The problem comes when toolbox tries to extract metadata for images from sidecar json and expects to find hMRI structure. When it fails, the defaults are used.

I see two posiibilities to make toolbox compatible:

1. Retrieve the metadata from json in bids

Make get_metadata_val function a front-end, which checks if acqpar is present in json structure, if so call the get_metadata_val_classic witch retrieves the hMRI parameters, else calls get_metadata_val_bids retrieving bids metadata.

Pros:

• Non invasive, should be immediately compatible with toolbox without further adjustments
• Easy to implement

Cons:

• Not all hMRI metadata has corresponding field in bids json, for example B1FAValues
• Some values may be defined differently, for ex ReadoutDuration in BIDS uses FSL definition and not SPM one.

2. Allow user to pass parameters directly from batch script

In batch interface add a menu called something like "Processing parameters", where user can add parameter in form: <key> <value> where key is hMRI metadata name, and value corresponds to value.

Then get_metadata_val checks first in these parameters and if it fails checks in json structure.

Pros:

• Add flexibility to processing data, allow to pass key parameters dynamically even if image files has no metadada

  Cons:

• Need to adapt all hMRI tools

[lukeje]

There is a now a wiki page to document the current status of BIDS compatibility: https://github.com/hMRI-group/hMRI-toolbox/wiki/BIDS