hMRI-group / hMRI-toolbox

A toolbox for quantitative MRI and in vivo histology using MRI (hMRI)
GNU General Public License v2.0
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Make hMRI toolbox compatible with BIDS #20

Open nbeliy opened 3 years ago

nbeliy commented 3 years ago

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:

Cons:

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:

lukeje commented 1 year ago

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