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EEG data conversion to BIDS

Wrapper around FieldTrip data2bids to facilitate conversion to BIDS.

Requirements

  • MATLAB - version ???? (not tested on Octave)
  • Fieldtrip - version ????
  • bids-matlab is already shipped as a library in the lib folder.

You can install Fieldtrip and update bids-matlab by running:

make install

Usage

Add the proper folder to the Matlab path. Running the init_env.m function will do this for you and also check that you have Fieldtrip installed.

Organize your source data

Rules

  • sujbect folder should start with a letter
  • run folders should start with the same prefix (in this case run)
  • one datafile per run folder
  • you can have one extra level for sessions (this folder can only include characters and/or numbers)
Example 
sourcedata
└── subject1
    ├── run1
    │   └── faces_run1.bdf
    └── run2
        └── faces_run2.bdf
Example with session level 
sourcedata
└── subject1
    └──day1
       ├── run1
       │   └── faces_run1.bdf
       └── run2
           └── faces_run2.bdf

You can use some of bids-matlab function to help you create this folder tree:

prfx = 'run';
subjects = {'BB1', 'sub-02', 'ReGa'};
sessions = {'day1', 'beh'};
runs = {[prfx '1'],[prfx '2'], [prfx '5']};

bids.util.mkdir('sourcedata', subjects, sessions, runs);

Will create this.

sourcedata
├── BB1
│   ├── beh
│   │   ├── run1
│   │   ├── run2
│   │   └── run5
│   └── day1
│       ├── run1
│       ├── run2
│       └── run5
├── ReGa
│   ├── beh
│   │   ├── run1
│   │   ├── run2
│   │   └── run5
│   └── day1
│       ├── run1
│       ├── run2
│       └── run5
└── sub-02
    ├── beh
    │   ├── run1
    │   ├── run2
    │   └── run5
    └── day1
        ├── run1
        ├── run2
        └── run5

Participant mapping

Create a TSV file that contains the information on how a given subject folder is mapped to a participant in the final BIDS data set.

The REQUIRED columns are label and source_folder, but it can contain extra info.

label	source_folder	age	gender	group	handedness
1	BB01	25	F	ctrl	r

Configuration

Create conversion_config.m file with the configuration details needed for the conversion. There is a template for this in the templates folder.

  cfg.run_folder_prefix = prefix_used_for_run_folder;
  cfg.extension = extension_of_the_data_file;

  cfg.bidsroot  = path_where_to_create_the_bids_data;
  cfg.source_data = path_to_the_source_data_is;

  cfg.participants_file = path_to_participant_map;

Run the conversion

init_env()
cfg = conversion_config();
convert_to_bids(cfg);

src/convert_to_bids.m which is a wrapper function around data2bids.m from Fieldtrip.

TODO

  • create a function to check the cfg structure content
  • labels cannot contain spaces otherwise we will have sub-01_task-foo bar_eeg.bdf and that's just not OK.
  • events.json not created
  • participants.json not created