Creating a default model

It is possible to write a “first draft” for your model by using Pybids or bids-matlab.

See below for code snippet showing how to do it with each package.

PyBIDS - auto_model

PyBIDS currently represents models as dictionaries. To generate a default model dictionary, use bids.modeling.auto_model(), and then use json.dump() to save it to a file.

from bids import BIDSLayout
from bids.modeling import auto_model
import json

# indexing the dataset
layout = BIDSLayout(path_to_dataset)

# creating the default model
model = auto_model(layout, one_vs_rest=True)

# saving to a JSON file
with open("model-default_smdl.json", "w") as outfile:
    json.dump(model[0], outfile, indent=2)

BIDS-MATLAB - Model.default

BIDS-MATLAB provides similar functionality through +bids.Model.default():

% indexing the dataset
BIDS = bids.layout(path_to_dataset);

% create an empty model
bm = bids.Model();
% creating the default model for our dataset
bm = bm.default(BIDS);

% saving to a JSON file
filename = fullfile(pwd, 'model-default_smdl.json');
bm.write(filename);