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Examples using API
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A rough example of usage when using the graynet API is shown below. However, we recommend using the command line interface given it is geared towards batch processing on HPC clusters and there is a `script <https://github.com/raamana/graynet/blob/master/scripts/generate_hpc_jobs.py>`_ to help you with large amount of processing.


.. code-block:: python


    import graynet
    import os

    base_project_dir = '/project/mydataset'
    input_dir = os.path.join(base_project_dir, 'freesurfer_v5.3')
    base_feature = 'thickness' # 'gmdensity', 'curv' or 'sulc' or 'gyrification'
    fwhm = 10
    atlas = 'GLASSER2016'
    patch_size = 'default' # number of vertices per patch in this case

    out_dir = os.path.join(base_project_dir, 'graynet', base_feature)

    graynet.extract(input_dir, base_feature, atlas, smoothing_param = fwhm, size = patch_size)