Examples using API

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 to help you with large amount of processing.

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)