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#!/usr/bin/env python3
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
__doc__ = """
Example showing how to use the parcel generator.
We load an image with ROI definitions and calculate the number of voxels in each
ROI.
"""
print(__doc__)
from os.path import dirname
from os.path import join as pjoin
import nipy
from nipy.core.utils.generators import parcels
OUR_PATH = dirname(__file__)
DATA_PATH = pjoin(OUR_PATH, '..', 'data')
BG_IMAGE_FNAME = pjoin(DATA_PATH, 'mni_basal_ganglia.nii.gz')
bg_img = nipy.load_image(BG_IMAGE_FNAME)
bg_data = bg_img.get_fdata()
"""
I happen to know that the image has these codes:
14 - Left striatum
16 - Right striatum
39 - Left caudate
53 - Right caudate
All the other voxels are zero, I don't want those.
"""
print("Number of voxels for L, R striatum; L, R caudate")
for mask in parcels(bg_data, exclude=(0,)):
print(mask.sum())
""" Given we know the codes we can also give them directly """
print("Again with the number of voxels for L, R striatum; L, R caudate")
for mask in parcels(bg_data, labels=(14, 16, 39, 53)):
print(mask.sum())
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