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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4 import nibabel
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5 import shutil
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6
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7 from dipy.data import fetch_sherbrooke_3shell
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11
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8 from matplotlib import pyplot
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9
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10 parser = argparse.ArgumentParser()
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11 parser.add_argument('--input', dest='input', help='Input dataset')
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12 parser.add_argument('--output', dest='output', help='Output dataset')
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13
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14 args = parser.parse_args()
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15
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10
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16 input_dir = 'sherbrooke_3shell'
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9
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17 # Get input data.
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18 fetch_sherbrooke_3shell()
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19 fdwi = os.path.join(input_dir, 'HARDI193.nii.gz')
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20 fbval = os.path.join(input_dir, 'HARDI193.bval')
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21 fbvec = os.path.join(input_dir, 'HARDI193.bvec')
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22 # Load the dMRI datasets.
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23 img = nibabel.load(fdwi)
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24 data = img.get_data()
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25 # data is a 4D array where the first 3 dimensions are the i, j,
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26 # k voxel coordinates and the last dimension is the number of
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27 # non-weighted (S0s) and diffusion-weighted volumes.
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28 # Visualize the results using matplotlib.
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29 axial_middle = data.shape[2] // 2
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30 pyplot.figure('Showing the datasets')
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31 pyplot.subplot(1, 2, 1).set_axis_off()
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32 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
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33 pyplot.subplot(1, 2, 2).set_axis_off()
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34 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
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35 pyplot.savefig('data.png', bbox_inches='tight')
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36 shutil.move('data.png', args.output)
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