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comparison dmri.py @ 8:a0d57df923d2 draft

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Uploaded
author greg
date Fri, 03 Nov 2017 13:33:58 -0400
parents 2b6708bc9391
children cf847e9f1a3a
comparison
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7:2b6708bc9391 8:a0d57df923d2
23 shutil.copy(source_entry, destination_directory) 23 shutil.copy(source_entry, destination_directory)
24 else: 24 else:
25 shutil.move(source_entry, destination_directory) 25 shutil.move(source_entry, destination_directory)
26 if remove_source_dir: 26 if remove_source_dir:
27 os.rmdir(source_directory) 27 os.rmdir(source_directory)
28
29 input_dir = 'input_dir'
30 # Get input data.
31 fetch_sherbrooke_3shell()
32 # MNove inputs to working directory.
33 source_dir = os.path.abspath(os.path.join('home', 'greg', '.dipy', 'sherbrooke_3shell')) 28 source_dir = os.path.abspath(os.path.join('home', 'greg', '.dipy', 'sherbrooke_3shell'))
34 move_directory_files(source_dir, input_dir) 29 dest_dir = 'input_dir'
35 fdwi = os.path.join(input_dir, 'HARDI193.nii.gz') 30 if not os.path.exists(source_dir):
36 fbval = os.path.join(input_dir, 'HARDI193.bval') 31 # Get input data.
37 fbvec = os.path.join(input_dir, 'HARDI193.bvec') 32 fetch_sherbrooke_3shell()
33 # Move inputs to working directory.
34 move_directory_files(source_dir, dest_dir, copy=True)
35 fdwi = os.path.join(dest_dir, 'HARDI193.nii.gz')
36 fbval = os.path.join(dest_dir, 'HARDI193.bval')
37 fbvec = os.path.join(dest_dir, 'HARDI193.bvec')
38 # Load the dMRI datasets. 38 # Load the dMRI datasets.
39 img = nibabel.load(fdwi) 39 img = nibabel.load(fdwi)
40 data = img.get_data() 40 data = img.get_data()
41 # data is a 4D array where the first 3 dimensions are the i, j, 41 # data is a 4D array where the first 3 dimensions are the i, j,
42 # k voxel coordinates and the last dimension is the number of 42 # k voxel coordinates and the last dimension is the number of