Mercurial > repos > greg > drmi

comparison dmri.py @ 30:6c1fd6d2c07e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 30 Nov 2017 09:39:31 -0500
parents 6e7ed2b633dc
children 221c1fe8be2c
comparison
equal deleted inserted replaced
29:da507620bd74 30:6c1fd6d2c07e
10 10
11 import nibabel 11 import nibabel
12 12
13 parser = argparse.ArgumentParser() 13 parser = argparse.ArgumentParser()
14 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset') 14 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset')
15 parser.add_argument('--drmi_dataset_type', dest='drmi_dataset_type', help='Input dataset type')
15 parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset') 16 parser.add_argument('--output_nifti1', dest='output_nifti1', help='Output Nifti1 dataset')
16 parser.add_argument('--output_nifti1_extra_files', dest='output_nifti1_extra_files', help='Output Nifti1 extra files') 17 parser.add_argument('--output_nifti1_extra_files', dest='output_nifti1_extra_files', help='Output Nifti1 extra files')
17 parser.add_argument('--output_png', dest='output_png', help='Output dataset') 18 parser.add_argument('--output_png', dest='output_png', help='Output dataset')
18 19
19 args = parser.parse_args() 20 args = parser.parse_args()
32 if remove_source_dir: 33 if remove_source_dir:
33 os.rmdir(source_directory) 34 os.rmdir(source_directory)
34 35
35 # Get input data. 36 # Get input data.
36 input_dir = args.drmi_dataset 37 input_dir = args.drmi_dataset
37 if input_dir == 'stanford_hardi': 38 #if input_dir == 'stanford_hardi':
39 if args.drmi_dataset_type == "dataset":
38 fetch_stanford_hardi() 40 fetch_stanford_hardi()
39 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz') 41 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
40 fbval = os.path.join(input_dir, 'HARDI150.bval') 42 fbval = os.path.join(input_dir, 'HARDI150.bval')
41 fbvec = os.path.join(input_dir, 'HARDI150.bvec') 43 fbvec = os.path.join(input_dir, 'HARDI150.bvec')
42 elif input_dir == 'sherbrooke_3shell': 44 img = nibabel.load(fdwi)
43 fetch_sherbrooke_3shell() 45 else:
44 fdwi = os.path.join(input_dir, 'HARDI193.nii.gz') 46 img, gtab, labels = read_stanford_labels()
45 fbval = os.path.join(input_dir, 'HARDI193.bval')
46 fbvec = os.path.join(input_dir, 'HARDI193.bvec')
47 # Load the dMRI datasets.
48 img = nibabel.load(fdwi)
49 data = img.get_data() 47 data = img.get_data()
50 # data is a 4D array where the first 3 dimensions are the i, j, 48 # data is a 4D array where the first 3 dimensions are the i, j,
51 # k voxel coordinates and the last dimension is the number of 49 # k voxel coordinates and the last dimension is the number of
52 # non-weighted (S0s) and diffusion-weighted volumes. 50 # non-weighted (S0s) and diffusion-weighted volumes.
53 # Visualize the results using matplotlib. 51 # Visualize the results using matplotlib.