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comparison dmri.py @ 37:d9c4ef2ee7c6 draft

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author greg
date Thu, 30 Nov 2017 10:51:01 -0500
parents 501221517d3f
children b054adc68274
comparison
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36:501221517d3f 37:d9c4ef2ee7c6
32 shutil.move(source_entry, destination_directory) 32 shutil.move(source_entry, destination_directory)
33 if remove_source_dir: 33 if remove_source_dir:
34 os.rmdir(source_directory) 34 os.rmdir(source_directory)
35 35
36 # Get input data. 36 # Get input data.
37 input_dir = args.drmi_dataset 37 input_dir = 'stanford_hardi'
38 if input_dir == 'stanford_hardi': 38 if args.drmi_dataset == 'stanford_hardi':
39 if args.drmi_dataset_type == "dataset": 39 if args.drmi_dataset_type == "dataset":
40 fetch_stanford_hardi() 40 fetch_stanford_hardi()
41 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz') 41 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
42 fbval = os.path.join(input_dir, 'HARDI150.bval') 42 fbval = os.path.join(input_dir, 'HARDI150.bval')
43 fbvec = os.path.join(input_dir, 'HARDI150.bvec') 43 fbvec = os.path.join(input_dir, 'HARDI150.bvec')
46 img, gtab, labels = read_stanford_labels() 46 img, gtab, labels = read_stanford_labels()
47 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz') 47 fdwi = os.path.join(input_dir, 'HARDI150.nii.gz')
48 fbval = os.path.join(input_dir, 'HARDI150.bval') 48 fbval = os.path.join(input_dir, 'HARDI150.bval')
49 fbvec = os.path.join(input_dir, 'HARDI150.bvec') 49 fbvec = os.path.join(input_dir, 'HARDI150.bvec')
50 else: 50 else:
51 # input_dir == 'stanford_t1 51 # args.drmi_dataset == 'stanford_t1
52 fetch_stanford_t1() 52 fetch_stanford_t1()
53 fdwi = os.path.join(input_dir, 't1.nii.gz') 53 fdwi = os.path.join(input_dir, 't1.nii.gz')
54 fbval = os.path.join(input_dir, 't1.bval') 54 fbval = os.path.join(input_dir, 't1.bval')
55 fbvec = os.path.join(input_dir, 't1.bvec') 55 fbvec = os.path.join(input_dir, 't1.bvec')
56 img = nibabel.load(fdwi) 56 img = nibabel.load(fdwi)