Mercurial > repos > greg > diffusion_signal_reconstruction

comparison diffusion_signal_reconstruction.py @ 10:7bcc39c8ccfd draft

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author greg
date Thu, 30 Nov 2017 08:51:01 -0500
parents dc700deb06c1
children bca3ded6d5cc
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9:dc700deb06c1 10:7bcc39c8ccfd
52 52
53 # Get input data. 53 # Get input data.
54 # TODO: do not hard-code 'stanford_hardi' 54 # TODO: do not hard-code 'stanford_hardi'
55 input_dir = 'stanford_hardi' 55 input_dir = 'stanford_hardi'
56 os.mkdir(input_dir) 56 os.mkdir(input_dir)
57 input_dir = args.drmi_dataset
58 for f in os.list_dir(args.input_extra_files_path): 57 for f in os.list_dir(args.input_extra_files_path):
59 shutil.copy(f, input_dir) 58 shutil.copy(os.path.join(args.input_extra_files_path, f), input_dir)
60 fetch_stanford_hardi()
61 img, gtab = read_stanford_hardi() 59 img, gtab = read_stanford_hardi()
62 60
63 data = img.get_data() 61 data = img.get_data()
64 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2) 62 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
65 63