Mercurial > repos > greg > diffusion_signal_reconstruction

comparison diffusion_signal_reconstruction.py @ 11:bca3ded6d5cc 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 08:56:23 -0500
parents 7bcc39c8ccfd
children 361bdd5fa8bc
comparison
equal deleted inserted replaced
10:7bcc39c8ccfd 11:bca3ded6d5cc
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 for f in os.list_dir(args.input_extra_files_path): 57 for f in os.listdir(args.input_extra_files_path):
58 shutil.copy(os.path.join(args.input_extra_files_path, f), input_dir) 58 shutil.copy(os.path.join(args.input_extra_files_path, f), input_dir)
59 img, gtab = read_stanford_hardi() 59 img, gtab = read_stanford_hardi()
60 60
61 data = img.get_data() 61 data = img.get_data()
62 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)