Mercurial > repos > greg > create_streamlines

comparison create_streamlines.py @ 3:51263bfe7b2c draft

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author greg
date Tue, 28 Nov 2017 14:23:27 -0500
parents 1c5508f627ec
children 3b5e09c727f5
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2:ef9b4bf2e9a4 3:51263bfe7b2c
27 27
28 hardi_img, gtab, labels_img = read_stanford_labels() 28 hardi_img, gtab, labels_img = read_stanford_labels()
29 data = hardi_img.get_data() 29 data = hardi_img.get_data()
30 labels = labels_img.get_data() 30 labels = labels_img.get_data()
31 31
32 if args.drmi_dataset == 'stanford_t1': 32 # For possible later use: if args.drmi_dataset == 'stanford_t1':
33 fetch_stanford_t1() 33 fetch_stanford_t1()
34 t1 = read_stanford_t1() 34 t1 = read_stanford_t1()
35 t1_data = t1.get_data() 35 t1_data = t1.get_data()
36 white_matter = (labels == 1) | (labels == 2) 36 white_matter = (labels == 1) | (labels == 2)
37 csamodel = shm.CsaOdfModel(gtab, 6) 37 csamodel = shm.CsaOdfModel(gtab, 6)
38 csapeaks = peaks.peaks_from_model(model=csamodel, data=data, sphere=peaks.default_sphere, relative_peak_threshold=.8, min_separation_angle=45, mask=white_matter) 38 csapeaks = peaks.peaks_from_model(model=csamodel, data=data, sphere=peaks.default_sphere, relative_peak_threshold=.8, min_separation_angle=45, mask=white_matter)
39 seeds = utils.seeds_from_mask(white_matter, density=2) 39 seeds = utils.seeds_from_mask(white_matter, density=2)