Mercurial > repos > greg > diffusion_signal_reconstruction

comparison diffusion_signal_reconstruction.py @ 12:361bdd5fa8bc draft default tip

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author greg
date Thu, 30 Nov 2017 09:02:37 -0500
parents bca3ded6d5cc
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11:bca3ded6d5cc 12:361bdd5fa8bc
75 fa = fractional_anisotropy(tenfit.evals) 75 fa = fractional_anisotropy(tenfit.evals)
76 fa[numpy.isnan(fa)] = 0 76 fa[numpy.isnan(fa)] = 0
77 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine) 77 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine)
78 nibabel.save(fa_img, 'output_fa.nii') 78 nibabel.save(fa_img, 'output_fa.nii')
79 shutil.move('output_fa.nii', args.output_nifti1_fa) 79 shutil.move('output_fa.nii', args.output_nifti1_fa)
80 move_directory_files(input_dir, args.output_nifti1_fa_files_path) 80 move_directory_files(input_dir, args.output_nifti1_fa_files_path, copy=True)
81 81
82 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine) 82 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine)
83 nibabel.save(evecs_img, 'output_evecs.nii') 83 nibabel.save(evecs_img, 'output_evecs.nii')
84 shutil.move('output_evecs.nii', args.output_nifti1_evecs) 84 shutil.move('output_evecs.nii', args.output_nifti1_evecs)
85 move_directory_files(input_dir, args.output_nifti1_evecs_files_path) 85 move_directory_files(input_dir, args.output_nifti1_evecs_files_path, copy=True)
86 86
87 md1 = dti.mean_diffusivity(tenfit.evals) 87 md1 = dti.mean_diffusivity(tenfit.evals)
88 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii') 88 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii')
89 shutil.move('output_md.nii', args.output_nifti1_md) 89 shutil.move('output_md.nii', args.output_nifti1_md)
90 move_directory_files(input_dir, args.output_nifti1_md_files_path) 90 move_directory_files(input_dir, args.output_nifti1_md_files_path, copy=True)
91 91
92 fa = numpy.clip(fa, 0, 1) 92 fa = numpy.clip(fa, 0, 1)
93 rgb = color_fa(fa, tenfit.evecs) 93 rgb = color_fa(fa, tenfit.evecs)
94 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii') 94 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii')
95 shutil.move('output_rgb.nii', args.output_nifti1_rgb) 95 shutil.move('output_rgb.nii', args.output_nifti1_rgb)
96 move_directory_files(input_dir, args.output_nifti1_rgb_files_path) 96 move_directory_files(input_dir, args.output_nifti1_rgb_files_path, copy=True)
97 97
98 sphere = get_sphere('symmetric724') 98 sphere = get_sphere('symmetric724')
99 ren = fvtk.ren() 99 ren = fvtk.ren()
100 100
101 evals = tenfit.evals[13:43, 44:74, 28:29] 101 evals = tenfit.evals[13:43, 44:74, 28:29]