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1 #!/usr/bin/env python
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2 import argparse
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3 import shutil
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4
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5 from dipy.data import fetch_sherbrooke_3shell
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6 from dipy.data import fetch_stanford_hardi
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7 from dipy.data import get_sphere
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8 from dipy.data import read_sherbrooke_3shell
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9 from dipy.data import read_stanford_hardi
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10 from dipy.reconst import dti
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11 from dipy.reconst.dti import color_fa
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12 from dipy.reconst.dti import fractional_anisotropy
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13 from dipy.segment.mask import median_otsu
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14 from dipy.viz import fvtk
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15 from matplotlib import pyplot
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16
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17 import nibabel
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18 import numpy
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19
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20 # http://nipy.org/dipy/examples_built/reconst_dti.html#example-reconst-dti
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21 parser = argparse.ArgumentParser()
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22 parser.add_argument('--drmi_dataset', dest='drmi_dataset', help='Input dataset')
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23 parser.add_argument('--output_nifti1_fa', dest='output_nifti1_fa', help='Output fractional anisotropy Nifti1 dataset')
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24 parser.add_argument('--output_nifti1_evecs', dest='output_nifti1_evecs', help='Output eigen vectors Nifti1 dataset')
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25 parser.add_argument('--output_nifti1_md', dest='output_nifti1_md', help='Output mean diffusivity Nifti1 dataset')
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26 parser.add_argument('--output_nifti1_rgb', dest='output_nifti1_rgb', help='Output RGB-map Nifti1 dataset')
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27 parser.add_argument('--output_png_ellipsoids', dest='output_png_ellipsoids', help='Output ellipsoids PNG dataset')
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28 parser.add_argument('--output_png_odfs', dest='output_png_odfs', help='Output orientation distribution functions PNG dataset')
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29 parser.add_argument('--output_png_middle_axial_slice', dest='output_png_middle_axial_slice', help='Output middle axial slice PNG dataset')
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30
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31 args = parser.parse_args()
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32
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33 # Get input data.
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34 input_dir = args.drmi_dataset
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35 if input_dir == 'sherbrooke_3shell':
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36 fetch_sherbrooke_3shell()
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37 img, gtab = read_sherbrooke_3shell()
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38 elif input_dir == 'stanford_hardi':
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39 fetch_stanford_hardi()
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40 img, gtab = read_stanford_hardi()
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41
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42 data = img.get_data()
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43 maskdata, mask = median_otsu(data, 3, 1, True, vol_idx=range(10, 50), dilate=2)
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44
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45 axial_middle = data.shape[2] // 2
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46 pyplot.subplot(1, 2, 1).set_axis_off()
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47 pyplot.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
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48 pyplot.subplot(1, 2, 2).set_axis_off()
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49 pyplot.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
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50 pyplot.savefig('middle_axial.png', bbox_inches='tight')
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51 shutil.move('middle_axial.png', args.output_png_middle_axial_slice)
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52
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53 tenmodel = dti.TensorModel(gtab)
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54 tenfit = tenmodel.fit(maskdata)
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55
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56 fa = fractional_anisotropy(tenfit.evals)
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57 fa[numpy.isnan(fa)] = 0
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58 fa_img = nibabel.Nifti1Image(fa.astype(numpy.float32), img.affine)
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59 nibabel.save(fa_img, 'output_fa.nii')
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60 shutil.move('output_fa.nii', args.output_nifti1_fa)
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61
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62 evecs_img = nibabel.Nifti1Image(tenfit.evecs.astype(numpy.float32), img.affine)
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63 nibabel.save(evecs_img, 'output_evecs.nii')
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64 shutil.move('output_evecs.nii', args.output_nifti1_evecs)
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65
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66 md1 = dti.mean_diffusivity(tenfit.evals)
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67 nibabel.save(nibabel.Nifti1Image(md1.astype(numpy.float32), img.affine), 'output_md.nii')
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68 shutil.move('output_md.nii', args.output_nifti1_md)
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69
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70 fa = numpy.clip(fa, 0, 1)
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71 rgb = color_fa(fa, tenfit.evecs)
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72 nibabel.save(nibabel.Nifti1Image(numpy.array(255 * rgb, 'uint8'), img.affine), 'output_rgb.nii')
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73 shutil.move('output_rgb.nii', args.output_nifti1_rgb)
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74
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75 sphere = get_sphere('symmetric724')
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76 ren = fvtk.ren()
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77
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78 evals = tenfit.evals[13:43, 44:74, 28:29]
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79 evecs = tenfit.evecs[13:43, 44:74, 28:29]
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80 cfa = rgb[13:43, 44:74, 28:29]
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81 cfa /= cfa.max()
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82 fvtk.add(ren, fvtk.tensor(evals, evecs, cfa, sphere))
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83 fvtk.record(ren, n_frames=1, out_path='tensor_ellipsoids.png', size=(600, 600))
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84 shutil.move('tensor_ellipsoids.png', args.output_png_ellipsoids)
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85
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86 fvtk.clear(ren)
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87
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88 tensor_odfs = tenmodel.fit(data[20:50, 55:85, 38:39]).odf(sphere)
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89 fvtk.add(ren, fvtk.sphere_funcs(tensor_odfs, sphere, colormap=None))
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90 fvtk.record(ren, n_frames=1, out_path='tensor_odfs.png', size=(600, 600))
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91 shutil.move('tensor_odfs.png', args.output_png_odfs)
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