In [1]:

    

import numpy as np
import nibabel as nib
import dipy.reconst.dti as dti
from dipy.data import fetch_stanford_hardi, read_stanford_hardi
from dipy.reconst.dti import quantize_evecs
from dipy.data import get_sphere
from dipy.reconst.dti import fractional_anisotropy, color_fa, lower_triangular
from dipy.segment.mask import median_otsu
from dipy.tracking.eudx import EuDX
from dipy.io.trackvis import save_trk


    

    




/home/jyeatman/anaconda/lib/python2.7/site-packages/skimage/filter/__init__.py:6: skimage_deprecation: The `skimage.filter` module has been renamed to `skimage.filters`.  This placeholder module will be removed in v0.13.
  warn(skimage_deprecation('The `skimage.filter` module has been renamed '

In [5]:

    

fetch_stanford_hardi()


    

    




Creating new directory /home/jyeatman/.dipy/stanford_hardi
Downloading raw HARDI data (87MB)...
Done.
Files copied in folder /home/jyeatman/.dipy/stanford_hardi

In [6]:

    

img, gtab = read_stanford_hardi()
data = img.get_data()


    

In [7]:

    

maskdata, mask = median_otsu(data, 3, 1, True,
                             vol_idx=range(10, 50), dilate=2)


    

In [8]:

    

tenmodel = dti.TensorModel(gtab)
tenfit = tenmodel.fit(maskdata)


    

In [9]:

    

FA = fractional_anisotropy(tenfit.evals)
FA[np.isnan(FA)] = 0
evecs = tenfit.evecs
fa_img = nib.Nifti1Image(FA.astype(np.float32), img.get_affine())


    

In [10]:

    

sphere = get_sphere('symmetric724')
peak_indices = quantize_evecs(evecs, sphere.vertices)
eu = EuDX(FA.astype('f8'), peak_indices, seeds=5000000, odf_vertices = sphere.vertices, a_low=0.2)

tensor_streamlines = [streamline for streamline in eu]


    

    




/home/jyeatman/git/dipy/dipy/reconst/dti.py:1802: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if odf_vertices == None:

In [14]:

    

#save_trk("./tensor_streamlines.trk", tensor_streamlines, fa_img.get_affine(), FA.shape)


    

In [11]:

    

len(tensor_streamlines)


    

    
Out[11]:





977354

In [1]:

    

tensor_streamlines[1000]


    

    




---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-1f73f118643b> in <module>()
----> 1 tensor_streamlines[1000]

NameError: name 'tensor_streamlines' is not defined

In [12]:

    

hdr = nib.trackvis.empty_header()
hdr['voxel_size'] = img.get_header().get_zooms()[:3]
hdr['voxel_order'] = 'RAS'
hdr['dim'] = FA.shape
hdr['vox_to_ras'] = img.get_affine()
tensor_streamlines_trk = ((sl, None, None) for sl in tensor_streamlines)
ten_sl_fname = 'tensor_streamlines.trk'
nib.trackvis.write(ten_sl_fname, tensor_streamlines_trk, hdr, points_space='rasmm')


    

In [13]:

    

hdr


    

    
Out[13]:





array(('TRACK', [71, 87, 62], [2.0, 2.0, 2.0], [0.0, 0.0, 0.0], 0, ['', '', '', '', '', '', '', '', '', ''], 0, ['', '', '', '', '', '', '', '', '', ''], [[2.0, 0.0, 0.0, -80.0], [0.0, 2.0, 0.0, -120.0], [0.0, 0.0, 2.0, -60.0], [0.0, 0.0, 0.0, 1.0]], '', 'RAS', '', [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], '', '', '', '', '', '', '', 0, 2, 1000), 
      dtype=[('id_string', 'S6'), ('dim', '<i2', (3,)), ('voxel_size', '<f4', (3,)), ('origin', '<f4', (3,)), ('n_scalars', '<i2'), ('scalar_name', 'S20', (10,)), ('n_properties', '<i2'), ('property_name', 'S20', (10,)), ('vox_to_ras', '<f4', (4, 4)), ('reserved', 'S444'), ('voxel_order', 'S4'), ('pad2', 'S4'), ('image_orientation_patient', '<f4', (6,)), ('pad1', 'S2'), ('invert_x', 'S1'), ('invert_y', 'S1'), ('invert_z', 'S1'), ('swap_xy', 'S1'), ('swap_yz', 'S1'), ('swap_zx', 'S1'), ('n_count', '<i4'), ('version', '<i4'), ('hdr_size', '<i4')])

In [14]:

    

len(tensor_streamlines)


    

    
Out[14]:





977354

In [12]:

    

tensor_streamlines[0]


    

    
Out[12]:





array([[ 26.4841423 ,  38.62833023,  55.76271439],
       [ 26.57774162,  38.49172211,  55.29093552],
       [ 26.64459229,  38.38281631,  54.80754089],
       [ 26.67384911,  38.28636551,  54.31780243],
       [ 26.67930412,  38.199646  ,  53.82541275],
       [ 26.65811348,  38.11829758,  53.33252716],
       [ 26.60972404,  38.04495239,  52.84030914],
       [ 26.54303741,  37.99626923,  52.3471756 ],
       [ 26.45503044,  37.96047974,  51.8562851 ],
       [ 26.32678413,  37.92443085,  51.37435532],
       [ 26.16465759,  37.89036942,  50.90259933],
       [ 25.99437714,  37.88658905,  50.43250275],
       [ 25.81068993,  37.91730118,  49.96848297],
       [ 25.60430717,  37.9600296 ,  49.51507187],
       [ 25.38165474,  38.02501678,  49.07212448],
       [ 25.16344643,  38.09794235,  48.62820435],
       [ 24.94886398,  38.17311859,  48.18289185],
       [ 24.7429409 ,  38.25121307,  47.73400497],
       [ 24.54547119,  38.33713531,  47.28276062],
       [ 24.36642075,  38.44501495,  46.82855606],
       [ 24.2315464 ,  38.60185242,  46.37335205],
       [ 24.14370537,  38.82037354,  45.93229294],
       [ 24.07652092,  39.07571793,  45.50769424],
       [ 24.02395821,  39.34848022,  45.09195328],
       [ 23.98945999,  39.61047745,  44.66749191],
       [ 23.97363091,  39.85165405,  44.22978973],
       [ 23.97454834,  40.06808472,  43.77906036],
       [ 23.98659134,  40.24941254,  43.31325531],
       [ 24.00270653,  40.40057373,  42.83692551],
       [ 24.01823044,  40.55133438,  42.36044693],
       [ 24.03686523,  40.6929245 ,  41.88127518],
       [ 24.06965828,  40.79943085,  41.39385223],
       [ 24.11989784,  40.8843956 ,  40.90369415],
       [ 24.19494057,  40.98794556,  40.42032242],
       [ 24.29132271,  41.09959793,  39.94257355],
       [ 24.39356995,  41.21032715,  39.46583176],
       [ 24.52283669,  41.31397247,  38.9940834 ],
       [ 24.6780262 ,  41.41601562,  38.52985764],
       [ 24.83321571,  41.51805496,  38.06563568],
       [ 25.0146122 ,  41.60752869,  37.60837173],
       [ 25.17758369,  41.69558716,  37.14395142],
       [ 25.31911469,  41.82216263,  36.68140793],
       [ 25.46059608,  41.945755  ,  36.21804047],
       [ 25.59143639,  42.03065109,  35.74298859]])

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