In [1]:
import analysis2 as a2
reload(a2)
Out[1]:
<module 'analysis2' from 'analysis2.pyc'>
In [2]:
import SimpleITK as sitk
In [3]:
from ndreg import *
import matplotlib
import ndio.remote.neurodata as neurodata
In [4]:
raw_s275 = sitk.ReadImage('/home/s275.nii')
In [5]:
ara3_atlas = sitk.ReadImage('/home/ara3.nii')
In [ ]:
ara3_annotations = sitk.ReadImage('/home/ara3_annotation.nii')
In [ ]:
inImg_lddmm, refAnnoImg = a2.register('s275', '/home/userToken.pem', 'IAL', raw_im = raw_s275, atlas=ara3_atlas, annotate=ara3_annotations);
Getting data from server...
(804, 979, 1114)
(1140, 800, 1320)
Finished data acquisition...
100
[0 0 0 ..., 0 0 1]
lower and upper thresholds:
100
63823
Begin CLARITY mask generation...
Begin affine transformation...
(56, 81, 98)
(114, 80, 132)
Step translation:
0. -0.112719540338
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Step scale:
0. -0.249186893234
1. -0.254721048378
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3. -0.284763018056
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Step rigid:
0. -0.277921104027
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99. -0.269834992795
Step affine:
0. -0.269113043198
1. -0.26738587891
2. -0.284953410045
3. -0.292871075121
4. -0.300539163913
5. -0.303800412264
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Begin LDDMM...
Step 0: alpha=0.05, beta=0.05, scale=1.0
In [ ]:
imShow(inImg_lddmm, vmax=1000);
In [ ]:
Content source: NeuroDataDesign/seelviz
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