import nibabel as ni
import osmosis.model.analysis as oza
import osmosis.model.sparse_deconvolution as ssd
import osmosis.model.dti as dti
import osmosis.viz.maya as viz
import osmosis.wm_mask as wm_mask
/usr/lib/python2.7/dist-packages/nose/util.py:14: DeprecationWarning: The compiler package is deprecated and removed in Python 3.x. from compiler.consts import CO_GENERATOR
import os
import osmosis as oz
import osmosis.io as oio
oio.data_path = os.path.join(oz.__path__[0], 'data')
subject = 'HT'
data_2k_1, data_2k_2 = oio.get_dwi_data(2000, subject)
seg_path = '%s/%s/%s_t1_class.nii.gz'%(oio.data_path, subject, subject)
dwi = dti.TensorModel(*data_2k_1, params_file='temp')
out_path = '%s/%s/%s_wm_mask.nii.gz'%(oio.data_path, subject, subject)
Loading from file: /home/arokem/usr/lib/python2.7/site-packages/osmosis/data/HT/0015_01_DTI_2mm_b2000_150dir_aligned_trilin.bvals Loading from file: /home/arokem/usr/lib/python2.7/site-packages/osmosis/data/HT/0015_01_DTI_2mm_b2000_150dir_aligned_trilin.bvecs
wm_mask.make_wm_mask(seg_path, dwi, out_path)
Loading from file: /home/arokem/usr/lib/python2.7/site-packages/osmosis/data/HT/0015_01_DTI_2mm_b2000_150dir_aligned_trilin.nii.gz Fitting TensorModel params using dipy
vol_anat = oio.get_t1(subject, resample=ni.load(oio.data_path + '/%s/%s_wm_mask.nii.gz'%(subject, subject)))
vol_mask = ni.load(out_path).get_data()
vol_mask[vol_mask<1] = np.nan
%gui wx
viz.plot_cut_planes(vol_anat,
overlay=vol_mask,
overlay_cmap="RdYlGn",
slice_coronal=40,
slice_saggital=15,
slice_axial=30,
view_azim=-40,
view_elev=60)
Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x9358cb0> Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x84fa9b0> Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x8506cb0> Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x8514d70> Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x84a6410> Cannot set extents for <mayavi.modules.image_plane_widget.ImagePlaneWidget object at 0x84a5710>
<mayavi.core.scene.Scene at 0x9333ad0>