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@chrisgorgo
Created September 25, 2012 18:23
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def plot_coregistration():
anat_file = "/Users/filo/data/rs_pipeline/GSDT/anat/mprage.nii"
func_file = "/Users/filo/workdir/rs_preprocessing/preprocess/preproc/take_mean_art/weighted_mean/corr_rest_roi_dtype.nii.gz"
affine_file = '/Users/filo/workdir/rs_preprocessing/preprocess/preproc/getmask/register/mapflow/_register0/corr_rest_roi_dtype_bbreg_recon_all.mat'
from nipy.labs import viz
from nipy.labs.viz_tools import anat_cache
import nibabel as nb
anat = nb.load(anat_file).get_data()
anat_affine = nb.load(anat_file).get_affine()
reference = nb.load(func_file).get_data()
reference_affine = nb.load(func_file).get_affine()
import numpy as np
slicer = viz.plot_anat(anat, anat_affine, dim=.2, black_bg=True)
slicer.edge_map(reference, reference_affine
fatal: No names found, cannot describe anything.
Traceback (most recent call last):
File "/Users/filo/Documents/workspace/pipelines/src/resting_state_preprocessing.py", line 69, in <module>
plot_coregistration()
File "/Users/filo/Documents/workspace/pipelines/src/resting_state_preprocessing.py", line 64, in plot_coregistration
slicer = viz.plot_anat(anat, anat_affine, dim=.2, black_bg=True)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipy/labs/viz_tools/activation_maps.py", line 335, in plot_anat
black_bg=black_bg)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipy/labs/viz_tools/slicers.py", line 246, in init_with_figure
cut_coords)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipy/labs/viz_tools/slicers.py", line 492, in find_cut_coords
activation_threshold=threshold)
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nipy/labs/viz_tools/coord_tools.py", line 117, in find_cut_coords
cut_coords = ndimage.center_of_mass(np.abs(my_map))
File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/ndimage/measurements.py", line 1151, in center_of_mass
return [tuple(v) for v in numpy.array(results).T]
TypeError: 'numpy.float64' object is not iterable
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