Hello HCP users,
We're doing our own preprocessing of a variety of datasets and are planning
on running HCP data through our pipeline. I'm trying to take one of the raw
images from HCP and do gradient distortion correction (using the HCP
gradunwarp package at https://github.com/Washington-University/gradunwarp).
I'm using the command-line tool, specifying a gradient coefficient file,
but am running into a problem.
Here's the error:
Traceback (most recent call last):
File "/usr/local/bin/gradient_unwarp.py", line 124, in <module>
grad_unwarp.run()
File "/usr/local/bin/gradient_unwarp.py", line 113, in run
self.unwarper.run()
File
"/usr/local/lib/python2.7/dist-packages/gradunwarp/core/unwarp_resample.py",
line 152, in run
m_rcs2lai, m_rcs2lai_nohalf, g_xyz2rcs)
File
"/usr/local/lib/python2.7/dist-packages/gradunwarp/core/unwarp_resample.py",
line 271, in non_linear_unwarp_siemens
order=self.order)
File "/usr/lib/python2.7/dist-packages/scipy/ndimage/interpolation.py",
line 299, in map_coordinates
raise RuntimeError('invalid shape for coordinate array')
RuntimeError: invalid shape for coordinate array
Digging into the code in some of those files, the problem seems to be
occurring with the 4-dimensional volume that is being passed to the NumPy
interpolation.
I'm running Ubuntu 14.04 with Python version 2.7.6, NumPy version 1.8.2 and
Scipy version 0.13.3.
Any help would be greatly appreciated!
Michael
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