Hi,
I was trying to do gradient nonlinearity correction as part of the structural
pre-processing pipeline, which failed. Calling gradient_unwarp.py independently
produces the same error:
gradient_unwarp.py T1w.nii.gz trilinear.nii.gz siemens -g coeff.grad -n
gradient_unwarp.py fails to read the file, the output is:
gradunwarp-INFO: Parsing coeff.grad for harmonics coeffs
Traceback (most recent call last):
File "/share/apps/python/Python-2.7.9/bin/gradient_unwarp.py", line 122, in
<module>
grad_unwarp.run()
File "/share/apps/python/Python-2.7.9/bin/gradient_unwarp.py", line 91, in run
self.args.gradfile)
File
"/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/core/coeffs.py",
line 30, in get_coefficients
return get_siemens_grad(cfile)
File
"/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/core/coeffs.py",
line 194, in get_siemens_grad
R0_m, max_ind = grad_file_parse(gfile, txt_var_map)
File
"/share/apps/python/Python-2.7.9/lib/python2.7/site-packages/gradunwarp/core/coeffs.py",
line 159, in grad_file_parse
txt_var_map['Alpha_z'][x,y] = float(line.split()[-2])
IndexError: index 15 is out of bounds for axis 0 with size 14
We have gradunwarp installed from
https://github.com/Washington-University/gradunwarp
I can successfully correct T1w images from Lifespan pilot data, using the Skyra
.grad file:
gradient_unwarp.py T1w.nii.gz trilinear.nii.gz siemens -g
coeff_SC72C_Skyra.grad -n
So I think the gradunwarp install is OK. I think the Prisma coeff file is also
correct, as we've checked it against the same file from another scanner. Has
anyone managed to do the GDC with Prisma coeffs?
Thanks
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