The Prisma coefficient file contains more harmonics than the original
gradient_unwarp.py could handle.
Although, I thought that we had fixed that in the version that we are
hosting on github…
(Tim Brown?)
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110Email: mha...@wustl.edu
On 5/9/17, 3:57 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Philip A Cook" <hcp-users-boun...@humanconnectome.org on behalf of
coo...@mail.med.upenn.edu> wrote:
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/cor
e/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/cor
e/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/cor
e/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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