Success - HCP-gradunwarp version 1.0.3 runs without errors. Thanks
> On May 10, 2017, at 1:50 PM, Philip A Cook <coo...@mail.med.upenn.edu> wrote: > > Thanks Michael, we have release 1.0.2. I will try 1.0.3 > > >> On May 9, 2017, at 5:27 PM, Harms, Michael <mha...@wustl.edu> wrote: >> >> >> 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 >> >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
