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
