Do you have the latest version of gradunwarp? Matt.
On 7/31/18, 11:32 PM, "hcp-users-boun...@humanconnectome.org on behalf of Marc Dubin" <hcp-users-boun...@humanconnectome.org on behalf of mrd9...@med.cornell.edu> wrote: >Hello All, When I run PreFreeSurferPipelineBatch.sh I get the following >error. I tried installing Python 2.7, but I still get the same error. > >Any thoughts on how to fix this would be appreciated! > >Thanks, > >Marc > >[mrd9035@localhost Scripts]$ ./PreFreeSurferPipelineBatch.sh >StudyFolder: /home/mrd9035/projects/Pipelines_ExampleData >Subjlist: 7467 >EnvironmentScript: >/home/mrd9035/projects/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh >Run locally: >This script must be SOURCED to correctly setup the environment prior to >running any of the other HCP scripts contained here >7467 >Found 1 T1w Images for subject 7467 >Found 1 T2w Images for subject 7467 >About to use fsl_sub to queue or run >/home/mrd9035/projects/Pipelines/PreFreeSurfer/PreFreeSurferPipeline.sh >/usr/lib/python2.6/site-packages/argparse.py:1575: DeprecationWarning: >The "version" argument to ArgumentParser is deprecated. Please use >"add_argument(..., action='version', version="N", ...)" instead > """instead""", DeprecationWarning) >gradunwarp-INFO: Parsing >/home/mrd9035/projects/Pipelines/global/config/coeff.grad for harmonics >coeffs >Traceback (most recent call last): > File "/usr/bin/gradient_unwarp.py", line 123, in <module> > grad_unwarp.run() > File "/usr/bin/gradient_unwarp.py", line 91, in run > self.args.gradfile) > File "/usr/lib64/python2.6/site-packages/gradunwarp/core/coeffs.py", >line 30, in get_coefficients > return get_siemens_grad(cfile) > File "/usr/lib64/python2.6/site-packages/gradunwarp/core/coeffs.py", >line 194, in get_siemens_grad > R0_m, max_ind = grad_file_parse(gfile, txt_var_map) > File "/usr/lib64/python2.6/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) out of range (0<=index<14) in dimension 0 >_______________________________________________ >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
