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
