Dear all:
I’m running HCP pipeline script on our Siemens Prisma data. I would like to see
whether gradient nonlinearity on Siemens Prisma scanner would cause visible
error on segmentation result. I got the gradient coefficient file from the
scanner.
If I set the variable of "GradientDistortionCoeffs" with our gradient
coefficient file in PreFreeSurferPipeline, I get following error.
************************************************************************************************************************************
gradunwarp-INFO: Parsing
/Users/sang-young/projects/Pipelines/global/config/coeff_AS82_Prisma.grad for
harmonics coeffs
Traceback (most recent call last):
File "/sw/bin/gradient_unwarp.py", line 123, in <module>
grad_unwarp.run()
File "/sw/bin/gradient_unwarp.py", line 91, in run
self.args.gradfile)
File "/sw/lib/python2.7/site-packages/gradunwarp/core/coeffs.py", line 30, in
get_coefficients
return get_siemens_grad(cfile)
File "/sw/lib/python2.7/site-packages/gradunwarp/core/coeffs.py", line 194,
in get_siemens_grad
R0_m, max_ind = grad_file_parse(gfile, txt_var_map)
File "/sw/lib/python2.7/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 is out of bounds for axis 0 with size 14
*******************************************************************************************************
Could someone else please help me fix the error?
Thanks in advance.
Sang-Young
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