Hi,
This came up on the list just earlier this week.  See this:
http://www.mail-archive.com/hcp-users@humanconnectome.org/msg04590.html


--
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  63110 Email: mha...@wustl.edu

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Sang-Young Kim <sykim...@gmail.com<mailto:sykim...@gmail.com>>
Date: Friday, May 12, 2017 at 1:41 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Cc: Tae Kim <ta...@pitt.edu<mailto:ta...@pitt.edu>>
Subject: [HCP-Users] Error for gradient nonlinearity correction on Siemens 
Prisma data

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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