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 _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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