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 http://lists.humanconnectome.org/mailman/listinfo/hcp-users