Hi Marc, You probably have multiple versions of python installed on your computer and pip has installed numpy for a different version of python than is used by the gradunwarp script. You can check this by running: $ which pip and $ which python My guess based on your screenshots and comments so far is that `which pip` will point to your python 2.7 installation, while `which python` still points to your python 2.6 installation. If that is the case, you will have to adjust your PATH environment variable to ensure that `which python` also points to your python 2.7 installation to fix this issue.
Good luck, Michiel On 2 Aug 2018, at 05:38, Marc Dubin <mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu>> wrote: Thanks, Matt. I did upgrade to the latest version of gradunwarp (forked to HCP). Now I am getting the error in the attached screenshot when I run PreFreesurfer… script <Screen Shot 2018-08-02 at 12.33.46 AM.png> I checked the output of “pip list” and I do have numpy 1.4.1 installed. Marc On 1 Aug 2018, at 7:35, Glasser, Matthew wrote: Do you have the latest version of gradunwarp? Matt. On 7/31/18, 11:32 PM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of Marc Dubin" <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on behalf of mrd9...@med.cornell.edu<mailto:mrd9...@med.cornell.edu>> wrote: 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<mailto:HCP-Users@humanconnectome.org> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwIFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=C9S_n0bF0p6dJ48M-Lgp1b9KBLxvTD5zOml7nDJ1vZU&m=IFVa_KMxOIHaKNEBXjw2lElahNY72GzoYWobG9KAXQs&s=QxQgKMh3JE6l649116S-Tfyvwm-ZL8Z2ifv5ys6IXb0&e= ________________________________ 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<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users <Screen Shot 2018-08-02 at 12.33.46 AM.png> _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
