Thanks vey much, Michael.
I actually have Centos 6 Linux which came with python 2.6 installed in
/usr/bin
I then installed Python 2.7.15 from compiling source and it installed in
/usr/local/bin
“Which python” gives /usr/local/bin/python
“Which pip” gives /usr/bin/pip
Do I need to install a pip that goes with python 2.7?
My PATH has /usr/local/bin prior to /usr/bin
Best,
Marc
On 2 Aug 2018, at 5:12, Michiel Cottaar wrote:
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
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