Vasudev,
It seems like you may need to provide the Python environment with some
indication of where to find the installation of numpy. I'm not sure why
this would be happening unless for some reason the Python installation
you are using when running the HCP Pipeline Scripts is different from
the Python installation that you would use if you simply entered python
at the command line.
Let's try the following.
First, you will need to know where numpy is installed on your system.
Based on the output from your apt-cache command, it looks to me like you are
working on an Ubuntu system and have installed numpy with a command something
like:
apt-get install python-numpy
If that is the case, you should be able to find out where numpy is installed by
starting up Python from a terminal/shell and issuing commands similar to the
following:
$ python
Python 2.7.9 (default, Apr 2 2015, 15:33:21)
[GCC 4.9.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import imp
>>> imp.find_module('numpy')
(None, '/usr/lib/python2.7/dist-packages/numpy', ('', '', 5))
>>> quit()
$
The directory listed after "None," should be where numpy is installed on
you system. In the above example, it is /usr/lib/python2.7/dist-
packages/numpy.
Once you have that information, try the following to see if we can get
numpy found when you are running PreFreeSurferPipeline.sh
Either in a script file that you source in order to set up your environment
before running the PreFreeSurferPipeline.sh script, or in your ~/.bash_profile
file set your PYTHONPATH environment variable with a command like the following:
export PYTHONPATH=/usr/lib/python2.7/dist-packages/numpy:${PYTHONPATH}
Of course, you will want to use the directory you found above in place
of /usr/lib/python2.7/dist-packages/numpy in the above command.
This form of setting the PYTHONPATH environment variable assumes you are
using the bash shell which is the default for most Linux environments.
If you do this in your ~/.bash_profile file, you should log out and log
back in to make sure that the PYTHONPATH environment variable gets set.
With the PYTHONPATH environment variable set, when your run the
PreFreeSurferPipeline.sh script and the Python environment is started in
order to run the aff2rigid command (which is a Python script), the
directories in your PYTHONPATH variable should be included in the list
of directories in which to look for items to import. So the from numpy
import * statement in the Python script should then work.
Give this a try and let me know how things work out.
Tim
On Thu, Mar 10, 2016, at 13:33, Dev vasu wrote:
> Dear Sir,
>
> I have started running PreFreeSurferPipeline.sh and every time i run
> , i am incurring following error,
>
> "START: ACPCAlignment
>
Final FOV is:
>
.000000 160.000000 0.000000 256.000000 86.000000 150.000000
>
>
Traceback (most recent call last):
>
File "/usr/share/fsl/5.0/bin/aff2rigid", line 75, in <module>
>
from numpy import *
>
ImportError: No module named numpy "
>
>
>
> Numpy is installed in my computer but the program could not
> import numpy.
>
>
> " vasudev@vasudev-OptiPlex-780:~/Documents/workbench/bin_linux64$ apt-
> cache policy python-numpy
>
python-numpy:
>
Installed: 1:1.8.2-0ubuntu0.1
>
Candidate: 1:1.8.2-0ubuntu0.1
>
Version table:
>
*** 1:1.8.2-0ubuntu0.1 0
>
500 http://de.archive.ubuntu.com/ubuntu/ trusty-updates/main
amd64 Packages
>
100 /var/lib/dpkg/status
>
1:1.8.1-1ubuntu1 0
>
500 http://de.archive.ubuntu.com/ubuntu/ trusty/main amd64 Packages "
>
>
> Could you please let me know how shall i resolve it.
>
>
>
> Thanks
> Vasudev
>
>
>
>
>
>
> _______________________________________________
>
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>
[email protected]
>
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--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
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