Hi again Vasudev,
>From what you've put in your message below, it looks to me like you may
be missing an important character in the following lines.
You have:
export FSLDIR=/usr/share/fsl/5.0
${FSLDIR}/etc/fslconf/fsl.sh
you should have:
export FSLDIR=/usr/share/fsl/5.0
. ${FSLDIR}/etc/fslconf/fsl.sh
Notice the "." at the beginning of the second line. That "." is very
important.
Please verify that it is there. You will also need to verify that
/usr/share/fsl/5.0 is the correct directory in which you have FSL
installed.
If /usr/share/fsl/5.0 is where you have FSL installed, you do have the
"." at the beginning of the second line above, and you still get the
"Permission denied" error, then try issuing the following command and
sending the output to me.
$ ls -l /usr/share/fsl/5.0/etc/fslconf
Regards,
Tim
On Thu, Mar 10, 2016, at 14:41, Dev vasu wrote:
> Dear Sir,
>
>
Thanks for this information i will try it now, i also had another doubt
>
>
> In the script the path to FSL directory suggested as follows
>
> " export FSLDIR=/usr/share/fsl/5.0
${FSLDIR}/etc/fslconf/fsl.sh
> and when i run the script i am incurring following error
>
> dev@dev-OptiPlex-780:~/Documents/Pipelines-master/PreFreeSurfer$
./PreFreeSurferPipeline.mine.sh
./PreFreeSurferPipeline.mine.sh: line
170: /usr/share/fsl/5.0/etc/fslconf/fsl.sh: Permission denied "
>
>
>
> Could you please let me know the reason for the error.
>
>
> Thanks
>
>
> Vasudev
>
> On 10 March 2016 at 21:36, Timothy B. Brown <[email protected]> wrote:
>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>>
HCP-Users mailing list
>>> [email protected]
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> --
>> Timothy B. Brown
>> Business & Technology Application Analyst III
>> Pipeline Developer (Human Connectome Project)
>> tbbrown(at)wustl.edu
>> ________________________________________
>> The material in this message is private and may contain Protected
>> Healthcare Information (PHI).
>> 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.
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Human Connectome Project)
tbbrown(at)wustl.edu
________________________________________
The material in this message is private and may contain Protected Healthcare
Information (PHI).
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.
_______________________________________________
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