e_surfaces so that when looking for shared
libraries it will look in your ${HOME}/shared_libraries/usr/lib directory
before looking in the remaining "standard" locations.
$ export LD_LIBRARY_PATH=${HOME}/shared_libraries/usr/lib
Note: If your LD_LIBRARY_PATH already has some value, you'll want to use a
command like:
$ export LD_LIBRARY_PATH=${HOME}/shared_libraries/usr/lib:${LD_LIBRARY_PATH}
instead of the earlier command.
Note: You only want to use version 6 of the libnetcdf library when using
FreeSurfer v5.3.0-HCP. You don't want to use it for any other software on your
system that happens to use libnetcdf because that other software may depend
upon behavior in later versions of the libnetcdf library. That is why it is
safer to not allow version 6 to be installed in /usr/lib where it might be
found by other software using the libnetcdf library. Basically, you don't want
to contaminate your standard library locations with old libraries.
That is also why you should only set the LD_LIBRARY_PATH environment variable
as shown above when you are running FreeSurfer v5.3.0-HCP.
Once you've installed version 6 of the libnetcdf library in a directory and
made sure LD_LIBRARY_PATH points to that directory, try running the
FreeSurferPipeline.sh script again.
Lastly, in the future please ask questions like this to the HCP-Users mailing
list. That way other people can either benefit from the answer if it is correct
or correct my answer if I've made mistakes. I've gone ahead and sent this
response to that list and to your email address too because I don't know if you
are subscribed to the list.
You can subscribe to the HCP-Users mailing list by visiting
https://www.humanconnectome.org/contact-us. There is a place to join our two
email lists, HCP-Announce and HCP-Users, on the right hand side of that page.
Hope that's helpful,
Tim
On 2018-07-12 04:51 PM, Boukhdhir Amal wrote:
Hello Tim,
After running the PreFreesurferHCP pipeline in the HCP connectome course and
reproducing that on my computer successfully, I am getting thgis issue with
the Freesurfer pipeline (as a second step in the structural pipeline).
I attached the reconn-all.log file and a screenshot of the error.
The freesurfer version I am using is:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
These are more informations related to the distribution I am using:
aboukhdhir@thuya:/mnt/home_sq/aboukhdhir$ cat /etc/os-release NAME="Ubuntu"
VERSION="16.04.3 LTS (Xenial Xerus)" ID=ubuntu ID_LIKE=debian
PRETTY_NAME="Ubuntu 16.04.3 LTS" VERSION_ID="16.04"
HOME_URL="http://www.ubuntu.com/"; SUPPORT_URL="http://help.ubuntu.com/";
BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"; VERSION_CODENAME=xenial
UBUNTU_CODENAME=xenial
I have also tried the same pipeline on 2 other computers with different RAMs
and I am getting the same error.
Do you please have an idea why I am getting this error and how can I solve it
?
Best, Amal
--
Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Connectome Coordination Facility)
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
