Hi Joe, The mris_make_surfaces binary in the HCP custom version of FreeSurfer (5.3.0-HCP) was linked using shared libraries. (My understanding is that the mris_make_surfaces binary in other releases of FreeSurfer is linked to static libraries so that the library code is included in the resulting binary and thus the library does not need to be installed on your system or located at run-time.) The mris_make_surfaces binary is looking for a specific version (version 6) of a shared library that it needs: the NetCDF (Network Common Data Form) library. You may have an older version of the NetCDF shared library installed on your system (e.g. libnetcdf.so.4), or even possibly a newer version of the NetCDF installed on your system (e.g. libnetcdf.so.7). Many binaries that use the NetCDF shared library will work fine because they are linked in such a way as to use the latest version of the shared library that you have installed. But in this case, mris_make_surfaces is trying to locate a very specific version of the library.
You (or your friendly, neighborhood systems administrator) will need to make sure libnetcf.so.6 is installed in a standard library directory location or in a directory referenced by the LD_LIBRARY_PATH environment variable. It would be preferable to install it in one of the standard library locations instead of using LD_LIBRARY_PATH to locate it. The standard locations may depend upon your exact platform (Ubuntu, Red Hat, Cent OS, etc.) but generally are: * /lib * /lib64 * /usr/lib * /usr/lib64 * /usr/local/lib * /usr/local/lib64 Unless you really, really know what you're doing, installing a library in /lib or /lib64 is not usually a good idea. I think you'll find that /usr/lib64 is probably your best bet. Also, you will probably actually end up having libnetcdf.so.6.0.0 installed and have libnetcdf.so.6 be a symbolic link to the libnetcdf.so.6.0.0 file. If you have problems finding the shared library version libnetcf.so.6 for your platform, please email back, and I'll see if our system administrators can help you locate the appropriate file and get it installed. As for the impacts of on your results of using release 5.3.0 instead of 5.3.0-HCP...changes to the mris_make_surfaces program were necessary to better handle the HCP data. It was these changes to the mris_make_surface program that actually prompted the creation of the 5.3.0-HCP version of FreeSurfer. These changes involved correct location of the pial surface. There are others who would be much better able to explain the differences between pial surface location using FreeSurfer 5.3.0 versus using FreeSurfer 5.3.0-HCP than I would. If you would like that better explanation, I suggest you re-post your question to this [email protected] list as a question about pial surface location. Hope that's helpful, Tim On Thu, Oct 23, 2014, at 11:06, Joseph Orr wrote: > Hi, I’m getting the below missing shared libraries error from > mris_make_surfaces with Freesurfer-5.3.0-HCP. Is it possible that I am > missing a required package/ file? I was able to run > FreeSurferPipeline.sh without error using the release version of > FS-5.3.0. What are the impacts on my results using release 5.3.0 and > the HCP version? I am running the pipeline on my own data from a > functional study. > > Thanks, Joe > >> mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs 2011 lh >> >> mris_make_surfaces: error while loading shared libraries: >> libnetcdf.so.6: cannot open shared object file: No such file or >> directory > > > -- > Joseph M. Orr, PhD. Postdoctoral Fellow Institute of Cognitive Science > 594 UCB - CINC 182D University of Colorado at Boulder Boulder, CO > 80309-0594 > _______________________________________________ > 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. _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
