From reading the email thread history, it appears you may have downloaded the apple OS X version of 3rvolreg.afni and overwrote the original, which is the cause of the error. Please extract the original version of that binary from the original tarball. If you no longer have it you can download it from this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke > On Jun 22, 2015, at 11:29 PM, Thục Trinh <thuctrinh...@gmail.com> wrote: > > hello, > I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. > I think that makes the confliction. > > 2015-06-23 8:26 GMT+07:00 Thục Trinh <thuctrinh...@gmail.com>: >> Hello Douglas and ZK, >> I set the path for shared library in my .basrch file, but it still does not >> work and comes up with this Error: >> 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF >> class: ELFCLASS32 >> ERROR: 3dvolreg.afni >> Invalid null command. >> >> Trinh >> >> 2015-06-23 3:03 GMT+07:00 Z K <zkauf...@nmr.mgh.harvard.edu>: >>> Trinh, >>> >>> Attempt to determine where libXp.so.6 was installed on your system after >>> you installed it using yum. For example, on my system libXp.so.6 exists >>> in directory "/usr/lib64". Once you determine the location where the >>> library resides, add that directory to your LD_LIBRARY_PATH after you >>> source freesurfer. >>> >>> $> source $FREESURFER_HOME/SetUpFreeSurfer.sh >>> $> export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH >>> $> preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh >>> -fwhm 5 -per-run >>> >>> -Zeke >>> >>> >>> >>> >>> On 06/22/2015 02:40 PM, Douglas Greve wrote: >>> > I'm not sure what to tell you. Zeke, do you have any ideas? >>> > Alternatively, you can just install afni on your machine. Once you >>> > verify that the installation works, copy 3dvolreg from the installation. >>> > >>> > On 6/21/15 3:55 PM, Thục Trinh wrote: >>> >> Hello Douglas, >>> >> I already had *3dvolreg.afni* in */freesurfer/bin/*, but I still >>> >> download the new one 3dvolreg.afni and replaced it in /freesurfer/bin. >>> >> But the Error still remain the same. >>> >> *3dvolreg.afni: error while loading shared libraries: libXp.so.6: >>> >> cannot open shared object file: No such file or directory* >>> >> *ERROR: 3dvolreg.afni* >>> >> *Invalid null command.* >>> >> >>> >> >>> >> 2015-06-19 16:04 GMT+07:00 Douglas Greve <gr...@nmr.mgh.harvard.edu >>> >> <mailto:gr...@nmr.mgh.harvard.edu>>: >>> >> >>> >> >>> >> See this thread >>> >> >>> >> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html >>> >> >>> >> >>> >> >>> >> >>> >> On 6/17/15 5:59 PM, Thục Trinh wrote: >>> >>> Hi freesurfer experts, >>> >>> I am practicing on the fsfast tutorial data that were given at >>> >>> Freesurfer website. >>> >>> I run the command to do the pre-processing on the sess01 <*noproc*>. >>> >>> *preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh >>> >>> -fwhm 5 -per-run* >>> >>> it was unfinished and failed with the ERROR: >>> >>> *3dvolreg.afni: error while loading shared libraries: libXp.so.6: >>> >>> cannot open shared object file: No such file or directory* >>> >>> *ERROR: 3dvolreg.afni* >>> >>> *Invalid null command.* >>> >>> so I run the command to install libXp.so.6 under root permission >>> >>> *yum install libXp.so.6 *and completely installed. >>> >>> I found the file *3dvolreg.afni *in the $FREESURFER_HOME/bin >>> >>> But the ERROR still remained unfixed. >>> >>> >>> >>> Please help me with any suggestions to finish the preproc-sesss >>> >>> Thankyou and have a nice day. >>> >>> Trinh Tran >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Freesurfer mailing list >>> >>> Freesurfer@nmr.mgh.harvard.edu >>> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >> >>> >> >>> >> The information in this e-mail is intended only for the person to >>> >> whom it is >>> >> addressed. If you believe this e-mail was sent to you in error and >>> >> the e-mail >>> >> contains patient information, please contact the Partners >>> >> Compliance HelpLine at >>> >> http://www.partners.org/complianceline . If the e-mail was sent to >>> >> you in error >>> >> but does not contain patient information, please contact the >>> >> sender and properly >>> >> dispose of the e-mail. >>> >> >>> >> >>> >> >>> >> >>> >> _______________________________________________ >>> >> Freesurfer mailing list >>> >> Freesurfer@nmr.mgh.harvard.edu >>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> > >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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