Hmmmm, it looks like you are missing a library. Do you have afni installed? Maybe Nick or Zeke can chime in. He's getting the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr When I run it on minerva (which I think is centos4.0 x64) I get: /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni: error while loading shared libraries: requires glibc 2.5 or later dynamic linker There is the same error when I run 3dvolreg from minerva: /usr/pubsw/packages/AFNI/2011_12_21_1014/3dvolreg Maybe our version of AFNI cannot be run under centos4? Yuhong, if you download and install AFNI (or if you have it), you can copy 3dvolreg to $FREESURFER_HOME/bin/3dvolreg.afni doug On 03/21/2013 02:14 PM, Y.V. Jiang wrote: > Hi Doug, > > Here's the output from cat /proc/version: > > Linux version 2.6.32-45-generic (buildd@batsu) (gcc version 4.4.3 > (Ubuntu 4.4.3-4ubuntu5.1) ) #101-Ubuntu SMP Mon Dec 3 15:39:38 UTC 2012 > > This is the result of cat $FREESURFER_HOME/build-stamp.txt > > freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 > > Thanks. > > -Yuhong > > On Thu, Mar 21, 2013 at 1:12 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > which version of CentOS? Also, can you send me the result of > cat $FREESURFER_HOME/build-stamp.txt > > > > On 03/21/2013 02:09 PM, Y.V. Jiang wrote: > > Hi Doug, > > I am using Linux: x86_64 GNU/Linux. Thanks. > > -Yuhong > > On Thu, Mar 21, 2013 at 12:57 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > what platform are you using? > > > On 03/21/2013 01:24 PM, Y.V. Jiang wrote: > > Hi Doug, > > Thanks for the reply. From the command line the command > 3dvolreg.afni returned the following error: > > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: > undefined > symbol: afni_ncerr > > -Yuhong > > On Thu, Mar 21, 2013 at 12:08 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote: > > > Hi Yuhong, > What happens when you run 3dvolreg.afni from the > command > line without > any args? > doug > > On 03/21/2013 12:38 PM, Y.V. Jiang wrote: > > Hi Doug, > > > > I was running preproc-sess in the newly released > freesurfer-5.2.0. The > > command I used was: > > > > preproc-sess -sf sessid -df sessdir -fsd bold > -surface > fsaverage lhr > > -mni305 -fwhm 6 -per-run > > > > The program failed with the following errors: > > > > 3dvolreg.afni -verbose -dfile 004/fmcpr.mcdat > -1Dmatrix_save > > 004/fmcpr.mat -base > 004/tmp.mc-afni2.29239/tempvol.nii.gz -prefix > > 004/tmp.mc-afni2.29239/outvol.nii.gz > 004/tmp.mc-afni2.29239/invol.nii.gz > > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: > undefined symbol: > > afni_ncerr > > ERROR: 3dvolreg.afni > > Invalid null command. > > > > I have the file 3dvolreg.afni in > $FREESURFER_HOME/bin. > There is > > another file of the same name under afni/bin. > Preproc-sess is > relying > > on the version in $FREESURFER_HOME/bin. > > > > Do you know what the problem is? Should I replace > freesurfer's > copy of > > 3dvolreg.afni with AFNI's copy of 3dvolreg.afni? > > > > Thanks. > > > > -Yuhong > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
