It should be in $FREESURFER_HOME/bin/3dvolreg.afni
On 05/21/2013 02:49 PM, Joseph Dien wrote: > Perhaps the problem has already been solved but I just ran into the > same issue (on OS X 10.8.2). After poking around, what I found was > that while the current AFNI distribution does not have a file > named 3dvolreg.afni, it does have one named 3dvolreg. I'm guessing > the problem is that it has been renamed. I fixed the problem by > creating a link: > > ln 3dvolreg 3dvolreg.afni > > I suppose FSFAST needs to be updated to take this new name into account. > > Cheers! > > Joe > >> 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 <http://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 <http://nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu >> >> <http://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 <http://nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu >> >> <http://nmr.mgh.harvard.edu>> >> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu >> >> <http://nmr.mgh.harvard.edu>> >> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu >> >> <http://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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> >> >> >> >> >https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >> -- >> >> Douglas N. Greve, Ph.D. >> >> MGH-NMR Center >> >> gr...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu >> >> <http://nmr.mgh.harvard.edu>> >> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu >> >> <http://nmr.mgh.harvard.edu>> >> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu >> >> <http://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<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<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/ <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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> > >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> >> >> >> >> >> >> >> >>https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 <http://nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu >> >> <http://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> >> >> >> >> <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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> > >> >> Outgoing: >> >> >> >>ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> >> >> >> > -- >> > Douglas N. Greve, Ph.D. >> > MGH-NMR Center >> > gr...@nmr.mgh.harvard.edu <http://nmr.mgh.harvard.edu> >> > Phone Number: 617-724-2358 >> > Fax: 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><http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > Outgoing:ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> > >> > >> _______________________________________________ >> 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. > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdie...@mac.com <mailto:jdie...@mac.com> > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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
