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>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<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<gr...@nmr.mgh.harvard.edu> > >> > > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> > >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > >> > > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > >> > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<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 > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> > >> > > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> > >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <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<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>> > >> > >> 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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > >> > > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> > >> > >> > >> <mailto:freesur...@nmr.mgh.**harvard.edu<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 > >> <mailto:gr...@nmr.mgh.harvard.**edu<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> > >> > >> <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/<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<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/ <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 > > > 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 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 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.
