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:
I suppose FSFAST needs to be updated to take this new name into account.
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
>> >
>> >
>> > ______________________________**_________________
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>> >
>>
>> <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
>>
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>> If the e-mail was sent to
>> you in error
>> but does not contain patient information, please contact the
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>>
>> -- 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/>
>
>
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