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.eduwrote:
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.**edugr...@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.**edugr...@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.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
<mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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 athttp://www.partners.org/**compliancelinehttp://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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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: jdien07@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//
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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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 listFreesurfer@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/**freesurferhttps://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 athttp://www.partners.org/**compliancelinehttp://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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://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/BugReportinghttp://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.htmlhttp://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: jdien07@mac.com mailto:jdien07@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//
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Joseph Dien