Hi all,
I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running
preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run
which provides the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I found this old communication https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html in which this user had the same problem. I found 3dvolreg.afni in the Freesurfer "bin" folder and copied to to my AFNI folder, but I still get the same error when running preproc-sess, even with 3dvolreg.afni now in the AFNI cluster.
Any idea what the problem might be?
Best, Adam Nitenson
Do the other programs in AFNI work on that computer? If 3dvolreg works, then copy that to 3dvolreg.afni in $FREESURFER_HOME/bin
doug
On 06/03/2014 12:01 PM, Nitenson, Adam wrote:
Hi all,
I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running
preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run
which provides the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I found this old communication https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html in which this user had the same problem. I found 3dvolreg.afni in the Freesurfer "bin" folder and copied to to my AFNI folder, but I still get the same error when running preproc-sess, even with 3dvolreg.afni now in the AFNI cluster.
Any idea what the problem might be?
Best, Adam Nitenson
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
Unfortunately that did not seem to work. I am normally able to run other AFNI programs on this computer (it's what I've been normally performing my data analyses with).
Best, Adam
On Wed, Jun 4, 2014 at 12:02 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
Do the other programs in AFNI work on that computer? If 3dvolreg works, then copy that to 3dvolreg.afni in $FREESURFER_HOME/bin
doug
On 06/03/2014 12:01 PM, Nitenson, Adam wrote:
Hi all,
I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running
preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run
which provides the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I found this old communication
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html
in which this user had the same problem. I found 3dvolreg.afni in the Freesurfer "bin" folder and copied to to my AFNI folder, but I still get the same error when running preproc-sess, even with 3dvolreg.afni now in the AFNI cluster.
Any idea what the problem might be?
Best, Adam Nitenson
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 greve@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
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.
Well, if you can't run any AFNI program, then that is the problem. doug
On 6/5/14 11:37 AM, Nitenson, Adam wrote:
Hi Doug,
Unfortunately that did not seem to work. I am normally able to run other AFNI programs on this computer (it's what I've been normally performing my data analyses with).
Best, Adam
On Wed, Jun 4, 2014 at 12:02 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Do the other programs in AFNI work on that computer? If 3dvolreg works, then copy that to 3dvolreg.afni in $FREESURFER_HOME/bin doug On 06/03/2014 12:01 PM, Nitenson, Adam wrote: > Hi all, > > I'm running version 5.2 off-site, and I keep running up against an > error for preproc-sess. From my SUBJECTS_DIR, I am running > > preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run > > which provides the following error: > > 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: > afni_ncerr > ERROR: 3dvolreg.afni > Invalid null command. > > I found this old communication > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html > in which this user had the same problem. I found 3dvolreg.afni in the > Freesurfer "bin" folder and copied to to my AFNI folder, but I still > get the same error when running preproc-sess, even with 3dvolreg.afni > now in the AFNI cluster. > > Any idea what the problem might be? > > Best, > Adam Nitenson > > > _______________________________________________ > Freesurfer mailing list > 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 greve@nmr.mgh.harvard.edu <mailto:greve@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: https://gate.nmr.mgh.harvard.edu/filedrop2 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> 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am able to run AFNI normally, it was just an issue with this particular command. I did however figure out a solution, which was just that I needed to use v5.3 instead of 5.2. I'm not sure if it's just our copy here that's outdated, but as soon as I loaded 5.3, I ran the same command I was trying before, and it ran appropriately, as well as the following spmregister command. I did not even know that we had the newest version since 5.2 was the default module on our systems.
Best, Adam
On Thu, Jun 5, 2014 at 11:43 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Well, if you can't run any AFNI program, then that is the problem. doug
On 6/5/14 11:37 AM, Nitenson, Adam wrote:
Hi Doug,
Unfortunately that did not seem to work. I am normally able to run other AFNI programs on this computer (it's what I've been normally performing my data analyses with).
Best, Adam
On Wed, Jun 4, 2014 at 12:02 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Do the other programs in AFNI work on that computer? If 3dvolreg works, then copy that to 3dvolreg.afni in $FREESURFER_HOME/bin
doug
On 06/03/2014 12:01 PM, Nitenson, Adam wrote:
Hi all,
I'm running version 5.2 off-site, and I keep running up against an error for preproc-sess. From my SUBJECTS_DIR, I am running
preproc-sess -fsd bold -s 608_Sess1 -fwhm 5 -per-run
which provides the following error:
3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr ERROR: 3dvolreg.afni Invalid null command.
I found this old communication
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28736.html
in which this user had the same problem. I found 3dvolreg.afni in the Freesurfer "bin" folder and copied to to my AFNI folder, but I still get the same error when running preproc-sess, even with 3dvolreg.afni now in the AFNI cluster.
Any idea what the problem might be?
Best, Adam Nitenson
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 greve@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
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.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Nitenson, Adam