Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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.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 http://nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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.**edugr...@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.eduFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@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.**edugr...@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
[Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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.
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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: 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.
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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 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: 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 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.
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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 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 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: 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. -- 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: 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
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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 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 https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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 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/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu 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 at http://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 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.
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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 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 mailto:gr...@nmr.mgh.harvard.edu mailto: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:Freesurfer@nmr.mgh.harvard.edu mailto: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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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 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/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs:
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
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/
Re: [Freesurfer] v5.2.0 preproc-sess failing on 3dvolreg.afni
H, it looks like you are missing a library. Do you have afni installed? Maybe Nick or Zeke can chime in. He's getting the following error: 3dvolreg.afni: symbol lookup error: 3dvolreg.afni: undefined symbol: afni_ncerr When I run it on minerva (which I think is centos4.0 x64) I get: /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni /space/freesurfer/centos4.0_x86_64/stable5_2_0/bin/3dvolreg.afni: error while loading shared libraries: requires glibc 2.5 or later dynamic linker There is the same error when I run 3dvolreg from minerva: /usr/pubsw/packages/AFNI/2011_12_21_1014/3dvolreg Maybe our version of AFNI cannot be run under centos4? Yuhong, if you download and install AFNI (or if you have it), you can copy 3dvolreg to $FREESURFER_HOME/bin/3dvolreg.afni doug On 03/21/2013 02:14 PM, Y.V. Jiang wrote: 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 mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto: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:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
