Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance.
Best,
Heather
what is your command line?
On 08/07/2013 10:19 AM, Heather L. Urry wrote:
Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance.
Best,
Heather
-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Here it is:
recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all &
(sorry for not thinking to include it originally)
Heather
On Wed, Aug 7, 2013 at 11:48 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
what is your command line?
On 08/07/2013 10:19 AM, Heather L. Urry wrote:
Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance.
Best,
Heather
-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
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.
and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote:
what is your command line?
On 08/07/2013 10:19 AM, Heather L. Urry wrote:
Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance.
Best,
Heather
-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah, sorry-- that too: tcsh 6.18.01.
(The command, which I just sent in a previous message, was as follows:
recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all &
)
Heather
On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote:
what is your command line?
On 08/07/2013 10:19 AM, Heather L. Urry wrote:
Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance.
Best,
Heather
-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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.
Hmm, not sure what is going on.
First, run it without the ampersand on the end.
If that still crashes, then run this and send me log.txt
recon-all -debug -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all |& tee log.txt
doug
On 08/07/2013 12:47 PM, Heather L. Urry wrote:
Ah, sorry-- that too: tcsh 6.18.01.
(The command, which I just sent in a previous message, was as follows:
recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all &
)
Heather
On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote: > what is your command line? > > > > > On 08/07/2013 10:19 AM, Heather L. Urry wrote: >> Hi folks, >> >> When issuing a recon-all command, I'm seeing the following message: >> >> set: Variable name must contain alphanumeric characters >> >> recon-all stalls and doesn't move forward (doesn't even create the >> subject directory). >> >> I'm using Freesurfer 5.3.0 >> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. >> In fact, we just upgraded to this version of Ubuntu from an older >> version of Mandriva and to this latest version of Freesurfer. >> recon-all did not produce this message before these two upgrades. Any >> help you can offer would be most appreciated! Thanks in advance. >> >> Best, >> >> Heather >> >> -- >> Heather L. Urry, Ph.D. >> Department of Psychology >> Tufts University >> 490 Boston Avenue >> Medford, MA 02155 >> >> email: heather.urry@tufts.edu <mailto:heather.urry@tufts.edu> <mailto:heather.urry@tufts.edu <mailto:heather.urry@tufts.edu>> >> phone: 617-627-3733 <tel:617-627-3733> >> fax: 617-627-3181 <tel:617-627-3181> >> >> http://ase.tufts.edu/psychology/ebbl >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Ah! That was helpful, Doug. While eliminating the & at the end didn't do anything, running the debug version of the command shows the following at the end of log.txt (attached):
set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /home/hurry01/.gvfs/ebblvm$ on callunavm.psy.tufts.edu/projects/resdep/data/mri/resdep214
This is where the set message gets spit out. It's - for obvious reasons - not happy with that path. I'll work with IT over on this end as it likely has something to do with the way we're mounting the Windows shares on which data are stored and processed.
Best,
Heather
On Wed, Aug 7, 2013 at 1:13 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Hmm, not sure what is going on.
First, run it without the ampersand on the end.
If that still crashes, then run this and send me log.txt
recon-all -debug -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all |& tee log.txt
doug
On 08/07/2013 12:47 PM, Heather L. Urry wrote:
Ah, sorry-- that too: tcsh 6.18.01.
(The command, which I just sent in a previous message, was as follows:
recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all &
)
Heather
On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote: > what is your command line? > > > > > On 08/07/2013 10:19 AM, Heather L. Urry wrote: >> Hi folks, >> >> When issuing a recon-all command, I'm seeing the followingmessage:
>> >> set: Variable name must contain alphanumeric characters >> >> recon-all stalls and doesn't move forward (doesn't even create the >> subject directory). >> >> I'm using Freesurfer 5.3.0 >> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. >> In fact, we just upgraded to this version of Ubuntu from an older >> version of Mandriva and to this latest version of Freesurfer. >> recon-all did not produce this message before these two upgrades. Any >> help you can offer would be most appreciated! Thanks in advance. >> >> Best, >> >> Heather >> >> -- >> Heather L. Urry, Ph.D. >> Department of Psychology >> Tufts University >> 490 Boston Avenue >> Medford, MA 02155 >> >> email: heather.urry@tufts.edu <mailto:heather.urry@tufts.edu> <mailto:heather.urry@tufts.edu <mailto:heather.urry@tufts.edu>> >> phone: 617-627-3733 <tel:617-627-3733> >> fax: 617-627-3181 <tel:617-627-3181> >> >> http://ase.tufts.edu/psychology/ebbl >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
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
you might try running
csh -V $FREESURFER_HOME/scripts/recon-all ....
and see where it crashes. It might be in one of your dot files and not in recon-all at all Bruce On Wed, 7 Aug 2013, Douglas N Greve wrote:
Hmm, not sure what is going on.
First, run it without the ampersand on the end.
If that still crashes, then run this and send me log.txt
recon-all -debug -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all |& tee log.txt
doug
On 08/07/2013 12:47 PM, Heather L. Urry wrote:
Ah, sorry-- that too: tcsh 6.18.01.
(The command, which I just sent in a previous message, was as follows:
recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all &
)
Heather
On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote:what is your command line?
On 08/07/2013 10:19 AM, Heather L. Urry wrote:
Hi folks,
When issuing a recon-all command, I'm seeing the following message:
set: Variable name must contain alphanumeric characters
recon-all stalls and doesn't move forward (doesn't even create the subject directory).
I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu
12.04.2.In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two
upgrades. Anyhelp you can offer would be most appreciated! Thanks in advance.
Best,
Heather
-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu
<mailto:heather.urry@tufts.edu <mailto:heather.urry@tufts.edu>>phone: 617-627-3733 tel:617-627-3733 fax: 617-627-3181 tel:617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.-- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155
email: heather.urry@tufts.edu mailto:heather.urry@tufts.edu phone: 617-627-3733 fax: 617-627-3181
http://ase.tufts.edu/psychology/ebbl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Heather L. Urry