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
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