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

--
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
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