[Freesurfer] set message
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.u...@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 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] set message
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 gr...@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.u...@tufts.edu mailto:heather.u...@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 gr...@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. -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.u...@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 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] set message
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 fis...@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.u...@tufts.edu mailto:heather.u...@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. -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.u...@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 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] set message
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 gr...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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.u...@tufts.edu mailto:heather.u...@tufts.edu mailto:heather.u...@tufts.edu mailto:heather.u...@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.u...@tufts.edu mailto:heather.u...@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 gr...@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 -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.u...@tufts.edu phone: 617-627-3733 fax: 617-627-3181 http://ase.tufts.edu/psychology/ebbl set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 5 != 0 ) set flag = $argv[1] ; shift
