It did not generate the error because the IsRunning file still exists. Can you delete this file
/autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/ scripts/IsRunning.lh+rh and re-run, capturing the output to send to me? doug On 08/27/2013 12:47 PM, pfot...@nmr.mgh.harvard.edu wrote: > Sure thing, I have attached it. > > Best, > Panos > >> Can you run it with -debug as the first option and send me the terminal >> output? >> On 08/27/2013 12:36 PM, pfot...@nmr.mgh.harvard.edu wrote: >>> Hi Doug, >>> >>> The same error message comes up. >>> >>> Panos >>> >>>> try this instead >>>> >>>> recon-all -all -subjid CAA_022_struc >>>> >>>> On 08/27/2013 11:23 AM, pfot...@nmr.mgh.harvard.edu wrote: >>>>> Hi FS Commuity, >>>>> >>>>> I am using the stable version 5.3 of FS to recon-all a subject of >>>>> mine, >>>>> but the job is aborted and gives the following message: >>>>> >>>>> The command that I ran is: recon-all -all -subjid >>>>> /cluster/ichresearch/Petechial/MEG/CAA_022_struc >>>>> >>>>> >>>>> Subject Stamp: >>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>>> Current Stamp: >>>>> freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 >>>>> INFO: SUBJECTS_DIR is /autofs/cluster/ichresearch/Petechial/MEG >>>>> Actual FREESURFER_HOME >>>>> /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 >>>>> Linux eesmith 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 >>>>> 03:10:46 >>>>> UTC >>>>> 2013 x86_64 x86_64 x86_64 GNU/Linux >>>>> #-------------------------------------------- >>>>> #@# MotionCor Tue Aug 27 11:09:19 EDT 2013 >>>>> Found 2 runs >>>>> >>>>> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/001.mgz >>>>> >>>>> /autofs/cluster/ichresearch/Petechial/MEG/CAA_022_struc/mri/orig/002.mgz >>>>> Checking for (invalid) multi-frame inputs... >>>>> if: Expression Syntax. >>>>> Exit 1 >>>>> >>>>> Also, I tried doing the same recon-all with the stable 5.0 version and >>>>> it >>>>> runs fine. Therefore, I was wondering whether you could tell me why is >>>>> this happening. By the way I have also attached the recon-all.log. >>>>> >>>>> Thank you for your time. >>>>> >>>>> Best, >>>>> Panos >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >> >> >> >> >> >> _______________________________________________ >> 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.
