HI Adam, what machine are you running from? This might be a case where a local machine cannot talk properly to the cluster disk space. You can try pbsubmit-ting the isxconcat-sess job.
doug Adam Nitenson wrote: > Hello Freesurfers, > > I'm having an odd problem with isxconcat. I tried running the command > for two separate groups (using Seymour): > > isxconcat-sess -sf > /cluster/roffman/users/Stable5_PerRun/Subject_Files/17_FB_Regression_Seed > -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 > -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix > -hemis -o /cluster/roffman/users/Stable5_PerRun/17_FB_Regression_Seed > > isxconcat-sess -sf > /cluster/roffman/users/Stable5_PerRun/Subject_Files/17_MTH_Regression_Seed > -d /cluster/roffman/users/Stable5_PerRun -analysis SIRP_Stable5 -c Cond1v3 > -c Cond1vFix -c Cond3vFix -c Cond1v5 -c Cond1v7 -c Cond5vFix -c Cond7vFix > -hemis -o /cluster/roffman/users/Stable5_PerRun/17_MTH_Regression_Seed > > About an hour in, both commands stop simultaneously and produce the error > > "MRISread(/cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg): > could not open file > Reading target registration > /cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg > No such file or directory > ERROR: could not read > /cluster/roffman/users/Stable5_PerRun/fsaverage/surf/lh.sphere.reg" > > I have since tried re-running the commands, but received the same error, > however both groups stopped during different subjects than last time. I'm > really not sure what the problem could be, as I have already concanenated > these groups for different analyses (including surface analyses, which > worked fine). It seems really odd that the commands for both would > simultaneously terminate. > > > Thanks, > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > niten...@nmr.mgh.harvard.edu > Phone: 617-643-3215 > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
