[Freesurfer] Permission denied - could not open lh.BA3b.thresh.label
Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 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 recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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] Permission denied - could not open lh.BA3b.thresh.label
Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 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 recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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.
Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label
It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 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 recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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.
Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label
Probably a network glitch? I'd try restarting it and seeing if the error persists. On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 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 recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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.
Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label
I am thinking that that's possible. Same command with same type of parameters executed successfully before the failure, and now previously failed command is working. I will try it again... Thanks for the input. -Ronny Probably a network glitch? I'd try restarting it and seeing if the error persists. On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: It looks like this is the first *thresh.* label that caused the problem. The following command ran and executed properly just before the error message on the log. mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface So looks like lh.BA3a.thresh.label ran just fine, but not lh.BA3b.thresh.label. This ran as part of recon-all and failed in the middle of executing that script so I hadn't even tried to run it any other way (without *.thresh.*) That said, I just ran the problematic piece line of code and it all of a sudden works just fine... mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface Any reason why it wouldn't have worked Friday near 7pm and works not? -Ronny Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or is BA3b.thresh the only one? If you remove the .thresh do you still get an error? Thanks, a.y On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello, I ran recon-all and left it running Friday afternoon/evening. When I next checked it this morning, the script had finished with errors. Looks like there was a problem with the file: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the script couldn't open it. Thoughts? -Ronny Further info below: machine: quito Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308 /usr/local/freesurfer/dev/bin/freesurfer SUBJECTS_DIR: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects Working Directory: /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig ** the exact command line I ran recon-all -autorecon2-cp -autorecon3 -subjid subj004 ** The command that caused the error (which was as a part of/ within the recon-all script) is mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface ** ERROR MESSAGE RECEIVED ** Permission denied mri_label2label: could not open label file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srclabel = /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = subj004 trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Invalid argument ERROR reading /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label Linux quito 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 recon-all -s subj004 exited with ERRORS at Fri Mar 8 21:04:18 EST 2013 For more details, see the log file /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ 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
