Nick or Doug could you help us here?
On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might
Bruce
On Fri, 3 Aug 2012, james pardon wrote:
Hi Bruce,
subject's folder is empty, there is no scripts folder, or anything else. Again if I omit -expert everything works fine.
Thanks
On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi James
what happens if you run: ls -l /home/dir/subject/subname/**scripts/expert-options touch /home/dir/subject/subname/**scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/**scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly, I checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, JamesThe 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/**compliancelinehttp://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.
So /home/dir/subject/subname/scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/scripts doug
On 08/03/2012 12:09 PM, james pardon wrote:
Nick or Doug could you help us here?
On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder, or anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/scripts/expert-options touch /home/dir/subject/subname/scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly, I checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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.
works fine. Even I can cp expert.opts to scripts folder on my own. Sorry forgot to reply all at first
On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
So /home/dir/subject/subname/**scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/**scripts doug
On 08/03/2012 12:09 PM, james pardon wrote:
Nick or Doug could you help us here?
On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto: fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>> wrote:
Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder, or anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu>wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/**scripts/expert-options touch /home/dir/subject/subname/**scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/**scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly, I checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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<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.-- 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Delete that dir and run recon-all with -debug as the first option. Pipe the output to a file, eg, recon-all -debug ... |& tee recon-all.log And send me recon-all.log. Note it will likely be very big! doug
On 08/03/2012 12:52 PM, james pardon wrote:
works fine. Even I can cp expert.opts to scripts folder on my own. Sorry forgot to reply all at first
On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So /home/dir/subject/subname/scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/scripts doug On 08/03/2012 12:09 PM, james pardon wrote: Nick or Doug could you help us here? On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder, or anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/scripts/expert-options touch /home/dir/subject/subname/scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly, I checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Hi James, I had the same issue. The following workaround was mentioned on the FS mailing list: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20335.html It works for me. Mehul
On Fri, Aug 3, 2012 at 10:11 AM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
Delete that dir and run recon-all with -debug as the first option. Pipe the output to a file, eg, recon-all -debug ... |& tee recon-all.log And send me recon-all.log. Note it will likely be very big! doug
On 08/03/2012 12:52 PM, james pardon wrote:
works fine. Even I can cp expert.opts to scripts folder on my own. Sorry forgot to reply all at first
On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So /home/dir/subject/subname/scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/scripts doug On 08/03/2012 12:09 PM, james pardon wrote: Nick or Doug could you help us here? On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder,or
anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/scripts/expert-options touch /home/dir/subject/subname/scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up). Secondly,I
checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>-- 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 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
All,
The solution suggested in the link that Mehul has sent works for me. It would be great to have this bug ironed out in future releases of FS :-)
Thanks
On Fri, Aug 3, 2012 at 11:45 PM, Mehul Sampat mehul.sampat@ieee.org wrote:
Hi James, I had the same issue. The following workaround was mentioned on the FS mailing list: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20335.html It works for me. Mehul
On Fri, Aug 3, 2012 at 10:11 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
Delete that dir and run recon-all with -debug as the first option. Pipe the output to a file, eg, recon-all -debug ... |& tee recon-all.log And send me recon-all.log. Note it will likely be very big! doug
On 08/03/2012 12:52 PM, james pardon wrote:
works fine. Even I can cp expert.opts to scripts folder on my own. Sorry forgot to reply all at first
On Fri, Aug 3, 2012 at 9:13 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
So /home/dir/subject/subname/scripts does not exist? If so that is wrong. What happens if you mkdir /home/dir/subject/subname/scripts doug On 08/03/2012 12:09 PM, james pardon wrote: Nick or Doug could you help us here? On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James can you post to the list so others can answer? I'm not sure what's going on, but Nick or Doug might Bruce On Fri, 3 Aug 2012, james pardon wrote: Hi Bruce, subject's folder is empty, there is no scripts folder,or
anything else. Again if I omit -expert everything works fine. Thanks On Fri, Aug 3, 2012 at 7:29 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> wrote: Hi James what happens if you run: ls -l /home/dir/subject/subname/scripts/expert-options touch /home/dir/subject/subname/scripts/expert-options Bruce On Fri, 3 Aug 2012, james pardon wrote: Dear all, I'm trying to pass the following flags for mri_normalize through -expert flag in recon-all, with a file, named expert.opts with the following single line: mri_normalize -b 20 -n 5 my command line is: recon-all -i inputfile -subject subname -all -expert <pathname>/expert.opts I receive the following error: cp: cannot create regular file: '/home/dir/subject/subname/scripts/expert-options' The directory of the subject has been created, but it is completely empty. At first glance I thought it might be some sort of permission problems, however I have rwx permission for all the paths (even running under the root username the same error comes up).Secondly, I
checked my disk quota, it is completely fine. Please note that, if I do not pass -expert flag recon-all works completely fine. Any input is much appreciated. Regards, James 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 thePartners
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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>-- 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 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
freesurfer@nmr.mgh.harvard.edu
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james pardon -
Mehul Sampat