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.