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