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 7:36 PM, james pardon james.pardon15@gmail.comwrote:

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.eduwrote:

...

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

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