On Fri, Aug 3, 2012 at 8:05 PM, Bruce Fischl <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>
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

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