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 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>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer