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
>
>
>
>
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> --
> 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>

>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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