Hi Tommi,
The mkdir error suggests to me that there is some system-level permissions thing going on. If it can't make the directory, then there is no directory into which fsl can write the refvol.fslregister.nii files, hence the final 2 errors.

>From the command line, are you able to navigate to directory:
/usr/pubsw/packages/fsl/current/data/standard/
And within that directory, execute:
mkdir <somedirectoryname>

My guess is that you will get a permission denied error. You can try using chmod to make the directory writable:
chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/
and see if you can now do a mkdir in that directory (you might have to be a superuser to do this)

Dear Surfers,

mni152reg --$SUBJECT exits with the error:

mkdir: cannot create directory
`/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402':
Permission denied

Thereafter, a couple consequential errors follow
...
niiWrite(): error opening file
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii
...
ERROR: failure writing
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii

This is on FS 5.1.0 stable. The error seems linux box independent. Please
let me know if you need further info. Thanks!

Bests,

Tommi

-- 
Chris McNorgan
Postdoctoral Researcher
Developmental Cognitive Neuroscience Laboratory
Northwestern University, Evanston, IL
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