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 --$SUBJECT exits with the error:
mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402': Permission denied
Thereafter, a couple consequential errors follow ... niiWrite(): error opening file /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii ... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.18402/refvol.fslregister.nii
This is on FS 5.1.0 stable. The error seems linux box independent. Please let me know if you need further info. Thanks!
Bests,
Tommi
Hi Tommi and Chris, this is a known bug that has been fixed in dev (and upcoming 5.2). Can you use the dev version just for this cmd? doug
On 01/24/2013 12:14 PM, Chris McNorgan wrote:
Hi Tommi, The mkdir error suggests to me that there is some system-level permissions thing going on. If it can't make the directory, then there is no directory into which fsl can write the refvol.fslregister.nii files, hence the final 2 errors.
From the command line, are you able to navigate to directory:
/usr/pubsw/packages/fsl/current/data/standard/ And within that directory, execute: mkdir <somedirectoryname>
My guess is that you will get a permission denied error. You can try using chmod to make the directory writable: chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/ and see if you can now do a mkdir in that directory (you might have to be a superuser to do this)
Dear Surfers, mni152reg --$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 DCNL Lab:http://tinyurl.com/9q35abd Frontiers Profile:http://tinyurl.com/aut488k
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