Hi Shanqing - You could try running FSL's bedpostx directly on /users/cais/STUT/tracula/S01/dmri. Our scripts have only been tested on our clusters running PBS, but the original FSL version is designed to work with SGE. If you find what's going wrong on SGE we'll be happy to incorporate any fixes of course!

a.y

On Fri, 27 May 2011, Shanqing Cai wrote:

Hi,

I am running Tracula on the MIT BCS cluster. The first step "-prep" finished without error. However, during the second step "-bedp" I received the following error messages.

ba3:~/STUT/tracula> trac-all -bedp -c ~/STUT/tracula/tracula.cfg INFO: SUBJECTS_DIR is /users/cais/STUT/FSDATA INFO: Diffusion root is /users/cais/STUT/tracula Actual FREESURFER_HOME /software/Freesurfer/5.1.0 ln -sf /users/cais/STUT/tracula/S01/dlabel/diff/anat_brain_mask.bbr.nii.gz /users/cais/STUT/tracula/S01/dmri/nodif_brain_mask.nii.gz ln -sf /users/cais/STUT/tracula/S01/dmri/dwi.nii.gz /users/cais/STUT/tracula/S01/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /users/cais/STUT/tracula/S01/dmri subjectdir is /users/cais/STUT/tracula/S01/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator Queuing parallel processing stage [: 223: SGE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x67: unexpected operator Queuing post processing stage [: 223: SGE: unexpected operator [: 314: SGE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator

It seems that there are errors related to SGE configurations. Anyone has any suggestions w.r.t. how to solve this problem?

Thanks!

Best regards, Shanqing _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer