what command are you running (I mean the full command line -- hard to debug without it). The preprocessing should not require matlab. Just guessing, this does not look like a FS problem.
doug

On 12/11/11 2:34 PM, Maryam Vaziri Pashkam wrote:

Hi,

I am running preprocessing on my data using freesurfer 5.1, fsl 4.1.7, and matlab R2009a (I also tried it with matlab 2007a) on Harvard cluster and I am receiving an error. I connect to the cluster using terminal and SSH connection in mac.

the preprocessing is stalled in the middle with this error:

++ Max displacement in automask = 0.79 (mm) at sub-brick 3
Can't connect? tcp_connect[connect]: Connection timed out
++ Wrote dataset to disk in 004/tmp.mc-afni2.20850/outvol.nii.gz
** Warning: overwriting file 004/fmcpr.mcdat
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out
Can't connect? tcp_connect[connect]: Connection timed out

It does not stop running and output an error. But rather keeps printing the last line and does not move forward. Any idea where the problem might be?

Thanks,

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