Hi,

I’m having difficulty making BedpostX work on non-tutorial data per the tutorial located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

The preprocessing has worked without errors, but now that I’m using BedpostX, the output is producing:

subjectdir is {subject's directory}/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed Queuing post processing stage

Obviously, it shouldn’t be going straight from 0 slices processed to the post processing stage. I’m running the command directly (i.e. bedpostx {subject's directory}/dmri ), and when the process is done ( it ends in 25 seconds) the dmri folder has files that are in the format data_slice_00**.nii.gz and nodif_brain_mask_slice_00**.nii.gz.

I’ve also tried running the command: trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial on a cluster, which produces the same output.

Has anyone else had this issue?

Thanks for any help, Anna