Hi Crystal - This is because of the way the B0 dewarping script is called during the pre-processing. It assumes that you have 2 phase images instead of the difference of 2 phase images (which is what you have). The next version actually accommodates both cases but for now you have 2 options:

1. Edit the script $FREESURFER_HOME/bin/trac-preproc and change this line: set cmd = ($cmd --ph $dwidir/b0pha.nii.gz) to this: set cmd = ($cmd --dph $dwidir/b0pha.nii.gz)

2. Be lazy and skip B0 dewarping!

Hope this helps, a.y

On Wed, 24 Oct 2012, Franklin, Crystal G wrote:

Freesurfer,

I am trying to run trac-all –prep and trac-preproc keeps exiting with errors.  It keeps saying the unwrappedphasemaps must contain at least two volumes.  My data only contains one phase image and 2 magnitude images.  Do you know what could be causing this error or how to get around it?

Thanks in advance, Crystal