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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
