Hi, 
  I've been trying to email out for help to the FreeSurfer community, using the below addresses. However, I am not receiving my own email back, though I am a member of the mailing list via this email address. Can you tell me what I'm doing wrong?

Thank you!
Susan Kuo

---------- Forwarded message ----------
From: Susan Kuo <susan.kuo.run@gmail.com>
Date: Wed, Feb 6, 2013 at 4:57 PM
Subject: Troubleshooting the preproc
To: ayendiki@nmr.mgh.harvard.edu
Cc: freesurfer@nmr.mgh.harvard.edu


Hi FreeSurfer community,
 
  I am currently trying to troubleshoot my preprocessing part of TRACULA with the tutorial dataset (for Diff001 as the subject, specifically), running trac-all -corr -c <config dmrirc>. I am running the commands in subjectID/scripts/trac-all.cmd one by one because I've had problems with some of the steps. Specifically, flip4fsl didn't work. I instead used fslswapdim -x -y z (flip4fsl uses fslswapdim x -y z, which doesn't generate the correct orientation for FSL in fact), followed by fslorient -forceradiological. I successfully ran eddy_current thereafter. Now I am stuck again, at FreeSurfer's xfmrot, which should look like: 

xfmrot <transform file> <input vector file> [<output vector file>]

I specifically typed in: 

xfmrot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/dwi.ecclog /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs.norot /j/dti7/Susie/freesurfer/subjects/diffusion_tutorial/Diff001/dmri/bvecs


and received the following iterative errors:

avscale: Command not found.
R: Subscript out of range.
R: Subscript out of range.
R: Subscript out of range.

Can any of you help me? 

Thank you, 
Susie K