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