Hi Susie - avscale is part of the FSL package. You have to make sure FSL is installed and in your path.

a.y

On Wed, 6 Feb 2013, Susan Kuo wrote:

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