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 . 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 []
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
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