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
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