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....@gmail.com> Date: Wed, Feb 6, 2013 at 4:57 PM Subject: Troubleshooting the preproc To: ayend...@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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
