Hi Kirstie - That's correct. The only difference between the anatorig and anat is in the orientation, where the latter is always in LAS so it looks straight if you open it in fslview. For the purposes of freeview and every other freesurfer program, the two are indistinguishable, and they should align with the volumes in your subject's mri/...

a.y

On Fri, 22 Aug 2014, Kirstie Whitaker wrote:

Hi

I have a very minor question about the naming scheme for tracula output.

I have the folders anat and anatorig in the dlabel folder. Am I right that:

• anatorig is the T1 image in "freesurfer space" (256 x 256 x 256; LIA)
• anat is a rotated version of the T1 image in freesurfer space that lines up with the standard orientation used by FSL (256 x 256 x 256; LAS)

So neither is actually in the same space as the *original* file that was passed to recon-all (176 x 240 x 256; LAS)?

I ran mri_label2vol with dlabel/anat/anat_brain_mask.nii.gz as the --temp argument and the labels didn't line up nicely. They did line up with anatorig though. Is this what you'd expect?

Kx

-- Kirstie Whitaker, PhD Research Associate

Department of Psychiatry University of Cambridge

Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB

Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com