Re: [Freesurfer] autorecon1 changes orientation

Hi Angela,

why do you care? We reslice to a coronal 1mm isotropic volume for ease of processing. All the coordinates should still be correct and all the transforms we compute account for the reslicing so I don't think it should mess anything up.

cheers, Bruce On Wed, 30 Sep 2009, Angela Y. Wang wrote:

Hi,

When I use autorecon1 it changes the orientation of my original image. My 001.mgz is in LAI. After autorecon1, I get rawavg.mgz is in LAI, however, orig.mgz, T1.mgz and brainmask.mgz are now in LIA. I checked the orientations using tkmedit.

How do I prevent this change in orientation? Thanks for any advice, Angela

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