Hi Stefano,

the orientation info is stored in the header, and can be accessed with mri_info. It should be propagated to AFNI, not sure why it's not. Bob and Ziad: have you had any trouble with losing the direction cosines when converting things from .mgz?

cheers, Bruce

On Thu, 23 Mar 2006, Pellegrini, Stefano (NIH/NINDS) [F] wrote:

thanks Bruce,

actually it is ok if I view it with tkmedit. But if I try to convert it to minc format and I try to view it with AFNI (for istance), I get the wrong orientation. Is there any way to automatically know which kind of orientation I am working with, so that I can include it in a script when I want to use the conversion to the minc format? thanks again,

   -stefano

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thu 3/23/2006 10:19 AM To: Pellegrini, Stefano (NIH/NINDS) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] --conform option

Hi Stefano,

the --conform does several things to the input volume to put it into a format we expect. If you bring it up in tkmedit and it properly shows you the various directions (e.g. the "coronal" view is indeed coronal) then you should be fine.

Bruce On Thu, 23 Mar 2006, Pellegrini, Stefano (NIH/NINDS) [F] wrote:

...

Hi everybody,

can anybody explain to me why when I use mri_convert with the --conform option with an input volume RAS oriented (let's say it is raw_mean.mgz) I get as output a volume LIA oriented (let's say it is orig.mgz)? is that ok? thanks,

 -stefano

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