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Thanks for your help, Bruce. This worked like a charm! How would I register the output segmentation back to the subject's T1.mgz? When I use mri_convert, the ROIs have a weird border around them.


thanks again,

Ryan 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Sent: Wednesday, December 19, 2018 11:43:03 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Setting the origin in native space
 
Hi Ryan

I think mri_convert -at <tal xform> <input vol> <output vol>

should do the trick.

cheers
Bruce


On Wed, 19 Dec
2018, Nillo, Ryan Michael R wrote:

>        External Email - Use Caution
>
> Hello FreeSurfer users,
>
> I want to use the suit software to segment the cerebellum, however the software requires the origin be set at the anterior composure. I know the Talairach image’s origin is set at the anterior commisure and that there is a Talairach transformation in mri/transforms. Is there a way to use this information to set the origin to the anterior commisure in the native space image?
>
> Thanks in advance,
> Ryan Nillo
> Staff Research Associate
> UCSF Department of Radiology and Biomedical Imaging
>
>
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