try using the switch:

mri_convert -rt nearest ...

to use nearest neighbor interpolation (which is what you need to resample a segmentation volume)

cheers Bruce

On Sun, 6 Jan 2019, Nillo, Ryan Michael R wrote:

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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

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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:

...

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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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