You can always run mri_convert with the -rl (“reslice like”) flag to achieve this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt float
If it’s a segmentation volume, you should add -rt nearest, in order to use nearest neighbor interpolation.
Cheers,
Eugenio

Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 10 Aug 2016, at 13:31, pierre deman <deman.pierre@gmail.com> wrote:

Hello,

I am trying to have the atlases aparc.a2009+aseg.mgz, hippocampal subfield etc ...
in a matrix with the same size as the input of recon-all (and not the cubic matrix 256x256x256) and with the same orientation.

what is the best way to do it ?

Cheers,
Pierre

--
DEMAN Pierre
Mobile : +33 7 82 57 80 94
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