On Aug 2, 2017 17:46, "Douglas Greve" <greve@nmr.mgh.harvard.edu> wrote:

what do you mean by referential? the coordinate system of the vertex coords?
On 8/2/17 4:49 AM, pierre deman-kibleur wrote:
Hi,

Is it possible to have the gifti output in the same referential as the orig nii file as well ?
I tried mris_convert lh.white lh.white.gii -rl mri/orig/001.mgz

but mris_convert doesn't have the -rl option.

Regards,

Pierre

On Wed, Aug 10, 2016 at 2:40 PM, Iglesias, Eugenio <e.iglesias@ucl.ac.uk> wrote:

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

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DEMAN Pierre
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