Try

mri_vol2vol --interp nearest --mov aparc+aseg.mgz --regheader --targ rawavg.mgz --o aparc+aseg.native.nii.gz

Natalia Sanchez wrote:

Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_convert and do cortical and subcoritcal segmentation in FreeSurfer. The outputs of the segmentation are the converted back into .nii.gz so I can use them in FSL, however, the dimensions of the Freesurfer outputs don't match with the FSL files. The freesurfer outputs are 256x256x256. Is there a way I can downsample this outputs to use them in FSL?

Thanks!

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