Re: [Freesurfer] aparc+aseg.mgz to nifti conversion

Hi Gabor

try adding:

-odt int

to the mri_convert command line. Because the rawavg.mgz is type uchar it wants to convert to uchar otherwise, which is messing things up.

cheers Bruce

On Thu, 11 Sep 2014, Gabor Perlaki wrote:

Dear all,

I'd like to convert the aparc+aseg.mgz to nifti and use it in the space of the original MR image. The basic conversion from mgz to nifti works fine "mri_convert aparc+aseg.mgz aparc+aseg.nii". However if I reslice it in the space of the original MRI than something fails and even negative intensities are presented in the converted aparc+aseg2raw.nii file " mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz aseg+aparc2raw.nii". Any idea how to convert it?

Best Regards, Gabor