[Freesurfer] Transforming Amygdala nuclei atlas to MNI space

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Dear all,

I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format.

I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz

then i convert .mgz file to NIFTI using

mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz.

Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place.

Kindly let me know what more i have to do , in order to transform .mgz label into MNI space.

Thanks Vasudev