Covert Mgz to Nifti

Mgh/Mgz is the MGH Freesurfer format, which means other software that only accept Nifti or Analyze7.5 (hdr/img pairs) can not read it. Here shows a way to convert the mgh/mgz format to nifti and swap the nifti image so that the FSLview can display it correctly.

For example we have an MRI image in mgz format and it is named A.mgz.

In the terminal,  type: mri_convert –out_orientation LAS A.mgz A_swap.nii.gz  press ‘Enter’.

To convert a hdr/img format mri:  mri_convert –out_orientation LAS A.img A_swap.nii.gz

These commands will give you A_swap.nii.gz which FSLview, mricro etc. could show in a correct orientation.

In the terminal type: FSLview

And load the A_swap.nii.gz image