Thanks Dr Douglas for your reply. Following is the list of command I used to generate brainstem mask.

• I first created from average subject directory, mask of brainstem using mri_binarize command: 
  

mri_binarize --match 16 --i aseg.mgz --o hc_brainstem.mgz

• Then converted to mni305 space using mri_convert command:

mri_convert mdd_brainstem.mgz mdd_brainstem.mni305.mgz --apply_transform transforms/talairach.xfm -oc 0 0 0 --conform

• Converted the .mgz to nii.gz with command:

mri_convert mdd_brainstem.mni305.mgz mdd_brainstem.mni305.nii.gz

Finally overlaid it on the mni_colin_t1hires atlas using mango.

Thanks and regards,

Sam

On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

how was it created?

On 6/20/17 9:41 AM, Dr Sampada Sinha wrote:

Dear freesurfer experts,

I am trying to over brainstem mask of my patients' group on mmi_colin_t1hires atlas. I had no problems in overlaying thalamus or amygdala mask, but somehow the midbrain mask is shifted from the actual place (please see attachment). Can you please let me know how do I correct this error?

Thanks for all your help.

Kind regards,

Sam

--

Dr Sampada Sinha

​Research medical scientist (B)​

Department of Geriatric Mental Health (DGMH)

King George Medical University

Lucknow-226003

​, Uttar Pradesh​

India

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Dr Sampada Sinha

​Research medical scientist (B)​

Department of Geriatric Mental Health (DGMH)

King George Medical University

Lucknow-226003

​, Uttar Pradesh​

India