Re: [Freesurfer] Regarding_ Midbrain_misalignment

And the same process worked for thalamus and amygdala? If so, then I don't know what is going wrong. Try doing the visualization in freeview. Also see if the amyg/thal seem to be in the right place relative to brainstem when you visualize all of them together.

On 6/25/17 9:31 AM, Dr Sampada Sinha wrote:

Hello Dr Greve,

Will you please let me know if the above said process I did to overlay brainstorm mask on colin atlas is correct?

Thanks and regards,

Sam

On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha <drsampadasinha@gmail.com mailto:drsampadasinha@gmail.com> wrote:

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 <mailto: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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