Hi Mohamad, For now, our brainstem module separates this structure into midbrain, pons, medulla and SCP - please see this link: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures If you want to segment more specific nuclei, we don’t have a tool capable of doing that yet. Cheers, /Eugenio

Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 30 Aug 2016, at 17:34, Alshikho, Mohamad J. <MALSHIKHO@mgh.harvard.edumailto:MALSHIKHO@mgh.harvard.edu> wrote:

Hi Iglesias, Kindly, we would like to know if there are any methods in Freesurfer that can help to segment thatbrain stem nucleus. I mean output the nucleus automatically as a small masks, so these small masks can be used in other analyses (e.g. fMRI)

I am thinking of creating masks for these nucleus depending on an atlas. I open the T1 image in Fslview and I create the mask for the nucleus of interest. But this is so hard, not accurate and time consuming. The reason for my question. We highly appreciate any suggestion!

Best, Mohamad

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