Hi Ella,

There are a number of options:
You can draw manual segmentations on individual subjects, though the time and cost required for this labor-intensive process of manual tracing has become prohibitive.  

Paul's suggestion would be a better one, maybe one of our protocols described in e.g. http://www.ncbi.nlm.nih.gov/pubmed/21733239 could be of use to you? In case of drawing on the fsaverage, I would add the suggestion to draw at least two times to see if you're segmentation is reliable (compare your two (or more) ROIs and check for overlap and non-overlapping parts, for non-overlap decide whether those voxels should be in- or excluded). Subsequently, you map your segmentation to individual subjects and check for correct registration.

Another approach would be to use the ROI from the Wake Forest University PickAtlas. You can map this to FS-space, and follow similar procedures to map to native space. Though I must note that this ROI is not perfect.

All depends on your research question of course, how detailed do you want your ROI to be.

Best of luck,
Cédric


----------------------------------------------------------------
  P.C.M.P. Koolschijn (Cédric), PhD 
  Dutch Autism & ADHD Research Center
  Brain and Cognition
  The Netherlands
  W http://www.dutcharc.nl/



On 3/18/14 1:04 PM, "Paul Beach" <pabeach1@gmail.com> wrote:


Ella,

My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against
the literature to see if your ROI performs well. It's not perfect, but it can give decent results.

Cheers,
Paul

Sent from my iPhone

On Mar 18, 2014, at 7:13 AM, Ella <ellahinton@hotmail.com> wrote:



Hi all,

I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus?

thanks in advance
Ella



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