Automate segmentation of ventricles from Brain MRI

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Automate segmentation of ventricles from Brain MRI

I have about 50 MRI series (T1, T2, Flair and T1 volumetric) that I would
like to segment out the ventricles to generate 3D models and to calculate
the volumes.  I would appreciate any input as to how best to go about doing
this in a manner that is as autonomous as possible.

One method I was considering was using one of the brain atlases to identify
and label all of the anatomy and then selectively export just the ventricles
for each MRI. At this point I am having some difficulty with using the
BRAINS fit to non rigidly register the atlas a subjects MRI in such a way
that the CSF space or ventricles are correctly labeled.

Any help would be great with this process or if someone has another
suggestion such as trying to automate the segmentation of just the
ventricles.  I did see in one of the tutorials where you can use a module to
label the CSF space, skull, white mattter and gray matter, maybe this would
be another step

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