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Dear Phil, FIRST is based on manual segmentations that come from the Centre for Morphometric Analysis (CMA) in Boston, as indicated in the documentation on FIRST. If you do a google search for "CMA segmentation manual" then you get the webpage: http://www.cma.mgh.harvard.edu/manuals/segmentation/ which contains all the information about how the CMA created these segmentations. All the best, Mark On 11 Mar 2013, at 09:26, philipp thomann <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Experts, this is a repost. I am quite dependant on a "good" answer since a reviewer asked us exactly this. Any help is highly appreciated. Thanks Phil -------- Original-Nachricht -------- Datum: Fri, 8 Mar 2013 19:59:07 +0100 Von: Philipp Thomann <[log in to unmask]<mailto:[log in to unmask]>> An: [log in to unmask]<mailto:[log in to unmask]> Betreff: Re: [FSL] Brainstem borders - FSL Hi, now I am a little confused. While I am well aware of the fact that the brainstem comprises midbrain, pons and medulla, I am wondering how the inferior border of the brainstem was defined during the manual tracing process as part of the development of FSL-FIRST. Can anyone of the FIRST experts/developers give me a clue? Thanks Philipp Am 08.03.2013 um 11:19 schrieb Andreas Bartsch: Hi, yes - you're right. The medulla oblongata (=myelencephalon) should also be included in the brainstem (truncus cerebri) - and not just the metencephalon (pons + cerebellum). So it is above the C1 level of the medulla spinalis up to the mesencephalon / diencephalon border. Cheers, Andreas Am 08.03.13 10:38 schrieb "Peter Foley" unter <[log in to unmask]<mailto:[log in to unmask]>>: Hi I'm a clinical neurologist. Not sure exactly how the caudal extent of the brainstem is defined by consensus but this should be available from a good neuroradiology text/friendly neuroradiologist. Just for the avoidance of doubt though, the term brainstem is clinically taken to include midbrain, pons and medulla. good luck. pete