[Brains-users] where to cut the brain stem

[Christoph Christmann]

We now decided to use all CSF and brainstem since we cannot find any 
valid reason to cut the brainstem or the CSF at a certain point 
except the transition to the spinal cord.
By including these parts we add only a small amount of CSF, GM and WM 
to the 'whole brain'.

Nevertheless, we are interested in contradicting and concurrent opinions.

Christoph

At Tuesday 21.03.2006 18:57, Ronald Pierson wrote:
>My opinion is that it probably doesn't make a big difference, unless you
>have a real interest in brainstem CSF.  To my knowledge, we haven't ever
>used brainstem volumes directly from these measures for anything.
>Indirectly, one could use them to remove the brainstem and cerebellum
>from whole brain volumes to get cerebral volumes.  For that purpose, the
>definition of the cutoff is irrelevant - it all gets subtracted.  Also,
>adding up the cortical lobes does the same thing, and you don't need the
>brainstem for that, either.  Maybe it will have a small affect on total
>brain compartment volume, if you use that for anything.
>
>However, that doesn't really help you make a decision about the cutoff.
>
>Vince Magnotta suggested something a few years ago that makes alot of
>sense.  Why not cut the brainstem at the bottom of the extended
>talairach bounds?  We add two rows of boxes below the normal talairach
>boxes to include the cerebellum.  To see them, load the Talairach.bnd,
>go to the selector, select the talairach bounds, click on object
>properties, then turn on the grid.  Then, simply trim the brain trace to
>cut off anything of the spinal cord/brainstem that extends below this.
>If the trace doesn't extend down far enough to reach the bottom of the
>grid, you will need to extend it down there.  I think this does a nice
>job as a guide and really takes away the hassle of finding the arteries,
>figuring out what to do when they don't look normal, etc.
>
>We haven't implemented it here because we have lots of longitudinal
>scans and need to continue doing it the same way to maintain continuity.
>However, if I were starting from scratch on a dataset, that is how I
>would do it.
>
>Ron
>
>On Tue, 2006-03-21 at 16:37 +0100, Christoph Christmann wrote:
> > Hi all,
> >
> > taking into account the manuals procedure to cut the brain at the
> > vertebral arteries I end up with a brain stem cutted oblique and the
> > lower part of the cerebellomedullar cinsterna is missing. However, if
> > I add the complete cisterna the measured occipital CSF is clearly
> > bigger than the Iowa norm. I am very interested in the procedures of
> > other groups - it seems necessary to me to include the whole cisterna
> > volume to get an overview over the CSF. But regarding the inclusion
> > of parts of the brain stem I am not quite sure.
> >
> > TIA
> >
> > Christoph
> >
> >
> >
> >
>--
>Ronald Pierson <ronald at psychiatry.uiowa.edu>

-- 
Christoph Christmann                  christma at as200.zi-mannheim.de
Psychologist, MEE                     Fon/Fax +49 621 1703 63 18/05
Central Institute of Mental Health    http://www.zi-mannheim.de
Department of Clinical                  D-68159 Mannheim J5
and Cognitive Psychology                       

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