Hi everybody,
I've been given that task of investigating whether it is possible to
perform VBM on rat brains.
Over the past few days I've been playing with the first stage in the
process namely brain extraction. My initial experiments indicate that
it will not work. The shape differences between the human and rat
brain are too great: the rat brain is too oblong by comparison and
bet is producing circular masks.
Even if I could replace FSL's bet with AFNI's 3dSkullStrip which does
a much better job at rat brain extraction, I'm then left with the
problem of the atlases and registration. Even if I could get the
Paxinos atlas in a computer file (and I don't know if i can), would
the registration tools even work with it (assuming I make appropriate
modifications to the scripts to accommodate the new atlas)?
In short am I asking too much of FSL to work with rat brains?
Thanks in advance,
Regards,
--
Dr Colm G. Connolly
School of Psychology and Institute of Neuroscience
The Lloyd Building
University of Dublin
Trinity College, Dublin 2, Éire
Tel: +353-1-896-8475
Fax: +353-1-671-3183
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