Hi Carles.
> Do the programs involved in SIENA recognize if images have axial, coronal or
> sagital format?
No - the Analyze image format does not unaombiguously provide that
information...but read on...
> Are, then, the options -b or -t affected in anyway by the
> images original orientation?
No - there is no problem here - because these options relate to the
up-down axis in standard space. So it doesn't matter what the orientation
of the input images is. Note though - if your orientation is very distant
from the standard-space images you might want to increase the flirt search
space by editing the siena script - find the "Talairach space masking"
flirt calls and add in the -xsearch (etc) options.
good luck! Steve.
Stephen M. Smith
Head of Image Analysis, FMRIB
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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