Hi. If you have some images acquired AP and some PA then affine
registration cannot fix the ordering as that would be an illegal
transformation (as you say - even if the "rotation" is done right, you
will then get LR wrong). You must first ensure that all images are
in the same APISLR universe. This is quite easy - in order to reverse the
ordering of an image you can just use avwswapdim - for example
avwswapdim IMAGE x y -z FLIPPED
Steve.
On Tue, 5 Nov 2002, carles wrote:
> Hi Stephen,
>
> sorry for asking again but there is a point that is not clear to me yet.
>
> We have some coronal volumes, some of them acquiered in AP order and the
> other in PA order. If I use -xsearch option to increase the angle search
> range in flirt, I could have a 180o rotation to match A with A and P with P
> but, in this case the images will be flipped in R-L direction, so this is
> not a good solution. My question is if I can ask flirt for checking if image
> must be flipped AP<->PA or TB<->BT to have a good registration between both
> images.
>
> Thanks again,
>
> Carles Falcon
> University of Barcelona
>
>
>
> -----Mensaje original-----
> De: FSL - FMRIB's Software Library [mailto:[log in to unmask]]En nombre
> de Stephen Smith
> Enviado el: jueves, 31 de octubre de 2002 16:25
> Para: [log in to unmask]
> Asunto: Re: [FSL] image order in SIENA
>
>
> 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
>
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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