> I am having trouble with image orientation in SPM99 following the
> conversion of my pet minc files to analyze format (using ana2mnc).
Not mnc2ana ? If you do this, ensure that the different planes are
intensity scaled correctly (there was a slight problem with some very
old SPM templates because of this).
>
> When viewing the analyze files using Display, the images in the two top
> windows (coronal and saggital views) are upside down- (i.e., top to bottom
> is actually inferior to superior). The axial image in the bottom window
> appears normal.
You could use SPM to do the conversion. e.g. via ImCalc, by evaluating the
simple expression "i1". Note also that you will need to be careful with the
left-right direction of the converted images. As you are using SPM99, you
will need to avoid the default behaviour of left-right flipping during the
spatial normalisation.
>
> I only experience this problem when using analyze files converted from minc
> in native space, when I use analyze files converted from talaraich-
> transformed minc images, all appears well.
I'm not surprised about this.
>
> First, I imagine that there is a relatively easy way to reorient the
> images, but I am not terribly familiar with SPM and would appreciate any
> advice on this matter.
You could also use the reorientation option of the Display function. Do a
search for "reorient display" through the JISCMail emails (possibly restricting
the search to emails from me).
>
> Second, is it possible to just use the converted talaraich-transformed
> images -which I will then normalize w/in SPM? - or is this generally not a
> good idea?
Probably not, as there is a good chance that there will be missing data within
the FOV, which could cause problems. Also, the affine registration in SPM
spatial normalisation assumes that the template brain is slightly bigger than
a typical brain, and will slightly bias the result. If your image has
been T&T transformed, then it is already the same size.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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