| I have 22 PET scans to process. When I perform a spatial normalization, it
| said that the images are flipped and a negative scale to X was given. So I
| swapped the data along X axis, then the result from spatial normalization
| said that the images are also flipped and a nearly same negative scale to X
| was give. Does anybody know why this will happen? Thanks a lot.
The first step in the spatial normalisation is an affine registration,
which takes its starting estimate from the defaults (which includes
a flip). To disable the flipping for the remainder of an SPM session
you need to modify the default starting estimates from
[0 0 0 0 0 0 -1 1 1 0 0 0] to [0 0 0 0 0 0 1 1 1 0 0 0]. This
can also be done for everyone who uses SPM99b by modifying spm_defaults.m
at around lines 137 and 138 so that they say something like:
% Orientation/position of images. Used as a starting estimate for
% affine normalisation.
%-----------------------------------------------------------------------
sptl_Ornt = [0 0 0 0 0 0 1 1 1 0 0 0]; % Neurological Convention (R is R)
%sptl_Ornt = [0 0 0 0 0 0 -1 1 1 0 0 0]; % Radiological Convention (L is R)
Proper transversely oriented Analyze format images are in Radiological
orientation, whereas the images after spatial normalization are in
Neurological orientation. This is why a flip is included by default.
I hope his helps,
-John
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