I think the email you read in the JISCmail archives only refers to SPM99. In
SPM99, the data were sometimes flipped during spatial normalisation
(depending on how sptl_Ornt was set).
Since SPM2, flipping no longer applies. In SPM2 (and SPM5b) you specify
whether all your data are stored left- or right- handed by setting the
appropriate value in spm_defaults.m. This is the value of the global
variable "defaults.analyze.flip". Most people have this set to a value of 1.
Once set, you should never change it, or use the same data with an
installation of SPM that uses a different value for defaults.analyze.flip,
because this can lead to unpredictable results.
See http://www.fil.ion.ucl.ac.uk/spm/software/spm2/#Compatability for more
information.
Best regards,
-John
> I searched the emaillist archives, and it was said SPM might flips the
> images by default in affine normalization, but I couldn't find the shown
> correspondent codes in both spm_normalise.m and spm_normalised_ui.m.
>
> % 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)
>
> Is flipping really the default set in normalization??
>
> In addition, if this is true, and if I normalize my data twice (which is
> needed in VBM, first normalized to MNI template and then normalized to my
> own template), does it mean that the images will be flipped twice and at
> last I still get the images with left is right and right is left? How
> could I change the setting to get the right orientation?
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