> My analyze files were produced through MRIcro. Since my last mail I have
> looked at phantom images with markers for left and right. I have set the
> default LR flip in MRIcro to ‘1: RPI --> LAS = SPM2’ and the
> defaults.analyze.flip value in SPM2 to 1. When I preview my phantom
> image in MRIcro, the image satisfies that if ‘defaults.analyze.flip=1’
> in ‘spm_defaults.m’ then left on right, right on left.
>
> If I then display this image in SPM2 the image returns to its left on
> left, right on right orientation with a negative x coordinate.
This is how it should be displayed.
> Am I to
> understand therefore that this negative x coordinate is just indicative of
> a flip having taken place so that my image displays on the screen in the
> same orientation as the template images (e.g. EPI.mcn).
Exactly.
> If so, will this
> flip automatically be applied during the normalization process due to the
> default.analyze.flip being 1?
The spatially normalised images will be saved with the voxels stored in the
same order as in your original images. When these are manipulated in SPM,
then a voxel-to-world transform will be applied so that (e.g.) the left will
continue to be displayed on the left, and your negative x T&T/MNI
co-ordinates will be the left half of the brain.
Best regards,
-John
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