| > I'm afraid I don't fully understand what you are doing. The origins
| > in normalised (nr*.img) images should differ from those of the
| > (r*.img) un-normalised images.
|
| there is obviously something fundamental I have misunderstood. When
| you say that normalisation changes the origin location, do you mean
| that it changes the voxel coordinates but the anatomical location remains
| the same, or vice versa?
SPM warps the images, so the origin in a normalised image is likely
to be in a completely different plave to the origin in the original.
Setting origins of images to be somewhere near the AC before spatially
normalising them helps by providing better starting estimates for the
affine part of the spatial normalisation.
| I change the origin on the r* files so that
| it is visually (using check reg)
| in the same spot as the origin of the EPI template. Following
| normalisation, the origin of the nr* files is no longer in register
| with that of the template - does this mean that normalisation has not
| occurred correctly?
It sounds like the spatial normalisation has not gone well. After spatial
normalisation, locations in the normalised images should be in the same
place as their corresponding locations in the template.
| Should I change the origin again to be in the
| same place as the EPI template before
| smoothing and estimating the model such that the activations in the
| glass brain are appropriately located?
If the spatial normalisation is failing, then there may be some things that
you can tweek to make it work better. (1) Disable the default brain masking
procedure. This is probably more of a hindrance than a help when spatially
normalising EPI images to match the EPI template. (2) Check to make sure the
contrast of the EPI template is the same as (or similar to) that of your EPI
files. If it is not, then you may need to try a different spatial normalisation
strategy. (3) Try increasing the amount of regularisation used by the nonlinear
part of the spatial normalisation (1 and 3 are done via the <Defaults> button).
Best regards,
-John
|