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. If you change the origin in a normalised
image, then SPM should recognise that it has changed. Normalised images
are not written with .mat files, so the origin and voxel size information
is read from their .hdr files.
There is no way using the buttons of SPM to modify the .mat files so that
the origin information is read from the .hdr files. A bit of extra
Matlab code would need to be written in order to do this.
Best regards,
-John
| we have a question about the output of the normalisation process for
| fMRI. We have noticed that the origin of the normalised nr* files differs from
| that of files at earlier stages (eg r* files). Despite the fact that
| we carefully change the origin of the files to equate with that of
| the EPI template image (using header edit) following normalisation
| it reverts to a more superior location and our normalised images turn
| out "squint".
|
| We suspect that this has to do with the fact that during
| normalisation, SPM reads origin information from the .mat files and
| not the header (is this right?). We cannot delete the .mat files, because these
| contain information about rotations which we have performed on the
| images such that the slices are at the correct angle. Our question
| is this: can you persuade SPM to read the origin location from the
| header without deleting the .mat files?
|
| the only solution we have come up with so far is to physically move
| the images (using the up, left, etc tools in the display window) until
| they align with the origin, rather than vice versa. Is this the only
| way to do it, or is there something we have misunderstood?
|