The <Check Reg> button is probably the best way of ensuring that
the images are in register. You can select a number of different
images, which will be displayed together as SPM understands their
relative orientations to be. You can click on different parts of the
orthogonal views, which will re-centre the cross-hairs.
The <Coregister> button should have a good go at registering the images
together. However, if this does not work well (e.g., because of low
grey/white contrast in your images), then you can try the Mutual Information
coregistration that you can get at via the <Defaults> button.
Before coregistering the images, the origin should be set to be somewhere
close to the AC (which can be done via the <Display> button). Repositioning
images in this way changes their .mat files. By default, SPM reads voxel
sizes and origins from the .mat files. However, if an image has no .mat
file, then the values are read from the image .hdr. The origin field
of the .hdr should contain the co-ordinate (rounded to the nearest voxel,
where the first voxel is at 1,1,1) of a voxel reasonably close to the AC.
After spatial normalisation, the origin is at the voxel that the spatial
normalisation deemed to be closest to the AC. There is more documentation
on this stuff available via the <Help> button (Data Formats).
Best regards,
-John
| Here is what I have:
| A T1 anatomical scan of 28 slices
|
| Spiral functional scans of 20 slices
|
| How can I ensure that the spiral scans are coregistered in the proper
| slice planes with the T1 anatomical scans?
|
|
| Second question:
| How is the origin field determined?
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