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- Open two instances of MATLAB, and open SPM in both ("SPM 1", "SPM 2").
- Shift the graphics window so you can see both images at the same time
- SPM 1:Open a template; select "Display" from the SPM menu, and select the single subject file in the .\canonical subfolder.
- SPM 1: Set Click "Origin" to set the location to 0 0 0.
- SPM 2: Open the T1 you want to register
- SPM 2: Set Click "Origin" to set the location to 0 0 0
- SPM 2: Adjust the shifts (x/y/z mm) and rotations (pitch/roll/yaw); this will move the T1. Enter values until Your aim is to have the T1 is registered aligned with the MNI template-space scan.
- Start with
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- rotations
- To set the x/y/z shifts, place the cross-hairs where you think the origin should be, and click "Set Origin"; this will automatically calculate the left/right, forward/back, and up/down shifts.
- A shift down is performed with negative "up" numbers (ditto for shifting left, use negative right numbers, etc.).
- Start with the most obvious changes: often "pitch" is the first to change, followed by resetting the origin.
- Cycle through the pitch/roll/yaw rotations, rather than trying to get one perfect then move to the next.
- Remember the rotations are in radians, so use small numbers; typically
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- the order of magnitude for pitch is 0.1-0.2
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- , and for roll/yaw 0.01-0.04.
- Keep an eye on the big picture; don't try to only match one feature.
- Features to note: angle of brainstem, 0 line just slicing superior cerebellum and gene and below of corpus callosum, origin at anterior commisure (where white matter "finger" ends).
- SPM 2: Save by clicking "Reorient"; the T1 will already be selected, so just click "Done". When asked, say "yes" to saving the parameters, and use the default file name.
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