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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 the location to 0 0 0.
- SPM 2: Open the T1 you want to registerShift the graphics window so you can see both images at the same time
- SPM 2: 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 the T1 is registered with the MNI template.
- Start with the most obvious changes: often "pitch" is the first to change, followed by "up".
- To shift a brain down, use negative up numbers (ditto for shifting left, use negative right numbers).
- Remember the rotations are in radians, so use small numbers; typically pitch could be 0.1-0.2 (or negative values), and 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.
For additional images, repeat steps 45-7.
Background: Process
Each subject's T1's go through this sequence:
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