Segmentation and spatial normalization sometimes require a manual registration of the T1 to the MNI space. Normalization and segmentation usually fail completely, and so problems are easy to see with a "checkreg" between normalized files and a template.
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Definition (simple)
Having the T1 "registered" to the MNI template means that the T1 and MNI images are in roughly the same space when they are opened. In other words, they overlap, the angle of the brain is similar, and the origins are in a similar place.
Manual registration means a user changes the location and angle of the T1 brain to make it visually match the MNI template.
Location of files to manually register
The T1 files to register are in T1_manual2MNI folders. Subject folders in T1preprocess contain three subfolders with T1 files, in the following order:
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| Fig. item | Meaning |
|---|---|
| 1 | subject folder in T1preprocess |
| 2 | individual series with nifti files (copied from rawimages) |
| 3 | average of T1 series; defines native space |
| 4 | copy of native space T1, which can optionally be manually registered |
| 5 | resliced versions of T1; two different reslice options are there (one with 0.7mm voxels the other with 0.9mm, according to the parameters in the Analysis GUI) |
Manually registering with SPM
- Open two instances of MATLAB, and open SPM in both ("SPM 1", "SPM 2").
- 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 register
- Shift 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 4-7.
Background: Process
Each subject's T1's go through this sequence:
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During preprocessing, CSPM checks to see whether the T1_manual2MNI file has shifted; if so, it re-runs subsequent steps, starting from the reslicing. The advantage of this approach is that we retain the original native space T1's, and at least in SPM12 we can save the re-orientation parameters for later use, in case we re-convert the nift files, or want to apply the reorientation to other images.
Manually registering with SPM
Open two instances of SPM. For one, open a template in Display (there is a single subject in spm..\canonical folder). Set the location to 0 0 0. In the second instance of SPM, open the T1 in T1_manual2MNI, and set the location to 0 0 0. Adjust the shift and rotation to match the reference. Save by clicking "Reorient" and selecting the file. In SPM12, the file is already selected, and you get the chance to save the parameters (do this - just go with the defaults).