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.

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 subfolders with T1 files, in the following order (numbers refer to image labels):

Subject in T1preprocess subfolder
- Parent folder is group, above that is project folder
Copies of individual series T1 images (some protocols use multiple T1 scans that are averaged to create a clean image).
T1_initnative_[N]seriesSingle
- T1 in original native space; if more than one series was collected, this file is the average of all series.
T1_manual2MNI
- A single T1 that can (optionally) be manually registered to the template. This initially is simply a copy of the native T1 (previous step).
T1_ref_vox...bb...
- A resliced version of the T1; this becomes the reference for native space.
- There may be more than one folder, since we sometimes use different resolutions

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; in this example, 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").
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: Click "Origin" to set the location to 0 0 0.
SPM 2: Open the T1 you want to register
SPM 2: 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. Your aim is to have the T1 aligned with the MNI-space scan.
- Start with 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 the order of magnitude for pitch is 0.1-0.2, 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 genu 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.

Step 8 completes the manual realigning. For additional studies, repeat steps 5-7.

Background Details: Process

Each subject's T1's go through this sequence:

DICOM Raw data folder => DICOM rawimages => nifti rawimages => same file to T1preprocess subject series folders => average of series to T1_initinative => same file to T1_manual2MNI => resliced in T1_ref_vox..bb...

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 nifti files, or want to apply the reorientation to other images.