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.
Location of files to manually register
Subject folders in T1preprocess contain three subfolders with T1 files, in the following order:
- T1_initnative_[N]series
- Single 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.
| 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) |
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 fiel 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 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).