In functional preprocessing, can co-registration FMRI images in the SPM using a template instead of the anatomical image of the subject?

In our study, multiple sclerosis patients and controls perform a task within the MRI and we want to know if in the functional pre-processing co-registration step a template image of the PMS can be used instead of the subject's own anatomical image, as sometimes errors occur that later interfere with the analysis.

Thank you!

Answer 1

[Jack]

Yes, it is possible to use a template image for co-registration in SPM instead of the subject’s own anatomical image, but there are some important factors to consider:

1. Standard Approach in SPM Co-Registration

• Typically, fMRI images are co-registered to the subject’s own T1-weighted anatomical image because it provides the best subject-specific alignment.
• This step ensures that the functional images align with anatomical structures unique to that individual.

2. Using a Template Instead of Subject’s Anatomy

• You can use a study-specific template (e.g., an averaged T1-weighted image from your cohort) or a standard MNI-space template like the ICBM152 or DARTEL template.
• This is sometimes done when individual anatomical images are low quality or contain artifacts that affect registration.

3. How to Implement This in SPM

• In the SPM GUI, instead of selecting each subject’s T1 image during co-registration, select the template image (e.g., a PMS-specific template).
• You might need to manually adjust the source and reference image selection to ensure alignment.
• After co-registration, check the results using Check Reg in SPM to verify alignment.

4. Potential Issues and Considerations

• Using a template instead of individual T1 scans can introduce registration errors, especially if there is significant anatomical variability among subjects.
• If errors in individual co-registration interfere with later analyses, consider using DARTEL-based normalization or rigid-body transformations to improve alignment.
• Another alternative is to use an initial affine registration with a template and then refine it using nonlinear warping.

5. Alternative: Direct Normalization Without Subject-Specific Co-Registration

• Instead of co-registering to a template, you can normalize the functional images directly to MNI space using SPM’s Segment + Normalize pipeline.
• This avoids co-registration errors but may lead to lower accuracy compared to subject-specific normalization.

For best results, it's recommended to visually inspect the co-registered images in SPM to ensure proper alignment. If errors persist, adjusting the cost function settings or using a study-specific template can improve results.

Let me know if you need further clarification! 🚀