Projects:RegistrationLibrary:RegLib C09
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Slicer Registration Library Exampe #9: Functional MRI aligned with structural reference MRI
RegLib 09: T1 SPGR RegLib 09: fMR
this is the fixed reference image. All images are aligned into this space | this is the moving image. The transform is calculated by matching this to the reference image
this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution | |
T1 structural reference | fMRI 4D volume | |
0.46 x 0.46 x 3.0 mm axial 512 x 512 x 46 RAS |
1.0 x 1.0 x 3.3 mm axial oblique 256 x 256 x 36 RAS |
Objective / Background
This is a typical example of fMRI pre-processing. Goal is to align the fMRI image with a structural scan that provides accuracte anatomical reference. The fMRI contains acquisition-related distortion and low contrast to discern much anatomical detail. We also have pathology (stroke) with variable contrast across different MRI protocols.
Keywords
MRI, brain, head, intra-subject, fMRI
Input Data
Registration Results
Download
- download entire package (Data,Presets,Tutorial, Solution, zip file 33.7 MB) (to be added: tutorial + presets)
- Presets
- Tutorial only
- Image Data only
Discussion: Registration Challenges
- the fMRI contains acquisition-related distortions that can make automated registration difficult.
- the fMRI contains low tissue contrast, making automated intensity-based registration difficult.
- the two images often have strong differences in voxel sizes and voxel anisotropy. If the orientation of the highest resolution is not the same in both images, finding a good match can be difficult.
- there may be widespread and extensive pathology (e.g stroke, tumor) that might affect the registration if its contrast is different in the baseline and structural reference scan
Discussion: Key Strategies
- masking is likely necessary to obtain good results.
- in this example the initial alignment of the two scans is not excessive.
- because speed is not that critical, we increase the sampling rate from the default 2% to 15%.
- we also expect larger differences in scale & distortion than with regular structural scane: so we significantly (2x-3x) increase the expected values for scale and skew from the defaults.
- a good affine alignment is important before proceeding to non-rigid alignment to further correct for distortions.