Difference between revisions of "Projects:RegistrationLibrary:RegLib C09"
m (→Download) |
|||
Line 40: | Line 40: | ||
===Download === | ===Download === | ||
− | *'''[[Media:RegLib_09_fMRI_full.zip|download entire package <small> (Data,Presets,Tutorial, Solution, zip file | + | *'''[[Media:RegLib_09_fMRI_full.zip|download entire package <small> (Data,Presets,Tutorial, Solution, zip file 39 MB) </small>]]''' |
*Presets | *Presets | ||
*Tutorial only | *Tutorial only |
Revision as of 18:35, 18 February 2010
Home < Projects:RegistrationLibrary:RegLib C09Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory
Contents
Slicer Registration Library Exampe #9: Functional MRI aligned with structural reference MRI
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 | LEGEND
|
![]() |
![]() | ||
0.5 x 0.5 x 1.0 mm axial 512 x 512 x 176 RAS |
1.8 x 1.8 x 4 mm axial oblique 128 x 128 x 19 x 125 timepoints 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 39 MB)
- Presets
- Tutorial only
- Image Data only
Link to User Guide: How to Load/Save Registration Parameter Presets
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.