View source for Vervet Atlas Construction:Debugging bspline registration

==Introduction==

Our goal is to construct probabilistic atlas of vervet monkey brain. We have 10 MR scans of vervet monkeys. Our plan is to initially select a template subject, register all subjects to the template subject. We then compute average template, and repeat the process by registering all subjects to the average template.

We use BRAINSFit Slicer plugin (latest svn checkout 327) to do all steps of registration. 

==Detailed description==

The input includes the following items:
* FIXED1.nrrd: Fixed image1: average over subjects registered to template 
* FIXED2.nrrd: Fixed image2: average with additional processing (histogram matching and bias correction), non-brain areas masked out
* MOVING.nrrd: Moving image: one of the vervet subjects
* FIXED_ROI.nrrd: brain mask for the fixed image
* MOVING_ROI.nrrd: brain mask for the moving image
* INITIAL_TFM.tfm: affine transform aligning MOVING with FIXED
* Everything in one package together with the Slicer scene:

{|
|[[Image:fixed1.jpg|thumb|300px|FIXED1]]
|[[Image:fixed2.jpg|thumb|300px|FIXED2]]
|[[Image:moving.jpg|thumb|300px|MOVING (under INITIAL_TFM)]]
|}


* '''Experiment1''': register MOVING/MOVING_ROI to FIXED1/FIXED_ROI. Initialize with INITIAL_TFM. Command line:
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* '''Experiment2''': register MOVING/MOVING_ROI to FIXED2/FIXED_ROI. Initialize with INITIAL_TFM Command line:
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