Projects:RegistrationLibrary:RegLib C19

From NAMIC Wiki
Revision as of 14:44, 2 July 2010 by Meier (talk | contribs)
Jump to: navigation, search
Home < Projects:RegistrationLibrary:RegLib C19

Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory

Slicer Registration Library Exampe #19: Multi-contrast group analysis: intra- and inter-subject registration of multi-contrast MRI

this is the main reference image. All images are aligned into this space this is the 1st intra-subject moving target, to be aligned with the main reference directly this is the 2nd intra-subject moving target, to be aligned with the main reference directly lleft this is both the fixed target for the 2nd subject and the moving image for inter-subject registration this is a moving image to be aligned indirectly to the main ref his is a moving image to be aligned indirectly to the main ref LEGEND

lleft this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution
lleft this indicates the moving image that determines the registration transform.

lleft reference T1, subject 1 lleft moving T2, subject 1 lleft moving MRA, subject 1 lleftlleft reference T1, subject 2 lleft moving T2, subject 2 lleft moving MRA, subject 2
1mm isotropic
176 x 256 x 176
PA 		1mm isotropic
192 x 256 x 128
PA 		0.51 x 0.51 x 0.8 mm
448 x 448 x 128
PA 		1mm isotropic
176 x 256 x 176
PA 		1mm isotropic
192 x 256 x 128
PA 		0.51 x 0.51 x 0.8 mm
448 x 448 x 128
PA


Objective / Background

This is an example of multi-stage registration containing both intra- and inter-subject alignment. We have two sets of multi-sequence MRI for two subjects, each comprised of a T1, T2 and perfusion MRA scan. We ant everything aligned to a single space to enable regional or voxel-based group comparison.

Keywords

multi-stage registration, MRI, brain, head, multi-contrast, inter-subject, group analysis, MRA, T2

Input Data

  • Button red fixed white.jpgreference/fixed : T1w coronal, 1mm isotropic. Called A1_gray
  • Button red fixed white.jpgreference/fixed : labelmap , aligned with above. Called A1_label
  • Button blue tag white.jpg moving: T1w coronal, 0.9 inplane, 1.5mm coronal slices. Called A0_gray
  • Button green moving white.jpg moving: labelmap , aligned with above. Called A0_label

Methods

  1. align T2 and MRA of each subject to their respective T1 via an affine transform
  2. align the T1 of subject 2 to the T1 of subject 1 via a non-rigid transform, this establishes the inter-subject mapping
  3. combine the affine transforms of subject 2 T2 and MRA with the above nonrigid and resample the two images into the reference space

Registration Results

unregistered
registered

Download

Link to User Guide: How to Load/Save Registration Parameter Presets

Discussion: Registration Challenges

  • We have two separate sets of registrations to combine. While theoretically possible to simply align every scan with the reference directly, this is likely to produce inferior results. Basic rule of thumb is to register to the image that is closest in anatomy and contrast, in that order.
  • the MRA has a strongly clipped FOV and low tissue contrast

Discussion: Key Strategies

  1. For the intra-subject affine portion: BRAINSfit
  2. For the inter-subject nonrigid portion: Fast nonrigid BSpline
  3. For combining the transforms: copy and paste in a Text Editor
  4. For applying the transforms and resampling: Resample Volume module


Acknowledgments

  • dataset provided by the
Retrieved from "https://www.na-mic.org/w/index.php?title=Projects:RegistrationLibrary:RegLib_C19&oldid=55735"