Projects:RegistrationLibrary:RegLib C02

Slicer Registration Use Case Exampe: Intra-subject Brain MR FLAIR to MR T1

T1 SPGR		T2 FLAIR	LABEL-MAP
1mm isotropic 256 x 256 x 146		1.2mm isotropic 256 x 256 x 116	1.2mm isotropic 256 x 256 x 116

Objective / Background

This scenario occurs in many forms whenever we wish to align all the series from a single MRI exam/session into a common space. Alignment is necessary because the subject likely has moved in between series.

Keywords

MRI, brain, head, intra-subject, FLAIR, T1, defacing, masking, labelmap, segmentation

Input Data

• reference: T1 SPGR , 1x1x1 mm voxel size, sagittal, RAS orientation
• moving: T2 FLAIR 1.2x1.2x1.2 mm voxel size, sagittal, RAS orientation
• quick view JPEG of a lighbox. Does your data look like this?
• download dataset to load into slicer

Registration Challenges

• we expect the amount of misalignment to be small
• we know the underlying structure/anatomy did not change, hence whatever residual misalignment remains is of technical origin.
• the different series may have different FOV. The additional image data may distract the algorithm and require masking
• the different series may have very different resolution and anisotropic voxel sizes
• hi-resolution datasets may have defacing applied to one or both sets, and the defacing-masks may not be available
• the different series may have different contrast.
• individual series may contain motion or other artifacts

Procedure

• step-by step text instruction
• recommended parameter settings

• guided video tutorial
• power point tutorial

Registration Results

• registration parameter presets file (load into slicer and run the registration)
• result transform file (load into slicer and apply to the target volume)
• result screenshots (compare with your results)
• result evaluations (metrics)