Slicer Registration Library Case 38: TBI
This is an example of a multi-contrast dataset acquired for traumatic brain injury (TBI). We have many scans we seek to align to a common reference. Since all scans are acquired in short succession, they have only little initial misalignment, but they may differ significantly in contrast and field of view.
Approach: we register all the scans within each exam to the T1. Because of the strong differences in field of view (FOV), we limit registration degree of freedom to 6 DOF (rigid transformation only).
Download (from NAMIC MIDAS)
- RegLib_C38.mrb (input data, Slicer mrb file. 42 MB).
- Load all datasets via drag&drop or via "AddData / AddVolume" ... do not center the volumes, since they have reasonable alignment at the outset
- the registration procedure below is identical for all other scans in the sequence, i.e. just replace the Moving Volume and the Slicer Linear Transform", everything else can stay at default
- open the General Registration (BRAINS) module
- Fixed Image Volume: T1
- Moving Image Volume: T2
- Output Settings:
- Slicer BSpline Transform": none
- Slicer Linear Transform: create new transform, rename to "Xf1_T2"
- Output Image Volume: none
- Registration Phases: check box for Rigid only
- leave all other settings at defaults
- click: Apply; runtime < 10 sec (MacPro QuadCore 2.4GHz)
- this will generate the alignment transform. The demo screencast above shows how to apply the result transforms without resampling and then saving the images under a new name. It also shows where in the saved image the new orientation is stored. Note that the screencast was done for version 4.2.0. If you're using a more recent version, the BRAINS registration tool may automatically place the moving image into the result transform.
- repeat steps above for all the other images: FLAIR, T1post, SWI,EP . The only 2 settings to change are the Moving Image and the Result Transform