Slicer3 Tutorial: Registration Library Case 19 Multi-stage registration for group analysis

1. Slicer3 Tutorial: Registration Library Case 19Multi-stage registration for group analysis Dominik Meier, Ron Kikinis July 2010, rev. Nov. 2010

2. Introduction / Scenario • 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. • 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 Subject 1 (N2) T1 T2 MRA Subject 2 (N4) T1 T2 MRA

3. Main Strategy • Align all scans within subject 1 (N2) • Align T2 -> T1 • Align MRA -> T1 • Align all scans within subject 2 (N4) • Align T2 -> T1 • Align MRA -> T1 • Align Subject 2 -> 1 • Align N4-T1 with N2-T1 -> Bspline Xform • Resample all MRA and T2 as registered above • Resample all MRA and T2 with Bspline Xform Note: if you wish to avoid a double resampling of the the T2 and MRA images to minimize interpolation blurring, you need to edit the BsplineXformwith a text editor. The procedure for this is discussed in later slides of this tutorial.

4. Modules Used • To accomplish this task we will use the following modules: • BRAINSfit Module • Fast Deformable BSpline Module • Resample Scalar/Vector/DWI Volume • Data Module • a Text Editor

5. Prerequisites • Slicer version 3.6.1 or later • Example Dataset: download and extract the dataset for this tutorial: RegLib_C19_DATA.zip, which should contain all original and intermediate solution data files. • Tutorials to complete first (optional): • Slicer3Minute Tutorial • Loading and Viewing Data

6. 1. Intra-Subject BRAINSfit:select: - initialize with center of head - include rigid registration phase - include scale Versor3D phase - include Affine phase - use default parameters for the rest - select a Slicer Linear Transform output

7. 2. Inter-Subject Fast Nonrigid Bspline , select: • Grid Size 3 • output transform & volume • defaults for the rest * note that the level of detail and the DOF used for inter-subject registration depends heavily on the application. Here we’re interested only in a low-level alignment that corrects the basic head shape. You may substitute this in your case with a different inter-subject registration.

8. 2. Inter-Subject: BRAINSFit BRAINSFit Module, select: • Registration Phases: BSpline • output transform & volume • 200,000 sampling points • 7x7x7 grid size * note that the level of detail and the DOF used for inter-subject registration depends heavily on the application. For illustration purposes the grid-size for this registration is twice the size of the previous one. How much deformation is permissible depends on the metrics to be derived from the final pooled cohort.

9. Resample • In DATA module, select the respective MRA or T2 volume, then via mouse right-click, select “Harden Transform” from the pop-up menu. When you release the mouse buttn, the node will move back out to the main level indicating that it has been resampled. It is not a bad idea at this point to rename the node to document this. • Once all MRA and T2 volumes have been resampled, apply the Bspline transform to those of subject 2 (N4_T2 and N4_MRA). • Module: Resample Scalar/Vector/DWI Volume • Reference Volume: N2_T1_Flash • Output Volume: create new, rename to N4_T2_Xf5 etc. • Transform Node: Xf5b_N4-N2_Bspline • Check “output-to-input” • Interpolation type: check “ws”

10. OPTIONAL: Combine Transforms This applies only if you wish to avoid the dual resampling of the MRA and T2 images outlined before: • Currently (Slicer 3.6) the concatenation of linear and nonlinear transforms is not (yet) supported directly in slicer. However this is an easy and fast procedure that can be done with any text editor. We merely copy the affine portion from one transform file and paste it into the nonrigid transform file: • Open Xform_N4_T2_Aff2.tfm • Duplicate Xform_N4-N2_BSpl1.tfm and rename to Xform_N4-N2_BSpl1+Aff2.tfm • Open both with any text editor • Find the highlighted text (on the right) in the affine file and paste it into the highlighted line on the nonrigid file • save & close. copy entire line

11. Resample • Finally we resample all the volumes with the obtained transform • For the images of subject 2 that undergo a nonrigid ransform, make sure to check the “output-to-input” box to have the affine and nonrigid transforms applied in the correct order. • As interpolation method you may select windowed sinc if slight blurring from linear interpolation is a concern.

12. Save • To enable concatenation of the transforms, we need to save them to file. • Select “Save” from the file menu, check all the transforms produced thus far. • Click ‘Save’

13. Results unregistered registered

14. What Next • Try the Manual Registration Tutorial or one of the tutorials from the Registration Case Library. • http://www.slicer.org/slicerWiki/index.php/Slicer3.4:Training • http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:UseCaseInventory • http://www.slicer.org/slicerWiki/index.php/Slicer3:Registration#Registration_in_3D_Slicer|Main • Feedback: anything amiss? If you have suggestions on how we can improve this and other documentation, please let us know: visit: • http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation

15. Acknowledgements National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center NIH P41RR013218 -12S1 (ARRA Suppl)