Proposal• Instead of doing whole brain nonlinear

registration, only register a cropped region– Previously we used a template to speed the

registration step• How do we determine the cropped region

automatically?

ROI Estimation• We want an estimate of the whole thalamus

– Can be conservative as we just want to crop a big enough region• Whole brain affine linear registration of priors’ whole

thalamus, then label fusion– In ANTS: maximum (very conservative), majority vote, STAPLE,

correlation vote– STEPS or PICSL?

• Use cross-validation to test 4 different methods

Registration• Register cropped priors to cropped image

– The cropped image is taken as the ROI estimate with a padding of 4 (2 on each side)

– The cropped priors are taken as the true whole thalamus ROI with a padding of 24• Larger to avoid missing data being warped into the region after registration• Arbitrary padding amount, tried 10, wasn’t enough

• ANTS options– Fixed space mask– Starting point affine transform– Continue affine transform

Registration• There are thus 6 permutations of ANTS options per

ROI estimate– With or without a fixed space mask (ROI estimate), i.e.

whole cropped region registration or limited to the ROI– With or without affine transform determined from

whole brain registration– Continue or don’t continue the affine registration search

Cross-Validation• Perform 20*19 whole brain affine registrations– Takes 5-10min on 20*16-cores

• Perform 20*19*4*6 cropped nonlinear registrations– Takes 1-2hrs with cropped region and 20*16-cores

• Probably <30min total pipeline once we pick the best registration method

Comparison of ROI Estimates

• Since coverage is our primary objective at this stage, maximum seems to be the clear winner

Comparison of Registration Quality

Targeted Registration• Correlation and majority voting

provide a better estimate of the thalamus– Let’s try telling the registration

to target those ROIs instead within the maximum-based crop

• Using the maximum-based ROI is (still) the best– More important to cover all

thalamus voxels with the registration than to be fine tuned on where the thalamus is exactly

– Plausible as it could permit crazy things happening outside the ROI

Registration Quality of 915 to ctrl_902

Actual Box

Box Affine

ROI[maximum] ROI[correlation]