Projects:DBP2:Harvard:Registration Documentation

Slicer 3 contains a number of different ways to register two images. In this document we will examine the results of these modules on three different cases. The convention used will be (moving image) -> (fixed image) = (resulting moved image). The cases are:

• Registering a t2 weighted image to an arbitrary t1, then registering this transformed image back to the original t2. Ideally this will produce a identical image.
• Registering a DTI baseline image to the corresponding realigned t2 weighted image, and vice-versa. This is a realistic test of one of our (the PNL) everyday uses of registration.
• Registering a realigned t2 weighted image to another t2.

There and back registration

Slicer modules

Affine

Affine case 1: Minor loss of detail.

• 53-t2 -> 31-t1 = aff1
• aff1 -> 53-t2 = aff2

The image shows these side by side. The are nearly the same except for the loss of fine detail.

Linear

Linear case 1: Minor shift at front, loss of detail.

• 53-t2 -> 31-t1 = lin1
• lin1 -> 53-t2 = lin2

The image shows lin2 and 53-t2 side by side. The image shows there appears to be some change beyond loss of detail, possibly a L-R shift in the front.

Rigid

Rigid case 1: Significant loss of detail.

• 53-t2 -> 31-t1 = rig1
• rig1 -> 53-t2 = rig2

Significant blurring, but every feature is in it's proper place.

Deformable B-spline

BSpline case 1: Frontal enlargement, rear upward shift, distortions throughout.

• 53-t2 -> 31-t1 = Bspline1
• Bspline1 -> 53-t2 = Bspline2

Superior frontal enlargement, odd upward shifting in rear of brain, distortions everywhere.

Diffeomorphic Demons

Demons case 1: Many minor deformations, clipping of brain at top, roughly correct placement overall.

• 53-t2 -> 31-t1 = Demons1
• Demons1 -> 52-t2 = Demons2

Multiple deformations. Much larger ventricles. Small errors everywhere, expansions, contractions, shifts. Roughly in the same place overall.

Register Images Module

Initial

Initial case 1: Minor shift down and anterior

Initial case 1: histograms of the two images.

• 53-t2 -> 31-t1 = init1
• init1 -> 53-t2 = init2

Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel.

Rigid

Rigid case 1: Shift in grey values.

• 53-t2 -> 31-t1 = rigid1
• rigid1 -> 53-t2 = rigid2

Shift in grey values. Few other problems.

Affine

Affine case 1: Slight posterior shift and grey value shift.

• 53-t2 -> 31-t1 = affine1
• affine1 -> 53-t2 = affine2

Again, shift in grey values, mostly okay otherwise. Slight posterior shift.

B-Spline

BSpline case 1: Minor distortions, grey value shifts.

• 53-t2 -> 31-t1 = Bspline1
• Bspline1 -> 53-t2 = Bspline2

Again grey values shift. Minor distortion in frontal lobe and cerebellum.

DTI Baseline to t2 registration

Slicer modules

affine

• DTI-baseline -> 53-t2 = aff3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Image shows the 53-t2 target image and the registered image side by side. DTI distortion remains but aligned well to ventricles in center.

• 53-t2 -> DTI-baseline = aff4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] The registered image does not stretch to the full extent of the DTI at the midline, though the match is quite close more laterally.

Linear

• DTI-baseline -> 53-t2 = lin3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Middle is clearly matched, coronal slices look okay, sagittal shows DTI distortions remain.

• 53-t2 -> DTI-baseline = lin4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Brainstem and cerebellum matched well, normal DTI distortions still present.

Rigid

• DTI-baseline -> 53-t2 = rig3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Brainstem aligned, normal DTI distortions present.

• 53-t2 -> DTI-baseline =rig4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Similar.

B-Spline

• DTI-baseline -> 53-t2 = Bspline3

BSpline case 2: Terrible distortion. Matches cortex to skull.

Fits the cortex on the baseline to the skull on the t2. Retry with a skull stripped t2.

• 53-t2 -> DTI-baseline = Bspline4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

• DTI-baseline-masked -> 53-t2-masked = Bspline3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Bad registration, numerous deformations, midline shift in frontal lobe, right side deformations, cerebellum doesn't fit any more.

Diffeomorphic Demons

• DTI-baseline -> 53-t2 = Demons3

Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.

• 53-t2 -> DTI-baseline = Demons 4

Register Images module

Initial

• DTI-baseline -> t2 = init3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

• t2 -> DTI-baseline = init4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Rigid

• DTI-baseline -> t2 = rigid3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

• t2 -> DTI-baseline = rigid4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Affine

• DTI-baseline -> t2 = affine3

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

• t2 -> DTI-baseline = affine4

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

B-Spline

• DTI-baseline -> t2

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]] Slow process. Inferior frontal, temporal, stretched downwards. Cerebellum is terrible. Very top of the brain is stretched. Pretty bad overall.

• t2 -> DTI-baseline

[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]

Different subject registration

Slicer modules

Rigid

01053>01031rigid.png = not bad... different brains of different sizes, but seem to be aligned in the ventricles so output seems okay. output slightly blurry. bad initial leveling displays.

Linear

01053>01031linear.png = not bad... different brains of different sizes, but seem to be aligned in the ventricles so output seems okay.output slightly blurry. bad initial leveling displays.

Affine

01053>01031_affine.png = looks good in terms of size. odd warping of frontal lobe and cerebellum area, but otherwise good coregistration.

B-spline

01053>01031_bspline.png = looks good in terms of size. odd warping of frontal/temporal lobe and cerebellum area, but otherwise good coregistration.

Diffeomorphic Demons

01053>01031_demons.png = 10 minutes. Window/leveling initially off. Otherwise, it looks really good. Not much distortion.

Register Images module

Initial

01053>01031_RI_initial.png - looks like the original 01053 image, but shifted, which is expected. resolultion a little worse.

Rigid

01053>01031_RI_rigid.png - center ventricles are mostly aligned, but not perfectly. in axial view, brain is more crooked than in initial scan... especially in frontal lobe.

Affine

01053>01031_RI_affine.png - ventricles aligned well. sizing decent. looks how one would expect affine to look. not perfect subcortically. some distortion, esp in temporal lobe.

B-spline

01053>01031_RI_bspline.png - good result. ventricles aligned well, but temporal lobe size is not the same as the target image.

Pipe Rigid

01053>01031_RI_pipe_rigid.png - shifted version of the original image. decent registration in the ventricles.

Pipe Affine

01053>01031_RI_pipe_affine.png - decent coreg. a bit of distortion in the frontal and temporal lobes, esp around the corpus collosum.

pipe B-spline

01053>01031_RI_pipe_bspline.png - good coregistration, but pretty blurred. also, I would have expected the temporal lobe to be coregistered better.