Difference between revisions of "Projects:DBP2:Harvard:Registration Documentation"
Line 1: | Line 1: | ||
− | |||
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: | 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 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 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. | * Registering a realigned t2 weighted image to another t2. | ||
+ | |||
+ | =There and back registration= | ||
==Slicer modules== | ==Slicer modules== | ||
Line 14: | Line 15: | ||
The image shows these side by side. The are nearly the same except for the loss of fine detail. | The image shows these side by side. The are nearly the same except for the loss of fine detail. | ||
+ | |||
+ | |||
+ | ===Linear=== | ||
+ | [[File:52-t2 lin.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 rig.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 Bspline.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 demons.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 RV initial.png|600px|thumb|left|Initial case 1: Minor shift down and anterior]] | ||
+ | [[File:53-t2 RV init histo.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 RV rigid.png|600px|thumb|left|Rigid case 1: Shift in grey values.]] | ||
+ | *53-t2 -> 31-t1 = rigid1 | ||
+ | *rigid1 -> 53-t2 = rigid2 | ||
+ | Shift in grey values. Few other problems. | ||
+ | |||
+ | |||
+ | ===Affine=== | ||
+ | [[File:53-t2 RV affine.png|600px|thumb|left|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=== | ||
+ | [[File:53-t2 RV bspline.png|600px|thumb|left|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 | *DTI-baseline -> 53-t2 = aff3 | ||
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
Line 23: | Line 94: | ||
===Linear=== | ===Linear=== | ||
− | |||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> 53-t2 = lin3 | *DTI-baseline -> 53-t2 = lin3 | ||
Line 38: | Line 104: | ||
===Rigid=== | ===Rigid=== | ||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> 53-t2 = rig3 | *DTI-baseline -> 53-t2 = rig3 | ||
Line 52: | Line 114: | ||
Similar. | Similar. | ||
− | === | + | ===B-Spline=== |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> 53-t2 = Bspline3 | *DTI-baseline -> 53-t2 = Bspline3 | ||
Line 74: | Line 130: | ||
===Diffeomorphic Demons=== | ===Diffeomorphic Demons=== | ||
− | |||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> 53-t2 = Demons3 | *DTI-baseline -> 53-t2 = Demons3 | ||
[[File:Basline-demons-t2.png|600px|thumb|left|Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.]] | [[File:Basline-demons-t2.png|600px|thumb|left|Demons case 2: Terrible distortions everywhere, unclear what it was trying to match.]] | ||
− | *53-t2 -> | + | *53-t2 -> DTI-baseline = Demons 4 |
+ | |||
+ | ==Register Images module== | ||
− | |||
===Initial=== | ===Initial=== | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> t2 = init3 | *DTI-baseline -> t2 = init3 | ||
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
Line 101: | Line 147: | ||
===Rigid=== | ===Rigid=== | ||
− | |||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> t2 = rigid3 | *DTI-baseline -> t2 = rigid3 | ||
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
Line 113: | Line 154: | ||
===Affine=== | ===Affine=== | ||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> t2 = affine3 | *DTI-baseline -> t2 = affine3 | ||
Line 125: | Line 162: | ||
===B-Spline=== | ===B-Spline=== | ||
− | |||
− | |||
− | |||
− | |||
*DTI-baseline -> t2 | *DTI-baseline -> t2 | ||
Line 137: | Line 170: | ||
*t2 -> DTI-baseline | *t2 -> DTI-baseline | ||
<nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
− | |||
= Different subject registration = | = Different subject registration = |
Revision as of 13:39, 23 April 2009
Home < Projects:DBP2:Harvard:Registration DocumentationSlicer 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.
Contents
There and back registration
Slicer modules
Affine
- 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
- 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
- 53-t2 -> 31-t1 = rig1
- rig1 -> 53-t2 = rig2
Significant blurring, but every feature is in it's proper place.
Deformable B-spline
- 53-t2 -> 31-t1 = Bspline1
- Bspline1 -> 53-t2 = Bspline2
Superior frontal enlargement, odd upward shifting in rear of brain, distortions everywhere.
Diffeomorphic Demons
- 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
- 53-t2 -> 31-t1 = init1
- init1 -> 53-t2 = init2
Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel.
Rigid
- 53-t2 -> 31-t1 = rigid1
- rigid1 -> 53-t2 = rigid2
Shift in grey values. Few other problems.
Affine
- 53-t2 -> 31-t1 = affine1
- affine1 -> 53-t2 = affine2
Again, shift in grey values, mostly okay otherwise. Slight posterior shift.
B-Spline
- 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
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
- 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.