Difference between revisions of "Projects:DBP2:Harvard:Registration Documentation"
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| − | = Registration = | + | = Same subject Registration = |
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. | ||
| Line 5: | Line 5: | ||
* Registering a realigned t2 weighted image to another t2. | * Registering a realigned t2 weighted image to another t2. | ||
| − | == | + | ==Slicer modules== |
===Affine=== | ===Affine=== | ||
| Line 15: | Line 15: | ||
*DTI-baseline -> 53-t2 = aff3 | *DTI-baseline -> 53-t2 = aff3 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
Image shows the 53-t2 target image and the registered image side by side. DTI distortion remains but aligned well to ventricles in center. | 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 | *53-t2 -> DTI-baseline = aff4 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
The registered image does not stretch to the full extent of the DTI at the midline, though the match is quite close more laterally. | The registered image does not stretch to the full extent of the DTI at the midline, though the match is quite close more laterally. | ||
| Line 30: | Line 30: | ||
*DTI-baseline -> 53-t2 = lin3 | *DTI-baseline -> 53-t2 = lin3 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
Middle is clearly matched, coronal slices look okay, sagittal shows DTI distortions remain. | Middle is clearly matched, coronal slices look okay, sagittal shows DTI distortions remain. | ||
*53-t2 -> DTI-baseline = lin4 | *53-t2 -> DTI-baseline = lin4 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
Brainstem and cerebellum matched well, normal DTI distortions still present. | Brainstem and cerebellum matched well, normal DTI distortions still present. | ||
| Line 45: | Line 45: | ||
*DTI-baseline -> 53-t2 = rig3 | *DTI-baseline -> 53-t2 = rig3 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
Brainstem aligned, normal DTI distortions present. | Brainstem aligned, normal DTI distortions present. | ||
*53-t2 -> DTI-baseline =rig4 | *53-t2 -> DTI-baseline =rig4 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
Similar. | Similar. | ||
===Deformable B-spline=== | ===Deformable B-spline=== | ||
| − | [[File:53-t2 Bspline.png|600px|thumb|left|BSpline case 1: | + | [[File:53-t2 Bspline.png|600px|thumb|left|BSpline case 1: Frontal enlargement, rear upward shift, distortions throughout.]] |
*53-t2 -> 31-t1 = Bspline1 | *53-t2 -> 31-t1 = Bspline1 | ||
*Bspline1 -> 53-t2 = Bspline2 | *Bspline1 -> 53-t2 = Bspline2 | ||
| Line 61: | Line 61: | ||
*DTI-baseline -> 53-t2 = Bspline3 | *DTI-baseline -> 53-t2 = Bspline3 | ||
| − | [[File:Baseline-bsp-t2-composite.png|600px|thumb|left|BSpline case 2: Matches cortex to skull. | + | [[File:Baseline-bsp-t2-composite.png|600px|thumb|left|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 | Fits the cortex on the baseline to the skull on the t2. Retry with a skull | ||
stripped t2. | stripped t2. | ||
| − | * | + | *53-t2 -> DTI-baseline = Bspline4 |
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | *DTI-baseline-masked -> 53-t2-masked = Bspline3 | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
Bad registration, numerous deformations, midline shift in frontal lobe, right | Bad registration, numerous deformations, midline shift in frontal lobe, right | ||
side deformations, cerebellum doesn't fit any more. | side deformations, cerebellum doesn't fit any more. | ||
===Diffeomorphic Demons=== | ===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 | *53-t2 -> 31-t1 = Demons1 | ||
*Demons1 -> 52-t2 = Demons2 | *Demons1 -> 52-t2 = Demons2 | ||
| Line 77: | Line 81: | ||
expansions, contractions, shifts. Roughly in the same place overall. | expansions, contractions, shifts. Roughly in the same place overall. | ||
| − | ===Register | + | *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.]] | ||
| + | |||
| + | *53-t2 -> | ||
| + | |||
| + | ==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 | *53-t2 -> 31-t1 = init1 | ||
*init1 -> 53-t2 = init2 | *init1 -> 53-t2 = init2 | ||
| − | |||
Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel. | Huge shift in count values, rigid translation down ~4 pixels, left ~1 pixel. | ||
| − | = | + | *DTI-baseline -> t2 = init3 |
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
| − | = | + | *t2 -> DTI-baseline = init4 |
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
| − | ====B-Spline==== | + | ===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. | ||
| + | |||
| + | *DTI-baseline -> t2 = rigid3 | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | |||
| + | *t2 -> DTI-baseline = rigid4 | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | |||
| + | ===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. | ||
| + | |||
| + | *DTI-baseline -> t2 = affine3 | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | |||
| + | *t2 -> DTI-baseline = affine4 | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | |||
| + | ===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. | Again grey values shift. Minor distortion in frontal lobe and cerebellum. | ||
*DTI-baseline -> t2 | *DTI-baseline -> t2 | ||
| − | + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | |
| + | Slow process. Inferior frontal, temporal, stretched downwards. Cerebellum is | ||
terrible. Very top of the brain is stretched. Pretty bad overall. | terrible. Very top of the brain is stretched. Pretty bad overall. | ||
| + | |||
| + | *t2 -> DTI-baseline | ||
| + | <nowiki>[[FILE:FILENAME|600px|thumb|left|TYPE case X: explanation]]</nowiki> | ||
| + | |||
| + | |||
| + | = Different subject registration = | ||
Revision as of 20:39, 22 April 2009
Home < Projects:DBP2:Harvard:Registration DocumentationContents
Same subject Registration
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.
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.
- 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
- 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.
- 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
- 53-t2 -> 31-t1 = rig1
- rig1 -> 53-t2 = rig2
Significant blurring, but every feature is in it's proper place.
- 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.
Deformable B-spline
- 53-t2 -> 31-t1 = Bspline1
- Bspline1 -> 53-t2 = Bspline2
Superior frontal enlargement, odd upward shifting in rear of brain, distortions everywhere.
- 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
- 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.
- DTI-baseline -> 53-t2 = Demons3
- 53-t2 ->
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.
- 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
- 53-t2 -> 31-t1 = rigid1
- rigid1 -> 53-t2 = rigid2
Shift in grey values. Few other problems.
- 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
- 53-t2 -> 31-t1 = affine1
- affine1 -> 53-t2 = affine2
Again, shift in grey values, mostly okay otherwise. Slight posterior shift.
- 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
- 53-t2 -> 31-t1 = Bspline1
- Bspline1 -> 53-t2 = Bspline2
Again grey values shift. Minor distortion in frontal lobe and cerebellum.
- 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]]
