The University of Chicago. Center for EPR Imaging in Vivo Physiology. Image Registration. Boris Epel
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1 The University of Chicago Center for EPR Imaging in Vivo Physiology Image Registration Boris Epel
2 Imaging Methods are Complimentary CT MRI EPRI High resolution anatomic images Quantitative Poor soft tissue contrast High resolution anatomic images High soft tissue contrast Less specific, since signal of interest is buried in water proton signals Less sensitive for species with low concentration (as compared to EPR) Measures environment parameters of interest Low resolution Spin-probe perfusion dependent Optics Ultra high resolution Very high sensitivity Mostly surface images Ultrasound, OMRI, PET, SPECT, MR Elastography. 2 EPR Oxygen Imaging Workshop 2014, Chicago
3 Localization of Information We are interested in obtaining various information from exactly the same location For example: po 2 (EPROI) from particular tumor area (MRI) IMRT beam (CT) targeting low po 2 area (EPROI) Oxygen delivery (MRI) correlated with tissue oxygenation (EPROI) Images should be registered, i.e. correspondence between locations in each image should be established 3 EPR Oxygen Imaging Workshop 2014, Chicago
4 Registration problems Images have different resolution Images have different dimensionality Images might not be sampled on Cartesian grid (for example various surfaces) Tissue might be damaged/distorted Images taken in longitudinal studies are impacted by tissue growth/shrinking Breathing impacts images Different physiologic states of animal (filling of bladder) 4 EPR Oxygen Imaging Workshop 2014, Chicago
5 Idea 1: Acquire all Images in the same Coordinate System Not always possible Requires complicated equipment (compatibility has a price) 5 EPR Oxygen Imaging Workshop 2014, Chicago
6 Idea 2: Register Images post Acquisition 6 EPR Oxygen Imaging Workshop 2014, Chicago
7 Linear Coordinate Transformation Images have different resolution Images have different dimensionality Images might be sampled on arbitrary plane (histological slices) (x,y,z) Z GG (x,y,z ) GG X Y 7 EPR Oxygen Imaging Workshop 2014, Chicago
8 Transformation Matrix Rotation 3x3 matrix Translation and Rotation 4x4 matrix tx ty tz 1 Coordinate Vector a = (x,y,z,1); a = a*r 8 EPR Oxygen Imaging Workshop 2014, Chicago
9 Coordinates for Matrices For a matrix one can define coordinate system associated with the voxel number (for example, 5 th in dimension 1, 23 rd in dimension 2, 4 th in third dimension The procedure to obtain the value will include interpolation (guessing of the value in between of voxels of the other image) 9 EPR Oxygen Imaging Workshop 2014, Chicago
10 How to Find Transformation Matrix Draw all images in some coordinate system Apply transformations until at least 4 non planar points of two images are aligned Objects visible in all images are required 10 EPR Oxygen Imaging Workshop 2014, Chicago
11 Anatomic Images 11 EPR Oxygen Imaging Workshop 2014, Chicago
12 Fiducials: EPR and MR Image Registration Mouse leg in the resonator. Polysiloxane half-cast with inserted fiducials 3D view of MRI and amplitude ESEI image registration. Fiducials are used to establish the coordinate transformation from MRI into ESE coordinate system EPRI 3mM deuterated FINLAND fiducials (~ 0.5 mm resolution) MRI water fiducials Haney C. et al., Concepts in Magnetic Resonance B (2008), 33, EPR Oxygen Imaging Workshop 2014, Chicago 12
13 The Protocol Define some coordinate system as a Reference Frame (typically associated with one of the image spatial representation) Find transformations that make all images aligned in the Reference frame Image I will have a R 1 = unit transformation (no changes) R for all other images, R j Resample image J in the coordinate system of I using transformation R j R -1 This creates image J representation in the coordinate system of image I 13 EPR Oxygen Imaging Workshop 2014, Chicago
14 ArbuzGUI: MATLAB Registration Toolbox 14 EPR Oxygen Imaging Workshop 2014, Chicago
15 Direct injection of spin probe into artery 51 mm diameter loop-gap resonator 4 cm VX2 carcinoma Spin probe was continuously injected directly into the artery feeding the leg. This allowed us to use only 1/4 of the calculated injection dose B. Epel et al. Medical Physics 37 (2010) EPR Oxygen Imaging Workshop 2014, Chicago
16 Multimodality Rat Imaging Multi-B ESE C po 2 A B 18 F-FDG PET C T 2 -weighted MRI D 16 EPR Oxygen Imaging Workshop 2014, Chicago
17 Volume Stain Image from Histology Slices Apply geometric restrictions Thick slab 17 Thin slice, visible light photography EPR Oxygen Imaging Workshop 2014, Chicago Align with fiducials Fluorescence photography
18 Summary Pimonidazol staining is localized primarily in tumor area. The correlation between areas of hypoxia and stain is not strong. In colorectal tumors stain is mostly localized close to tumor periphery or in small pockets inside the tumors. EPROI is much more specific in determination of hypoxia. Photograph Pimonidazole po 2 18 EPR Oxygen Imaging Workshop 2014, Chicago (green)
19 ESE and MRI Image Registration 19 EPR Oxygen Imaging Workshop 2014, Chicago
20 20 EPR Oxygen Imaging Workshop 2014, Chicago
21 Training: ArbuzGUI toolbox Load MRI, EPR fiducials and EPR po 2 images Segment tumor area from MRI Register MRI and EPR Transfer tumor area from MRI to EPR po 2 image Obtain po 2 statistics 21 EPR Oxygen Imaging Workshop 2014, Chicago
22 ArbugGUI MATLAB toolbox for image registration Developed by the Center for EPR Imaging in vivo Physiology Uses MATLAB image processing toolbox Uses ibgui toolbox developed by Center for image statistics and ortho-slice visualization Consists of the main shell for data management and plugins for registration and data processing Support for Bruker MRI, CT (DICOM), Amira, EPROI, histology etc data files 22 EPR Oxygen Imaging Workshop 2014, Chicago
23 ArbuzGUI: Main Window List all images, masks, surfaces etc Loads projects and data, save results Visualize the scenes Selects registration stages 23 EPR Oxygen Imaging Workshop 2014, Chicago
24 ArbuzGUI: SliceMaskEditPLG Manual and automatic image segmentation Anchors for image registration Conversion of masks into 3D surfaces for visualization 24 EPR Oxygen Imaging Workshop 2014, Chicago
25 ArbuzGUI: ImageTransform Resamples one image into the frame of another image Transfer segmentation results from one image to another (mask transfer) 25 EPR Oxygen Imaging Workshop 2014, Chicago
26 ibgui: Image Browser 2D, 3D and 4D images Loading of generic data from workspace and EPR specific data Slice-wise image visualization Manual image segmentation Statistics 26 EPR Oxygen Imaging Workshop 2014, Chicago
27 Training: ArbuzGUI toolbox Load MRI, EPR fiducials and EPR po 2 images Segment tumor area from MRI Register MRI and EPR Transfer tumor area from MRI to EPR po 2 image Obtain po 2 statistics 27 EPR Oxygen Imaging Workshop 2014, Chicago
28 Thank you 28 EPR Oxygen Imaging Workshop 2014, Chicago
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