Image registration in DataViewer
Contents
1. 2D registration e Actions View Options Input images for registration 4 Ol Q oj i Image Min Max File Reference 0 255 Preview0000 bmp Target 0 255 Preview0180 bmp Fusion a Alpha blending with selected or contrast colors lt 1 r Options r riena ia meena d Display parameters T t R 50 50 atte Registration parameters Target gt Reference Hide VOI f 0 108 4x t 6 Om L7it EN 0 479 Alpha Foie a 1952 0um 1952pixels 240 0 e 210 0 180 0 150 0 F 120 0 90 0 60 0 I 30 0 on 0 0 200 0 400 0 600 0 800 0 1000 0 1200 0 1400 0 1600 0 1800 0 2000 T Global scal Si 22 0 1144 Zoom 32 PESER se Fig 2 2 Main window for 2D image registration The registration can also be done automatically using buttons Register after selecting VOI carefully Itis generally recommended to shift rotate manually first so that the 2 images are sufficiently close to each other before using the automatic function You can alter the searching range using button Options Once the images are registered a saving function with button Save will allow you to save the transformed image It saves optionally also the reference image This makes sense if there is resampling during loading A difference image can be saved too The grey values in the difference image are calculated as such Diff 256 target2. and 8 bit 0 255 images although images displayed on the screen are always 8 bit To maximize flexibility a 3 layer data structure is used internally bottom middle and top layer The bottom layer is the raw data of both target and reference images which are loaded into memory either in 16 bit or 8 bit as it is in the original images Resampling and undersampling may occur as explained in the paragraph below At this layer no image transformation takes place The middle layer is always 8 bit and is extracted from the bottom layer with image transformation applied to target image Only the 3 orthogonal views are extracted and kept User defined dynamic range with the guidance of a corresponding histogram is applied to convert 16 bit 8 bit raw data to 8 bit display data This allows a user to choose image contrast properly Images at middle layer are the basis for image registration and profiling The top layer is the image displayed on the screen Artificial colors color look up table and contrast stretching and zooming are applied to the 8 bit middle layer images For registration the target image and reference image are not required to have the same matrix size or pixel size This implies that re sampling is unavoidable At loading time a common matrix is calculated based on one simple rule just large enough to contain both image sets with the chosen pixel size by default the pixel size in the reference image In 2D case no down
3. Even if the registration window is toggled off the registration procedure maintains its status until another task e g open a new dataset start 2D registration is started explicitly For registration two datasets are needed a reference image volume and a target image volume During registration the target image is transformed into the coordinate system of the reference image which stays stationary By double clicking the corresponding line in the list with left mouse button one can browse to select the corresponding image volume Once both volumes are selected one can load by clicking on the Load button The screen image shown above is when the reference and target image volumes are loaded successfully Once loaded the target image and reference image can be displayed either individually or as fused image by clicking on the corresponding line in the list Once highlighted you can use Page Up and Page Down button to switch In the fusion mode a slider is provided to vary the weights blending The images are shown in the main window as 3 orthogonal views the x y view transaxial view at bottom left the x z view coronal view at top and the z y view sagittal view at right When target reference image is shown alone one can change the color options and the dynamic range using the histogram shown Ee m Input image volumes for registration n Optone am 3H 12 Q QiB El emad_before_0107 bmp VC1Sb_rec0 115 png i
4. Inverted colors to show differences FF Flip target in Y Display parameters T 50 m Registration parameters Target gt Reference X Z COR R 18 207 x 19 414 Alpha Reset ts m 2654 Y 0601 Beta Reload 4 12 521 4 2 340 385 Gamma ES ee fi oa R k 500 e5 Shift to the right by 1 000 pixel in X Y TRA X Z COR view For Help press Fl 174 86 173 Fig 3 2 Main window for 3D image registration To visually examine how good the registration is one can alternate between target and reference images or view the fusion images with various settings Alternatively you can also check profile along any line right mouse click and drag The target image can be shifted and rotated manually using the arrow buttons or keyboard shortcuts see below for detailed key combinations There are 3 sets of arrow buttons Each of them corresponds to a given view the controls and the views are arranged in the same way topologically You can alter the shift rotation steps using button Options The registration can also be done automatically using buttons R and Register all after selecting VOI carefully It is generally recommended to shift rotate manually first so that the 2 sets of images are sufficiently close to each other before using the automatic function You can alter the searching range using button Options On each set of the arrow windows
5. there is a button R standing for register This action would do automatic registration on the corresponding view only The Register all button does registration on the 3 views alternatively in a few loops after registration on one view all 3 views are retrieved again using the newly obtained transformation parameters All these actions can be applied repeatedly and on different location of the volume A Volume Of Interest VOT is defined for automatic match only the area within the VOI is used for calculating matching criteria by default the square difference This can be crucial for registration the intuition is to use an area with clear and similar features for registration The VOI can be hidden if desired or be shown only so that you can move around to visualize the images at any location or be enabled for drawing To keep the transformation parameters three actions are provided Reset Reload and Keep The parameters can be kept in the original log file if absent one log file will be created in the target dataset Reload would simply read the parameters back and apply the transformation Reset is to discard all shifts and rotations in the current session Once the parameters are saved in the log file they will be loaded back automatically when you open the same set of data back again for 3D registration Once the images are registered a saving function with button Save will allow you to save the transformed images It saves op
6. reference 2 The resulting images will be saved in the target folder with _tar _ref and _diff attached to the file name Keyboard shortcuts For the keyboard shortcuts to work click at an empty place on the main window so that it is on focus to respond to the shortcut signals Shift lt shift target image to the left x axis by one step Shift shift target image to the right x axis by one step Shift 7 shift target image further y axis by one step Shift shift target image closer y axis by one step Ctrl Shift lt rotate to the left anti clock wise by one rotation step Ctrl Shift rotate to the right clock wise by one rotation step 3 3D registration This function can be activated via menu Actions gt 3D registration as shown in fig 3 1 G EL United Data Vee es View Options Animation Animation reverse Open Ctrl O Load for 3D viewing 2D registration 3D registration Save Exit Fig 3 1 How to activate 3D image registration function The 3D registration window as shown in fig 3 2 will appear and the normal image control window will be toggled off For the first time use of this function you might need to re adjust the window size so that all controls are shown properly This window is a floating window meaning that it cannot be attached to the main window but it can be toggled on and off with Actions gt 3D registration at any time
7. sampling is applied In 3D case both image volumes are loaded into computer memory Therefore down sampling is often necessary The down sampling factor is kept as an integer number and is determined by the max preview dimension as defined in options if N max preview dimension the maximum number of voxels is then N and the available physical memory on the PC Noting that 3D registration is very memory demanding it is therefore very important to install a 64 bit DataViewer on a 64 bit computer as a 32 bit application has the intrinsic limitation of maximum usable memory 2GB The registered images can be visualized immediately There are several ways to examine it Show the reference and target images alternatively on the screen by selecting with mouse or with keyboard keys T Page Up or Page Down Show fusion images Fusion is done with alpha blending Simply explained each grey value pixel is mapped into a so called RGB triplet R red G green B blue to be displayed on the screen if we denote a RGB triplet pixel in target image as R G B and the corresponding pixel in reference image as Rr Gr Br the pixel will be displayed as aRi 1 a R aG 1 a G oB 1 a B with ae 0 1 The mapping between a grey value and a RGB triplet is done using a look up table there are a few of them in DataViewer grey color 1 color 2 etc w o inverting w o contrast stretching The colors are chosen in different
8. Image registration in DataViewer A brief user guide Starting from version 1 5 0 0 DataViewer provides tools for image registration for both 2D and 3D In both cases only rigid transformation is considered Two sets of images are required as input a reference image which stays stationary and a target image which needs to be transformed to match the reference image 1 In a nutshell The aim of the registration option is to provide a basic tool for volume registration The emphasis is more on visualization speed and interactivity rather than a fully automatic registration which is extremely challenging We use an intensity based registration method for registration There are three important components transformation method rigid or non rigid similarity dissimilarity measure or matching criteria and the searching algorithm Currently only rigid transformation is used to transform the target image More specifically the rigid transform contains x y z translations and 3D rotation which is expressed internally using Euler angles z x z convention There are many different similarity dissimilarity measures for registration For the time being we use sum of square difference as criteria which is suitable for images coming from the same modality e g CT and when the 2 images are not too different in geometry and image intensity from each other For the searching engine we use Powell s method see Numerical recipes in C to fin
9. ation two images are needed a reference image and a target image During registration the target image is transformed into the coordinate system of the reference image which stays stationary By double clicking the corresponding line in the list with left mouse button one can browse to select the corresponding image Once both images are selected one can load by clicking on the Load button The screen image shown above is when the reference and target images are loaded successfully Once loaded the target image and reference image can be displayed either individually or as fused image by clicking on the corresponding line in the list Once highlighted you can use Page Up and Page Down button to switch In the fusion mode a slider is provided to vary the weights blending The images are shown in the main window When target reference image is shown alone one can change the color options and the dynamic range using the histogram shown To visually examine how good the registration is one can alternate between target and reference images or view the fusion images with various settings Alternatively you can also check profile along any line right mouse click and drag The target image can be shifted and rotated manually using the arrow buttons or keyboard shortcuts see below for detailed key combinations You can alter the shift rotation steps using button Options o 8 Untitled DataViewer
10. d the transformation parameters To speed up registration we use a pseudo 3D registration method Instead of searching all 6 parameters simultaneously using the 3D volumes we break the searching task into smaller and easier steps The viewing option in DataViewer displays three orthogonal views at any given location the x y plane transaxial view the x z plane coronal view and the z y plane rotated sagittal view We perform a 2D registration two shifts and one rotation on each of the views iteratively to achieve volume registration The number of loops is default to 3 which works fine in most cases One can change this number in the options If the improvement becomes very small the registration will stop automatically before the number of loops is done Due to the decomposition of a 3D task to many 2D tasks the registration can be done almost instantly in a semi automatic fashion A complete comparison in speed and accuracy is yet to be done the truly 3D registration is still to be implemented In this interactive registration mode it is important to choose a proper region for comparison The Volume Of Interest VOI can be defined interactively The smaller the VOI is the faster the calculation will be The VOI is chosen based on intuition for the automatic registration to succeed it should contain similar and clear structures in both volumes The 3D registration module in DataViewer accepts both 16 bit grey value ranging 0 65535
11. ther development As a beta release of image registration the available functionalities are quite limited New functions and features will be gradually added in the next releases A brief list of these functions is given below Truly 3D registration as an alternative Alternative similarity dissimilarity measures e g co variance mutual information in addition to the sum of square difference Alternative views for the pseudo 3D registration e g MIP images in addition to the usual orthogonal views Transformation scaling factor in addition to translation and rotation Pre processing of the image views Saving images in a resolution different than the loaded resolution e g the original resolution within given volume of interest Alternative visualization method for registered images e g check board viewing difference image Some of these come from the feedback we received on user sales meeting in 2013 We appreciate a lot these invaluable suggestions and hope for more feedback from our users on the beta release via info skyscan be
12. tionally also the reference volume This makes sense if there is resampling during loading A difference image can be saved too The grey values in the difference image are calculated as such Diff 256 target reference 2 The resulting images will be saved in the sub folder Registration in the target folder automatically created if absent Keyboard shortcuts For the keyboard shortcuts to work click at an empty place on the main window so that it is on focus to respond to the shortcut signals Shift lt shift target image to the left x axis by one step Shift shift target image to the right x axis by one step Shift 7 shift target image further y axis by one step Shift shift target image closer y axis by one step Shift Page Up shift target image up z axis by one step Shift Page Down shift target image down z axis by one step Ctrl Shift lt rotate x y tra view to the left around the z axis by one rotation step Ctrl Shift rotate x y tra view to the right around the z axis by one step Ctrl Shift 7 rotate x z cor view to the left around the y axis by one rotation step Ctrl Shift rotate x z cor view to the right around the y axis by one step Ctrl Shift Page Up rotate z y sag view to the left around the x axis by one rotation step Ctrl Shift Page Down rotate z y sag view to the right around the x axis by one rotation step 4 Fur
13. ways In fusion mode a if the user has selected different color for each image these colors are used otherwise a set of pre defined contrast colors are used instead In fusion mode i inverted grey colors are chosen to enhance the differences between the 2 set of images Draw a profile on the fusion image This draws a profile on each of the two images and shows the difference at pixel level not only in geometry but also in image intensity As mentioned above the profiles are extracted from the middle layer 2 2D registration This function is activated via menu Actions gt 2D registration as shown in fig 2 1 Untitled DataViewer View Options Animation Animation reverse Open Load for 3D viewing 2D registration 3D registration Save Exit Fig 2 1 How to activate 2D image registration function The 2D registration window as shown in fig 2 2 will appear and the normal image control window will be toggled off For the first time use of this function you might need to re adjust the window size so that all controls are shown properly This window is a floating window meaning that it cannot be attached to the main window but it can be toggled on and off with Actions gt 2D registration at any time Even if the registration window is toggled off the registration procedure maintains its status until another task e g open a new dataset start 3D registration is started explicitly For registr
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