Tutorial Visualization and Interaction

Transcription

1 m a k i n g f u n c t i o n a l M R I e a s y n o r d i c B r a i n E x Tutorial Visualization and Interaction Please note that this tutorial is for the latest released nordicbrainex. If you are using an older version please upgrade. NordicNeuroLab AS Møllendalsveien 65c N-5009 Bergen, Norway Phone: CustomerSupport@nordicneurolab.com

2 Contents 1 Coregistration Inter-modality coregistration Motion correction (BOLD/DTI/DSC/DCE) Eddy current correction (DTI) Visualization panels and thumbnails The menu Interacting with the 2D MPR views Overlays and palette scale information The slice editor Interacting with the 3D viewer Interacting with the thumbnails Volume of Interest (VOI) Creating VOIs Modifying VOIs VOI functionality Using VOIs with DTI fiber tracking VOI statitics Creating time intensity curves Using the scatter VOI to inspect time intensity curves Creating histograms Report Global report functions Report element functions Date modified: Page 2 of 33

3 1 Coregistration 1.1 Inter-modality coregistration Automatic inter-modality coregistration uses a mutual information based algorithm to search an optimal rigid transformation that aligns the two datasets. The implementation is based on an article by H. Sundar et al. (Sundar et al. MICCAI (Pt 1):950-8). Coregistration is turned on/off in the Settings menu. If turned on, then after loading of datasets have completed nordicbrainex checks if the image series are already coregistered. The functional image series are coregistered against the structural image series. If they are, nordicbrainex asks if the coregistration should be done over again. Figure 1: Redo coregistration? If the user chooses to redo the coregistration or if the image series has not already been coregistered against the structural series, automatic coregistration is started. When the coregistration is finished the user is notified that the coregistration result needs to be verified. Figure 2: Automatic coregistration is finished. In the interaction panel the icons of the two image series that are coregistered against each other appear along with a Please verify coreg button. To start the verification process press this button. Figure 3: Verify the coregistration. Date modified: Page 3 of 33

4 The image series that is coregistered against the structural series will be shown as an overlay on the structural image series, enabling a visual inspection of the coregistration. In Figure 4 the tools for adjusting and visualizing the coregistration result are shown. You can change the opacity of the overlay, switch to another overlay palette, or use a checker board visualization. At the top of this panel are the controls for interaction with the coregistration. There are basically three options: Figure 4: Working with the coregistration. Verify the automatic coregistration results If the results of the automatic coregistration are acceptable, then verify the results by clicking on Verify button. Manually coregister the data If manual adjustments are necessary click on the two Manual coregistration buttons (or press Ctrl+t/Ctrl+r) in order to enable manual translation and/or rotation. When these modes are enabled you can interactively adjust the overlaid dataset to align with the structural by using your mouse. Alternatively you alter the translations and rotations by manually changing the coregistration parameters. The MPRcrosshair can be helpful during visual inspection and can be toggle on/off using the checkbox. Restart coregistration Click on Redo button to restart automatic coregistration. The algorithm will start the search for a good match from the present coregistration settings. If you check the Use Brain Extraction option, the image Date modified: Page 4 of 33

5 series will be brain extracted before the coregistration is started. This might in some cases give a better result. You have to verify the coregistration first before the analysis of BOLD, DTI, or DSC data starts. 1.2 Motion correction (BOLD/DTI/DSC/DCE) The motion correction is an optional preprocessing step in the BOLD, DTI, DSC and DCE analysis that you can tick off in the respective settings interface, see sections DSC settings in Tutorial DSC, DCE settings in Tutorial DCE, BOLD design files in Tutorial BOLD, and DTI settings in Tutorial DTI. For each source volume the rotation and translation parameters are estimated, in an iterative manner, with regards to the first volume which is the reference volume. These parameters are saved internally so that the user can display them at a later stage by rightclicking on the icon of the dynamic series and choose Motion Correction Results. Because of the optimization nature of these algorithms, for certain datasets it may result in local, incorrect, minima that are indistinguishable from the true global minimum. Therefore, it is recommended to inspect the motion correction results for any obvious misalignments. 1.3 Eddy current correction (DTI) The Eddy current correction is an optional preprocessing step in DTI analysis, see section Details on configuring DTI settings in Tutorial DTI. The transformation model used in motion and eddy current correction of diffusion weighted images is based on an article published in 2004 by Rohde et al. Magn. Reson. Med : Certain approximations of the deformations due to Eddy currents allows us to describe the transformation as x = MDx mapping a voxel x from the distorted diffusion weighted volume space to the undistorted space of the reference volume. M is the rigid transformation matrix, while D written out is 1 c ( 1 c 2 c ) where c 1, c 2 and c 3 are the first order terms (from Eddy current artifacts) mentioned in Rohde's article. The optimization method is based on an article from 2001 by T. Netsch et al. titled Towards real-time multi-modality 3D medical image registration, which uses local correlation as the cost function. Date modified: Page 5 of 33

6 2 Visualization panels and thumbnails 2.1 The menu File Use this menu to open the database or save the session. Settings Synchronize 3D and MPR view. If ticked on, the position of the crosshair / planes in MPR and 3D viewer are synchronized. Export results as This setting will decide which export format that is used for BOLD/DTI/DSC/DCE results that are to be exported into neuronavigation systems. Smooth fibers on export. If ticked on, this will smooth the DTI fiber group before it is merged into the structural series/geometry for export to neuronavigation systems. This smoothing will also apply to DTI fiber groups displayed in MPR. Turning the smoothing off will increase the speed of Merge and View in MPR in the DTI interaction tab. Limit displayed resolution in MPR. If the user experiences problems with the application running out of memory, limit the displayed resolution in the MPR can help mitigate this problem. The data will then be resampled into the chosen resolution. Note that only the displayed resolution in MPR is reduced, and this will affect any Create snapshot / Slice selection / and Slice all outputs created, but not any merged output maps. Merged series will keep the original resolution. Use coregistration. If this is not checked, the analysis will be done without coregistrating / aligning the different series to the structural underlay. Using coregistration is recommended. 2.2 Interacting with the 2D MPR views The 2D Multiplanar Reconstruction (MPR) views display one underlay volume which can have several overlays. There are multiple interaction options available for the 2D MPR views which you can access by right clicking one of the 2D MPR views or one of the thumbnails in the data panel. We will go through these options in detail in this section. In addition to right-clicking you can also interact with the 2D MPR views using the mouse in the following way: Left clicking one of the 2D MPR views will move the two other MPR views to visualize the point in the brain were you clicked. You can also move around by holding the left mouse key down and move the mouse over the image. Holding down the middle mouse key while moving the mouse over the image will change the window level and the window width (described below). If your mouse has a wheel and you roll it over one of the 2D MPR views that plane will be moved slice by slice through the brain. Date modified: Page 6 of 33

7 Note that these interactions in the 2D MPR views also can update the 3D viewer. Go to File -> Settings and check Synchronize 3D and MPR view if you want the 3D viewer to be synchronized with the 2D MPR. Figure 5: Interaction options in the 2D multiplanar views. Right clicking one of the 2D MPR views will give you the following options: Overlay Interact with the Overlay options, delete them etc. By clicking Overlay options you can open/close that section in the interaction panel to the right. Acquisition parameters Display patient and dataset information in the 2D MPR views (see Figure 5). Add distance measure tool Add a distance measure tool to the current view (see Figure 5). Date modified: Page 7 of 33

8 Remove all distance measure tools Remove all distance measure tools that have been added. Slice selection Open the slice selection tool where you can select the area to slice, see Figure 6. Selecting Slice will open the slice editor. See section 2.3 The slice editor for more deitals. Start slicing Figure 6: Slice selection in the axial view. In the axial view slices in coronal or sagittal orientation can be generated. You can flip the orientation of the selection interface by ticking off the Horizontal checkbox. If fixed width is selected, the width can be specified by the user. Otherwise, the slice distance is generated by the number of slices and the slab thickness (the green lines). Slice all Generates a set of slices that mimics the original slices of the underlay with regard to number of slices and slice positions. Note that this equivalence only applies when this option is run from the frame in the 2D MPR with the same orientation as the slice direction of the underlay. The slicing includes all current overlays and VOIs present. When slicing is done you get a thumbnail under Derived data and the slice editor window opens up where you can send and save slices (See section 2.3 The slice editor for more deitals). Create snapshot Create a snapshot of the current view. The slice editor window opens up where you can send and save the snapshot (See section 2.3 The slice editor below for more deitals). Date modified: Page 8 of 33

9 Create snapshot of MPR Create a snapshot of the MPR in the same way as for Create snapshot above. Copy Copy the current 2D view to clipboard, you can then paste it where you want. Enable zoom/pan mode Enabling zoom and pan mode will allow you to hold down the right mouse key and move the mouse to zoom in and out, and in the same way hold the left key to pan. A miniature of the frame in the top right corner will show you which part of the frame you are looking at, see the axial view in Figure 5. Clicking the cross in this miniature turns off zoom/pan mode. Toggle window size Toggle between showing the MPR and the 3D, and to see only the current image. This feature can also be toggled by double clicking in the window. Window level/width Image contrast and intensity is often referred to as window width (contrast) and window level (intensity). This information is read from the DICOM header if available. When you open the Window level/width option you get a list of your current overlay and underlay, select the one to adjust and then click Toggle window level. You can change both values by keeping the left or the middle mouse button down and move the mouse in horizontal (contrast) or in vertical (intensity) direction on top of one of the 2D MPR views, or you can type in a particular value for maximum or minimum. The current window level and window width is shown in the MPR views (see Figure 7). Right-click to finish. Figure 7: A CBV map is added as an overlay, and toggle window level for CBV has been selected. On the right, the minimum value has been increased to exclude the lowest values from the visualization. Note that for a CBV map, this can also be done using the CBV thresholding in the DSC tab Overlays and palette scale information Overlays will be displayed with a palette/color scale. The palette scale will only be displayed when one overlay is shown, i.e. the following applies: Date modified: Page 9 of 33

10 The palette scale will be displayed if one overlay is added, but will be removed if more than one overlay is added. If BOLD analysis is done, the palette scale will be displayed if one BOLD contrast is selected, but not if more than one contrast are selected. If BOLD overlays are combined with other overlays, no palette scale will be displayed. To display the palette scale, simply select to display one overlay at the time. The numerical pixel value mappings for the palette scale will be visible when hovering the mouse pointer over the scale. If several overlays uses the same palette, it will not be possible to add to create a slice package (see next section). This is to avoid confusion when several overlays look similar. This also applies to situations where one of the overlays is a BOLD contrast (e.g. if a BOLD contrast with the hot palette is combined with an overlay with the same hot palette). The max and min values for the scale are included in the slice packages. Date modified: Page 10 of 33

11 2.3 The slice editor Figure 8: The slice editor displays the slice package selected in the MPR through slice all / slice selection or create snapshot. In the example in this figure, a study with perfusion is loaded, and the CBV map is displayed as overlays. Two VOIs have been created, their statistical values have been displayed, as well as histogram for CBV and DSC time curves for the two VOIs. This information is displayed together with the slice package, and can be saved to PACS. Date modified: Page 11 of 33

12 The purpose of the slice editor (Figure 8 and Figure 9) is to allow for easy saving of results to PACS or other remote entities. The output is a derived series without geometry, showing components from the MPR and any interactions (overlays, VOIs and VOI statistics, histograms, intensity curves, BOLD threshold etc.). The slice editor will display the slice / slice package as defined by the slice all / slice selection or create snapshot from MPR. The following options are available: Close: Will close the slice editor. The series will be saved as a thumbnail, but not saved automatically. The thumbnail can be saved manually later. Save and send: will save the slice package to the database as a new derived series, and open a dialog box with the defined remote entities for sending of the series to PACS. Save to database: will save the series to the local database only. Orientation images: will display the current position of the main orientation by crosshairs/lines on the two other orientations. In the example above, the position of the axial slice is indicated as a blue line on the coronal and sagittal views. The line with the slice position will automatically updates when scrolling through the slices. Per default, the orientation images are displayed. Cross hair: Enable if you want crosshair to show in the main frame. BOLD activation info: If any BOLD activation maps are present, this will display the current BOLD T-/Pvalue of the selected BOLD activation maps as displayed in MPR. Per default, the BOLD activation info is displayed. VOI statistics: If any VOIs have been created in the MPR, and the VOI statistics for those VOIs have been selected in the interaction and visualization panel, this will display the statistical information from the selected VOIs. Per default, VOI statistics is displayed. Histogram: If any VOIs have been created in the MPR, and the histogram for those VOIs have been selected in the interaction and visualization panel, this will display the histogram from the selected VOIs. Per default, histograms are displayed if they exist. Intensity Curves: If any VOIs have been created in the MPR, and the intensity curves for those VOIs have been selected in the interaction and visualization panel, this will display the intensity curves from the selected VOIs. Per default, intensity curves are displayed if they exist. Date modified: Page 12 of 33

13 Figure 9: The slice editor displays the slice package selected in the MPR through slice all / slice selection or create snapshot. In the example in this figure, a study with BOLD and one contrast is analyzed. One overlay VOI of the BOLD activation has been created, and the statistical values for the BOLD activations (the overlay VOI) is displayed as intensity curves. This information is displayed together with the slice package, and can be saved to PACS. Date modified: Page 13 of 33

14 2.4 Interacting with the 3D viewer The 3D viewing window enables visualization of the white matter fiber tracts as output from the DTI analysis. It can also be combined with BOLD activations by rendering the activations as 3D blobs. Figure 10: Interaction options in the 3D window in nordicbrainex. The 3D viewing window in nordicbrainex is illustrated in Figure 10. There are various features and controls embedded within the window for manipulating the current view: Fiber opacity Move the mouse over this text field located in the top row of the window to display a slider that can be used to change the opacity (transparency) of the visualized fibers. Note that using reduced opacity on interleaved objects like fiber-tracts might cause object to be visualized wrong with regards to what objects are visualized in front of what objects. Plane opacity Move the mouse over this text field located in the top row of the window to display a slider that can be used to change the opacity (transparency) of the image planes. Note that using reduced opacity on interleaved objects might cause object like planes to be visualized wrong with regards to what objects are visualized in front of what objects in different areas. AXIAL/CORONAL/SAGITTAL Date modified: Page 14 of 33

15 Move the mouse over any of these words located in the bottom row of the window to display a slider that can be used to scroll through the slices of the image volume. 3D Options Move the mouse over this button located in the upper left corner to open the 3D options. It can also be opened by right-clicking in the 3D window. Add to report Click this button located in the bottom left corner to add a snapshot of the current view to the report, see section Report. The basic navigation is done by using your mouse in the following way: Rotation of the image volume Hold down the left mouse key and move the mouse. Panning the image volume Hold down the middle mouse key and move the mouse. Alternatively you can hold down the SHIFT button when holding down the left mouse key. Zooming the image volume Hold down the right mouse key and move the mouse up/down to zoom in/out respectively. Information about a tube Hold down shift and click on a tube to get the information about it. Hold down shift and click outside the tube to remove the information. This feature is only available if a DTI dataset has been loaded. Figure 11: The animation tool in the 3D view. Right clicking in the 3D window (or clicking the 3D Options button) will give you the following 3D options: Date modified: Page 15 of 33

16 Toggle window size Toggle between showing the 3D window in full screen mode or normal view. This feature can also be toggled by double clicking in the window. Reset 3D viewer Reset all options you have chosen in the 3D visualization. Note that all the fiber groups will be lost. Create snapshots/animation Enables animation mode. Various screen captures and animations can be created of the 3D window, see Figure 11. Specify the amount of Rotation/Zoom using the corresponding drop down menu and value field, rotation values are given in degrees. Specify the number of Steps to be included in the animation. When you create an animation a new thumbnail holding the resulting snapshots will be created under Derived data. Right-click the thumbnail and select View slices to open the slice viewer window Figure 14). In this window you can save the animation in the AVI format, send it to the report, save it to the database or send it to a remote DICOM node, like e.g. a PACS system. Hide plane Toggle the visibility of any image plane (AXIAL/CORONAL/SAGITTAL). Reset view to... Reset the view to any of the orientations (AXIAL/CORONAL/SAGITTAL). Interaction mode Select between different interaction modes, i.e. how the view is updated during rotation/ panning/zooming. Default is Trackball. Plane interpolation Toggle on/off interpolation of the visualized image planes. The interpolation uses a nearest neighbor approach. Render fibers Toggle on/off the rendering of the fibers. This option is only available if a DTI dataset has been loaded and fiber tracking is performed. Hide group properties Toggle the visibility of any fiber group properties. Color fibers by direction Toggle the coloring scheme of the visualized fibers. When enabled, the fibers are colored according to their direction (Red: Left right, Green: Anterior Posterior, Blue: Inferior Superior). When disabled, the fibers have one single color as defined by the Set fiber color... menu entry, see below. Set fiber color... Set the color of the visualized fibers. Render fibers as tubes Visualize fibers as thicker tubes. Note that this may reduce the performance and interactivity of the 3D window depending on the number of fibers currently being visualized. Render volume Render volume as shown in Figure 12. Note that the volume will be rendered in a cropping box and that the basic navigation described above (using the left, middle or right mouse key) only works if you click outside this box. By clicking inside the box you move the box itself. You can also grab the bullets in the box Date modified: Page 16 of 33

17 to resize it. Also note that when Render volume is selected more options appear in the popup. These options are explained below. Hide Orientation Box Toggle the visibility of the orientation box located at the bottom right corner of the 3D window. Figure 12: Render volume in the 3D window. Note that this gives you a set of new options in the popup. When you select the 3D option Render volume the right-click menu will give you these additional options (see Figure 12): Opacity Function Shows the window for working with the opacity transfer function. Ray casting Turn on/off rendering using ray casting. Switching it off may improve performance. Cropping Box Show cropping box used for cropping the dataset. Clipping Plane Show a clipping plane used for clipping the dataset. Reset clipping/cropping Resets all clipping and cropping done by the clipping planes and the cropping box. Clip/crop overlays Toggles whether or not the clipping planes or cropping box should clip/crop through the overlay. Unselecting this option makes overlays such as BOLD activations appear as 3D-volumes. Shadow overlays Toggles the rendering option of adding shadows to the overlays on/off. Date modified: Page 17 of 33

18 2.5 Interacting with the thumbnails Figure 13: The right click menu of the structural and functional data differs slightly. Underlay and overlay datasets in the 2D and 3D multiplanar view can be changed by right clicking the thumbnails in the data panel. There are different options for structural and functional data which will be listed in the popup menu that appears when you right click the thumbnail, see Figure 13. Right clicking a thumbnail in the data panel will give you some of the following options: View as underlay Displays the dataset which corresponds to the thumbnail as underlay in the 2D multiplanar view. Only one of the datasets can be an underlay at the time. There must always be an underlay. View as overlay Displays the dataset which corresponds to the thumbnail as overlay in the 2D multiplanar view. You can add and remove overlays to view several, one or none overlays. View in 3D Displays the dataset which corresponds to the thumbnail as underlay in the 3D viewer. View slices View slices of the dataset in the slice viewer window (see Figure 14). Date modified: Page 18 of 33

19 Figure 14: The slice viewer. View dicom header: available once the derived series is saved to the local database. Send Send the dataset to a remote DICOM node, like e.g. a PACS system. You need to set up remote entities to use this functionality. Go to File -> Database -> Settings to add a remote entity (see Tutorial Handling Image Data for additional information). Note that you cannot send a dataset unless it is saved in the database (if you have a derived dataset you have to save it before you can send it). Show dicom info Show dicom information for the dataset. Note that this option is only available for datasets that are saved in the database (if you have a derived dataset you have to save it before you get this option). View dynamic series The dynamic series will be displayed volume wise in the 2D MPR views. Change the displayed volume by using the white slider in the axial view, see Figure 15. BOLD / DTI / DSC / DCE settings A BOLD dataset s thumbnail will give you the option to edit and save the settings/design file, import or create a new design file. For a DTI, DCE or DSC dataset the settings window will open so that changes can be made. See Tutorial BOLD, Tutorial DTI, Tutorial DCE and Tutorial DSC for more information on settings. Spike detection The Spike Detection window gives you the opportunity to discard slices that you find have spikes and rerun the analysis. See section Spike detection in BOLD in Tutorial BOLD and section DTI spike detecion in Tutorial DTI. Motion correction results Date modified: Page 19 of 33

20 This option gives you a pop-window with the results from the motion correction and/or eddy current correction graphically displayed. The results from motion correction are given in the graphs called Translation parameters and Translation parameters, while the results from the eddy current correction are called Deformation parameters. This option is only available for functional datasets where either motion correction or eddy current correction was performed. See section Motion correction (BOLD/DTI/DSC/DCE). Remove Remove the dataset from this session. You have to re-load it or generate it again if you want to have it back. Figure 15: View dynamic series enabled. Date modified: Page 20 of 33

21 3 Volume of Interest (VOI) 3.1 Creating VOIs The Volume of Interest (VOI) tool in nordicbrainex encompass some of the core features in the Visualization step as it offers comprehensive functionality for interacting with both the BOLD, DTI, DCE and DSC data. The Volumeof-Interest section is situated in the interaction panel to the right, see Figure 16. Figure 16: The interaction with Volume-of-Interest (VOI) tool is done on the right-hand side of the Visualization and Interaction panel (indicated with a red square). When a VOI is added, it will be shown with a bounding box in the Multiplanar Reconstruction views and the 3D viewer (with the exception of the Scatter VOIs). In order to add a VOI click on the button Add new VOI in the Volume-of-Interest section (Figure 16). A drop down menu allows you to choose the VOI type: Ellipsoid Add a VOI with an ellipsoid shape. The VOI will initially be positioned at the location of the cross hairs in the MPR view. Cube Add a VOI with a cubic shape. The VOI will initially be positioned at the location of the cross hairs in the MPR view. Polygon Date modified: Page 21 of 33

22 Add a polygon VOI. When choosing this VOI; use your mouse to draw a polygon on one of the MPR planes; click to add the points to the polygon. When you have finished you click the Finish button and the polygon will be added to the list of VOIs. Free-hand Add a free-hand VOI. When choosing this VOI; use your mouse to draw the VOI on one of the MPR planes. The drawing is done by holding down the left mouse button while drawing, and the drawing is finished when the mouse button is released. Scatter Add a scatter VOI. When choosing this VOI the Create scatter VOI - tool will open, see Figure 17. By using the slider you can move through all the slices in the current underlay s scan orientation. Choose Brush and click on the pixels you want to add to the VOI. You can select the pixels one by one or 9 at a time (see Figure 17). When Eraser is chosen you can remove already selected pixels from the VOI. Before you start to select pixels you might want to zoom in the area of interest. You can turn on/off the Zoom/Pan-mode by clicking the Zoom/Pan button. When in Zoom/Pan-mode you can zoom by moving the mouse holding down the right mouse key and pan by holding down the left mouse key. To start to select pixels you have to leave Zoom/Pan-mode by clicking this button once more. When the desired set of pixels are selected you can click Save to actually create the VOI. With the Cancel button you cancel the creation of this scatter VOI. Note that the Create scatter VOI - tool also has a checkbox to show/hide current overlays. Only overlay datasets that are derived from the underlay can be visualized in the tool. The checkbox to show/hide grid will toggle a grid that will be overlaid the visualized images reflecting the inherit resolution of the dataset and making it easier to see the actual pixel size. NOTE: This VOI type can typically be used to inspect time intensity curves, see section Creating time intensity curves. Figure 17: Tool to create a scatter VOI. Date modified: Page 22 of 33

23 3.2 Modifying VOIs A VOI can be translated, rotated and scaled, and the MPR views and the 3D viewer will then be updated accordingly. You can transform the VOI in three ways in the 2D MPR views: Translation Translate the VOI by interacting with the red point in the middle of the shape. Scaling Scale the VOI by interacting with the four yellow corner points. Rotation Rotate the VOI by using the green point in the lower right corner. Rotation can only be performed in the 2D MPR views (see Figure 18). Figure 18: Rotation of a VOI is done by moving the green dot. In the 3D viewer the VOI is displayed inside a box with 7 interaction handles, shown as spheres. These can be used to translate and scale the VOI (rotation is not possible in the 3D view): Translation in 3D viewer Translate the VOI by clicking on the handle in the center of the box. Alternatively you can click on the bounding box with the middle mouse button. Scaling in 3D viewer Scale the VOI by interacting with the six outer handles of the box. Alternatively you can click on the bounding box with the right mouse button to scale the box. Date modified: Page 23 of 33

24 3.3 VOI functionality All the added VOIs are listed in the Volume-of-Interest section (Figure 19). Figure 19: Two VOIs are created and displayed in the Volume of interest list (left). When clicking on the color box, additional options are opened (right). For each VOI you have a set of icons/options to interact with that specific VOI: Visibility checkbox for the VOI If checked the VOI is visible in the 2D MPR views and in the 3D viewer. Name of the VOI You can edit the default name of the VOI by clicking on the field and write. Color/visualization options Click the color icon to open an option panel: - Change the VOI s color and its opacity - Toggle whether the bounding box should be visible or not. - Find VOI (binoculars) By clicking the binoculars button the planes will adjust themselves so that the VOI is in the center of the planes shown. This button can help you re-find your VOI if you have navigated away from the VOI and can no longer see it in any of the views. Show/Hide VOI statitics Click to open the VOI statistical information for the current VOI. See section VOI statitics. Show/Hide intensity curve Click to open this VOI s intensity curve for a dynamic dataset, i.e. you need to load at least one dynamic dataset to use this option. Note that if you click this button for several VOIs their curves will all come up Date modified: Page 24 of 33

25 in the same diagram, distinguished by their color. Right-click the diagram to add the design graph or to add this curve to the report or save as text-file. See section Creating time intensity curves. Show/Hide histogram Click to open this VOI s histogram. Note that if you click this button for several VOIs their histograms will all come up in the same diagram, distinguished by their color. Right-click the diagram to add it to the report or save to text-file. See section Creating histograms. Logical operator In this dropdown you can mark the VOI with AND, OR, NOT or Seed. The section Using VOIs with DTI fiber tracking explains how the logical operators are used and how they are read in nordicbrainex. Delete VOI Click to delete this VOI. Click on the larger x-symbol on the top of the list to delete all VOIs. Create segmented VOI Create a new VOI based on the signal level of the selected map (e.g. BOLD contrast, CBV map, FA map, structural) inside the current VOI, i.e. the new VOI will contain all the pixels in the current VOI that is above the BOLD threshold / window level, see Figure 20. Due to differences in resolution, the activation VOI might not match pixel by pixel with the overlaying map. Figure 20: How to create a segmented VOI. 1) set the BOLD threshold / window level of underlay / overlay to a desired level; 2) create a VOI (ellipsoid or cube) around the area of interest; 3) select Create segmented VOI of the VOI created in step 2, and select the desired map from the dropdown; 4) This will turn the signal within large VOI which is above the chosen threshold / window level into a VOI. In the example above, we see that the BOLD activation is shown in pink, which is the color of the VOI. This VOI can be used further to inspect the VOI statistics, intensity curve, histogram etc. Note that in order for maps to be available for this functionality (visible in the dropdown), they have to be added as overlay. The current underlay and any BOLD contrast will always be available for this functionality. 3.4 Using VOIs with DTI fiber tracking One or multiple VOIs can be used to explore DTI fiber connectivity between different regions in the 3D viewer or define a Seed for narrowing down the search premises for Fiber Tracking (see Tutorial DTI for more details). In order to use a VOI for fiber selection, start by creating and positioning the VOI as explained in the section Creating VOIs. You can then mark the VOI with a logical operator from its drop down menu with AND, OR, NOT or Seed. If a VOI is marked with Seed it means that it is defined as a Seed region for fiber tracking. You are then asked if you want to rerun the fiber tracking, and the Fiber Tracking search algorithm will then start from the voxels within this VOI. Note that you will also get this question if you change a VOI to no longer be marked with Seed. Date modified: Page 25 of 33

26 It is important to notice that the logical operators in BrainEx are read in a certain order: 1. The fibers going through all the VOIs marked with AND are selected. 2. The fibers going through one or more of the OR VOIs are added. 3. The fibers going through one or more of the NOT VOIs are excluded. Note: with no logical operators on your VOIs, all the fibers are shown. Adding an AND to one VOI will remove all the fibers that don t go through that VOI. If you have no logical operators (all fibers are shown) and then add an OR to one of your VOIs then nothing happens. This is because OR only adds all the fibers inside it to the selection you already have (in this case: all fibers). When a VOI with an assigned AND/OR/NOT attribute is moved/scaled/resized, the fiber view will be updated to reflect the changes. 3.5 VOI statitics When VOIs are created, the VOI statistical information can be displayed on a list, by selecting the VOI statistics button next to the VOI (the i ). The i must be selected for all VOIs where the VOI statistics is to be displayed. Figure 21: The VOI statistics of the two VOIs are displayed by selecting the i next to the VOI name and color indicator box. Series to be displayed in the list is selected from the Select datasets dropdown. By default, the overlay that was added last is the default selection in the list. Any structural source data and any derived map can be displayed, and multiple maps from multiple VOIs can be displayed simultaneously, as shown in Figure 22. Dynamic source data are not available. Date modified: Page 26 of 33

27 Figure 22: Any derived map is available from the VOI statistics dropdown list. Here, ncbv and ncbf from perfusion analysis, and ADC from DTI analysis from two different VOIs are listed. The list can be saved to text-file by right-clicking on the list. Additionally, the VOI statistical information can be displayed on slice packages that are saved to PACS using Create snapshot, Slice selection or Slice all in the MPR (see Figure 8). 3.6 Creating time intensity curves You can use the VOI tool to inspect the time intensity curves for dynamic datasets. This allows you to visualize the dynamic signal in a BOLD, DTI, DCE or DSC dataset. In order to create a time intensity curve start by creating and positioning a VOI as explained in section Creating VOIs. You can then create a curve for this VOI by clicking on the time intensity curve symbol next to the VOI, see Figure 23. Figure 23: Intensity curves can be displayed by clicking on the intensity curve symbol in the VOI list. This will display the intensity curve in the lower right panel. If you have loaded more than one dynamic series, a drop down menu enables you to choose the series you want to see the time intensity curve for. If you right-click on the diagram you get the option to add the design graph (BOLD only, see Figure 24, left), save to text-file or add curve to the report. Intensity curves from multiple VOIs can be displayed simultaneously, as shown in Figure 24 (right). Date modified: Page 27 of 33

28 Figure 24: Left: the intensity curve (time curve) of a BOLD activation (VOI created by selecting an overlay VOI of the BOLD signal as explained in Modifying VOIs). The BOLD design graph can be displayed by right-clicking. Right: Intensity curves from a perfusion series from two different regions (VOIs). Whenever the VOI is moved/scaled/resized the curve will be updated to reflect the signal curve in the current VOI Using the scatter VOI to inspect time intensity curves The scatter VOI type has some additional features compared to other VOI types that allows interactive inspection of time intensity curves within individual pixels. This can be done by following these steps: Figure 25: Tool to create a scatter VOI: a dynamic dataset is selected as underlay and therefore the time intensity curves at the current mouse position is visualized. In the above example, a BOLD dynamic series is selected as an underlay. This can also be used to investigate the time curves of a perfusion series. 1. Right click on the thumbnail (in the data panel to the left) of the dynamic dataset to be inspected and select View as underlay. This will change the current visualized volume in the MPR views to the first volume of the dynamic dataset. Date modified: Page 28 of 33

29 2. Add a scatter VOI as explained in the section Creating VOIs on page 21. This time when the tool to create a scatter VOI opens (Figure 17) it will also show the time intensity curves for each of the pixels in a 3 3 matrix (Figure 25). The reason for this is that a dynamic dataset is selected as underlay. 3. Move the mouse over one of the pixels. That pixel s intensity curve is the green curve in the middle of the matrix, and its adjacent pixels have their intensity curves shown in red around it (see Figure 25). The 3 3 matrix of time intensity curves will update to always show the curves at the current mouse position. 4. You can use the Zoom/Pan-mode as described in section Creating VOIs on page 21. If you want to create a scatter VOI and not only investigate the time intensity curves for the pixels use the buttons and options above the curves (they are all described in the section Creating VOIs on page 21). 3.7 Creating histograms You can also use a VOI to create histograms of various parametric values. In order to create a histogram, start by creating and positioning a VOI as explained in section Creating VOIs on page 21. You can then open its histogram by clicking on the histogram symbol for that VOI in the list, see Figure 26. Figure 26: The histogram can be displayed by clicking on the histogram symbol in the VOI list. The histogram will open in the lower right panel and a drop down menu enables you to choose which dataset should be used as the source data for the curve. Whenever the VOI is moved/scaled/resized the histogram will be updated to reflect the signal curve in the current VOI. If you want to add the histogram to the report you rightclick on the histogram and select Add histogram to report. The histogram can also be saved as a text file by rightclicking on the histogram. Figure 27: Histograms from two VOIs on a normalized CBV map are shown. In this example, the two VOIs are measuring the signal in the normal tissue and tumor tissue, illustrating an increased CBV in the tumor tissue (see Figure 21). Date modified: Page 29 of 33

30 4 Report 4.1 Global report functions The nordicbrainex report module provides tools for generating a report based on the analysis results. The report can include screenshots from the visualization step, in addition to text, headlines and an appendix which is a summary of the image data that were used and the analysis that has been performed. You can go back and forth between the visualization view and the report by using the navigation buttons in the upper right corner of nordicbrainex. Figure 28: The report interface in nordicbrainex. If you start nordicbrainex and load new patient data an empty report will be opened, only containing information about the patient that is automatically extracted from the image. You can add images, text and an appendix to this report, or you can open an existing report. You can only open an existing report for the same patient. You can also create a new report. Note that if you open a saved session you will get the report that was saved in that session. Date modified: Page 30 of 33

31 All buttons on top of the report preview (Figure 28) are global report functions. The available buttons are shown in Figure 29 and gives you the following features: Back Go to the previous page of the report. Next Go to the next page of the report. Zoom in Zoom in the report preview. Zoom out Zoom out the report preview. New Create a new report. You are informed that you will lose the current report if you have not saved it. Open Open an existing report which was saved in the nordicbrainex report format. It is only possible to open reports that have been generated for the same patient, whose image data are currently opened. Save Save the report as a pdf file, a DICOM file or a nordicbrainex report. A nordicbrainex report can be re opened and modified later on. Note that when you save a session the report you are currently working on will be saved and re-opened when you re-load that session. Save to database Save the report to the database. You will not be able to modify the report afterwards, you can only save additional reports to the database. Refresh Refresh the report preview. Print Print the current report. Printer settings Define settings for your local printer. Figure 29: Interaction buttons on top of the report preview. Date modified: Page 31 of 33

32 4.2 Report element functions You can add different types of elements to the report: image, text, graph, appendix etc. When an element is added it will show up in the tree structure (Figure 28). In order to modify elements, e.g. edit the text or scale images, choose the element you want to modify in the tree structure. Its interaction tab will then open so that you can interact with that report element. Note that some of the nodes in the tree can be opened to see/select their subnodes. If you want to change the order of report elements you select an element that you want to move up or down in the tree structure and click on the Up and Down button (described below). If you want to add a text component to the report click the Add text button described below, and then click on the text component that appears in the tree structure. This will open the text interaction tab where you can edit the text. The result will be displayed in the Report preview. Graphs can be added by right clicking on them and select Add to report, e.g. histogram and intensity curves for VOIs (described in section Modifying VOIs ). Screenshots can be added to the report by clicking on Add to report in the lower left corner of each visualization view, see Figure 30. You can also add images when you have performed slicing by clicking on the Report buttons in the slice viewer window (see Figure 14). When an image is added you can select it in the tree structure to open it in the interaction tab below. In the interaction tab you can then scale the image, give it a name and add markers (circle or arrow). To edit the text for the marker select the marker in the tree structure and write in the Edit field in the interaction tab. You can also change the color or shape of the marker at any time by selecting it and then click Edit marker in the interaction tab. Date modified: Page 32 of 33

33 Figure 30: Adding a screenshot by clicking on Add to report in the MPR views and the 3D viewer. You can add an appendix to the end of the report by clicking on the Add appendix button. This will summarize which image data were used and which analysis steps were performed. If motion correction and/or eddy current correction was performed the results will be displayed as graphs in the appendix. The buttons above the tree structure in Figure 28 are used to interact with the components in the tree structure. The available functions are: Navigation Up and Down buttons for changing the order of the elements in the report, e.g. select an element in the three structure and click the Up button will make this element raise above the element above it. Add text A text component will be added to the report. You can also choose to enter a headline. Add appendix The appendix adds a summary of the image acquisition parameters and of the analysis that has been performed at the end of the report. Delete element You can at any time delete an element from the report: text, images, markers etc. Select the element you wish to delete and then click the Delete element button. Date modified: Page 33 of 33