Contents About InVesalius ........................................................................................................................... 3 Chapter 1....................................................................................................................................... 4 Introduction ............................................................................................................................... 4 1.1 Important Concepts ........................................................................................................... 4 1.1.1 DICOM (Digital Image Communications in Medicine) .......................................... 4 1.1.2 CT - Medical .................................................................................................................. 4 1.1.3 CT - Dental .................................................................................................................... 5 1.1.4 MRI .................................................................................................................................. 6 1.2 Resources required ............................................................................................................. 8 1.2.1 Minimum settings .......................................................................................................... 8 Chapter 3....................................................................................................................................... 8 Import ......................................................................................................................................... 8 DICOM 3.1 .................................................................................................................................. 8 3.2 Analyze ............................................................................................................................... 12 Chapter 4..................................................................................................................................... 13 4.1 Reconstruction Multiplanar ............................................................................................. 13 4.1.1 Axial Guidance .......................................................................................................... 15 4.1.2 sagittal orientation ..................................................................................................... 15 4.1.3 Coronal orientation ................................................................................................... 17 4.2 Correspondence between the axial directions, sagittal and coronal ..................... 17 4.3 Move................................................................................................................................... 18 4.4 Rotate ................................................................................................................................. 19 4.5 Enlarge (Zoom) .................................................................................................................. 20 4.5.1 Maximizing the windows guidance ......................................................................... 20 4.5.2 Enlarging or reducing an image .............................................................................. 21 4.5.3 Enlarging an image area .......................................................................................... 21 4.6 Brightness and contrast (Windows) ................................................................................ 22 4.7 Pseudocolor....................................................................................................................... 25 4.8 Type of projection............................................................................................................. 29

4.8.1 Normal ......................................................................................................................... 30 4.8.2 MaxiP............................................................................................................................ 30 4.8.3 MinIP ............................................................................................................................. 31 4.8.4 MeanIP......................................................................................................................... 32 4.8.5 MIDA ............................................................................................................................ 33 4.8.6 Outline MaxiP .............................................................................................................. 35 4.8.7 Outline MIDA............................................................................................................... 35 Chapter 5 Segmentation .......................................................................................................... 36 5.1 Threshold (Threshold) ........................................................................................................ 36 5.2 Manual Segmentation (Image Editing) ......................................................................... 40 Chapter 6 Surface (triangle mesh) .......................................................................................... 45 6.1 Creating surfaces ............................................................................................................. 45 6.2 Transparency ..................................................................................................................... 48 6.3 Color ................................................................................................................................... 49 6.4 Separating disconnected regions .................................................................................. 50 6.4.1 Separating the largest surface ................................................................................. 50 6.4.2 Select the regions of interest .................................................................................... 51 6.4.3 Separate all disconnected regions ......................................................................... 52 Chapter 7 Measurements ......................................................................................................... 52 7.1 Linear Measurement ........................................................................................................ 53 7.2 Angle Measurement ........................................................................................................ 54 7.3 Volumetric Measurement ................................................................................................ 55 Chapter 8 Data Management ................................................................................................. 56 8.1 Masks .................................................................................................................................. 57 8.2 3D Surfaces ........................................................................................................................ 57 8.3 Measurements................................................................................................................... 58 Chapter 9 Simultaneous display of images and surface ...................................................... 58 Chapter 10 Volume rendering.................................................................................................. 60 10.1 Standards viewing .......................................................................................................... 61 10.2 Customization of default ............................................................................................... 64 10.3 Customizing standard with Brightness and Contrast ................................................. 67

10.4 Cut .................................................................................................................................... 68 Chapter 11 Exporting Data ....................................................................................................... 69 11.1 Surface ............................................................................................................................. 69 11.2 Picture .............................................................................................................................. 70 Chapter 12 Customization ........................................................................................................ 71 12.1 Menu Tool ........................................................................................................................ 71 12.2 Automatic positioning of volume / surface ................................................................ 72 12.3 Background color of window volume / surface ........................................................ 72 12.4 Show / Hide Text in 2D window ..................................................................................... 73

About InVesalius InVesalius is a public software for the healthcare that performs analysis and segmentation of virtual anatomic models, enabling the manufacture of physical models with the aid of rapid prototyping. From pictures two-dimensional (2D) obtained by Computed Tomography (CT) or Magnetic Resonance Imaging (MRI) equipment, the program allows to create virtual models in three dimensions (3D) corresponding to anatomic structures of patients under care. The name is a tribute to the Belgian physician Andreas Vesalius (1514-1564), considered the "father of modern anatomy." InVesalius The software is developed by CTI (Center for Information Technology Renato Archer), a unit of the Ministry of Science and Technology (MCT) since 2001. Initially, only the installation program was distributed free. From November 2007, InVesalius was available as software free in the Public (www.softwarepublico.gov.br) Portal Software, consolidating communities of users and developers. This is a simple, free and open, robust, cross-platform tool with commands in Portuguese, with fast clear and direct functions, easy to use and when performed on PC microcomputer. The use of visualization technologies and three-dimensional image analysis medical, whether or not integrated rapid prototyping, assist the surgeon in diagnosis of disease and allow a detailed surgical planning is performed, simulating complex interventions in advance, which may involve, for example, a high degree of facial deformity or placing prostheses. The InVesalius has shown great versatility and has contributed with several areas, among them medicine, dentistry, veterinary medicine, archeology and engineering.

Chapter 1 Introduction This manual aims to show the use of tools InVesalius and also present some concepts to facilitate the use of the software. The InVesalius is a software to assist health professionals in the diagnosis and surgical planning. It is worth noting, however, that all software in the context of diagnosis is totally extra, and since all any act committed is the responsibility of the health professional. Apart from medicine, you can use the software in other areas such as archeology, veterinary, or even in industrial applications. As a prerequisite Basic, just that the images to be analyzed are the DICOM standard (Digital Imaging Communications in Medicine). To date, InVesalius stemmed reconstructs images from scanners and devices MRI. To operate the software, just have basic computer knowledge. Understanding medical images can contribute to a better understanding of the operations.

1.1 Important Concepts In this section, we discuss some concepts necessary for better understanding and operation of the software. 1.1.1 DICOM (Digital Image Communications in Medicine) DICOM is a standard relating to the transmission, storage and processing of medical images. The standard provides various imaging modalities medical, as images stemmed from CT equipment, MRI, ultrasound, electrocardiogram, among others. A DICOM image consists of 2 main components, a matrix containing the image pixels and a set of meta-information. Those information contains, for example, the name of the patient, the mode of image and position of the image relative to space (in the case of CT and resonance). 1.1.2 CT - Medical A CT scan shows the radiodensity of the tissue, i.e., the average X-ray absorption by the tissues. The radiodensity is translated for the image in gray levels on a scale called Hounsfield, name given in honor of Godfrey Newbold Hounsfield, one of the creators of first machine CT.

Figure 1.1: Medical Tomography - www.toshibamedical.com.br In modern appliances, with a radiation emitter and a bank sensor (also called channels, ranging from 2 to 256), which surround the patient while the stretcher is busy forming a spiral, you can generate a large amount of images simultaneously with low energy X-rays. Hounsfield scale As mentioned in the previous section, the computed tomography images are generated in gray levels, which are then translated into the scale Hounsfield (HU). The lighter shades represent denser tissues, and the darker, less dense tissues such as skin and brain. Table 1.1 presents some materials and their values in HU (Hounsfield Unit). Table 1.1: Range of Hounsfield Material HU Air -1000 or less Fat -120 Water 0 Muscle 40 Contrast 130 Bone 400 or more 1.1.3 CT - Dental A dental CT scan commonly works with less emission of radiation compared to computed tomography and medical, consequently, makes it possible to view more details of sensitive regions, such as alveolar cortex.

Image acquisition is done with the patient upright (unlike medical tomography, the patient is horizontal). A transmitter and a X-ray sensor surrounding the skull of the patient, an arc 180 or 360 . The images generated by the scanner can be interpreted as a volume with the patient's skull immersed. This volume is "sliced" by the instrument software, being able to generate images with different spacing or other types of images such as panoramic view of the region of interest.

Figure 1.2: dental CT scanner - www.kavo.com.br The images acquired by dental CT scanners often require greater post-processing when it is necessary to separate (segment) determined structures using other software such as InVesalius. This is because normally these images have more gray levels than the Hounsfield scale, which makes the use of segmentation patterns (preset) less efficient. Another fairly common feature in the images emanating from dental CT scanners is the high presence of speckle noise type and the presence of other noises typically caused by use of prostheses amalgamation by the patient. 1.1.4 MRI MRI is an examination performed without the use of ionizing radiation. Instead, there is used a strong magnetic field to align the some atoms present in our body, most commonly the element hydrogen. After alignment, the radio waves are triggered, and the atoms are excited. The sensors measure the time it takes the hydrogen atoms to align again. With this, you can determine which is the tissue type because different tissues have different amounts of hydrogen atoms. To avoid interference and improve the quality of the RF signal, and the patient get inside the machine, is placed a coil in the region of interest.

Figure 1.3: MRI Equipment - www.gehealthcare.com

Figure 1.4: Coil - www.healthcare.philips.com

1.2 Resources required The InVesalius is designed to run on personal computers, as desktops and notebooks. Currently, it is compatible with the following systems operational: - MS-Windows (XP, Vista, Windows 7) - GNU / Linux (Ubuntu, Mandriva, Fedora) - Apple Mac OS X The InVesalius performance mainly depends on the amount of reconstructed slices (images open by the software), the amount of available RAM, the processor frequency and architecture operating system (32 bit or 64 bit). It is worth mentioning, as a general rule, the higher the amount of RAM available on the system, the greater the number of slices that can be open simultaneously for a given study. For example, 1 GB of available memory, you can open about 300 slices with a resolution of 512x512 pixels. Already with 4 GB of memory, you can open around 1000 images with the same resolution. 1.2.1 Minimum settings  Operating System 32-bit  Intel Pentium 4 or equivalent, with a frequency of 1.5 GHz  1GB of RAM  80 GB hard drive  Graphics card with 64 MB memory  Video resolution of 1024x768 pixels  1.2.2 Recommended Configurations  Operating System 64-bit  Intel Core 2 Duo or equivalent, with a frequency of 2.5 GHz  4 GB of RAM  180 GB hard drive  NVidia or ATI graphics card with 128 MB memory  Video resolution of 1024x768 pixels

Chapter 3 Import The InVesalius matter in DICOM format files, including compressed files (JPEG lossless and lossy) files in Analyze format

DICOM 3.1 On the File menu, click Import DICOM option .... If you prefer, use the keyboard shortcut Ctrl + I. The import can also be triggered by toolbar icon shown in figure 3.1.

Figure 3.1: Shortcut for Import DICOM Then select the directory containing DICOM files, as in Figure 3.2. The InVesalius will also search for files in subdirectories of the selected directory, if any. Click OK.

Figure 3.2: Selection of directory While InVesalius demand for DICOM files in the directory is displayed in the progress of loading of files scanned, as shown in Figure 3.3.

Figure 3.3: Status of verification and loading files If DICOM files are found, a window opens (Figure 3.4) to select the patient and their series that you want to open. Also You can skip images for reconstruction.

Figure 3.4: Screen import If you want to import a series with all the images present, click "+" Next to the name of the patient to expand the series belonging to it. Double click with the left mouse button on the description of series. See figure 3.5.

Figure 3.5: Selection of series

In some cases, particularly when not have a computer memory and / or processing to work satisfactory with many images in a series, it may be advisable to skip (ignore) some of them. To do this, click once with the left mouse button on the description series (Figure 3.5) and select how many images will be skipped (Figure 3.6). Click OK.

Figure 3.6: Jumping pictures If detected insufficient amount of memory available in time to load the images is not recommended to reduce the resolution of the slices to work with volume and surface display, as shown in 3.7 window. The slices are resized according to the percentage compared to the original resolution. For example, if each slice of the examination contains the dimension of 512 x 512 pixels and is suggested to "Percentage of resolution Original "at 60%, each resulting image will be 307 x 307 pixels. If you want open with the original resolution select the value 100.

Figure 3.7: Reduced dimension image After the above procedures, a window (FIG. be displayed 3.8) with the progress of reconstruction (when images are stacked and interpolated).

Figure 3.8: Progress of reconstruction

3.2 Analyze To import files into Analyze format from the File menu, click the Import option other files ... then the Analyze option to shown in Figure 3.9.

Figure 3.9: Menu for importing images in analyze format Select the file type Analyze the extension. Hdr and click Open. (Figure 3.10).

Figure 3.10: Importing images in analyze format

Chapter 4 Image Manipulation (2D)

4.1 Reconstruction Multiplanar When importing DICOM images, InVesalius automatically shows the multiplanar reconstruction guidelines Axial, Sagittal, and Coronal and as a window to 3D manipulation. See figure 4.1.

Figure 4.1: multiplanar reconstruction In addition to creating the multiplanar reconstruction image InVesalius segments, especially, for example, the bones and soft tissues. The highlight is represented by means of applying color on the segmented structure, that is, the colors forming a mask over the image highlighting the structure (Figure 4.1). This will be discussed in more detail in later chapters. To hide the mask, we use the data manager, located in lower left corner of the screen. Simply choose the Masks tab and click once with the left mouse button on the icon next to the eye "Mask 1". See figure 4.2.

Figure 4.2: Mask Manager The icon disappears from the eye, and the colors of the mask segmentation are hidden (Figure 4.3). 4.1.1 Axial Guidance The axial orientation is composed of the region of interest transverse sections ie, parallel to the axial plane of the human body cuts. In Figure 4.4, is displayed an image in axial orientation of the skull region. 4.1.2 sagittal orientation The sagittal orientation is composed of sections performed laterally relative The region of interest, ie parallel to the sagittal plane of the body sections human which divides the left and right portions. Figure 4.5 shows an image of the skull in sagittal orientation.

Figure 4.3: Reconstruction of multiplanar unmasked segmentation

Figure 4.4: Axial

4.1.3 Coronal orientation The coronal orientation is composed of cuts parallel to the coronal plane, which divides the body into dorsal and ventral halves. Figure 4.6 shows an image of the skull in coronal orientation.

Figure 4.5: Sagittal section

Figure 4.6: Coronal

4.2 Correspondence between the axial directions, sagittal and coronal To find the common point of images in different orientations, just trigger the "Cross intersection of slices" feature from the shortcut icon located on the toolbar. See figure 4.7.

Figure 4.7: Shortcut to show common point between different orientations When the feature is activated, two line segments that intersect at right angles are displayed on each (Figure 4.8) image. The point of intersection of each pair of segments is the common point between different orientations. To modify the point, hold down the left button mouse and drag. Automatically, the corresponding points will be updated at each image.

Figure 4.8: Common point between different orientations To disable the feature, simply click on the shortcut again (Figure 4.7). This feature can be used in conjunction with the editor slices (which will be discussed later).

4.3 Move To move an image on the screen, you can use the shortcut icon "Move" in the toolbar (Figure 4.9). Click on the icon to activate the resource and then with the left mouse button on the image, drag it to the desired direction. The figure shows a 4:10 image displaced (moved).

Figure 4.9: Shortcut for moving images

Figure 4.10: Offset Image

4.4 Rotate The image rotation can be activated by the shortcut icon "Rotate" the toolbar (Figure 4.11). To rotate an image, click on the icon and then with the left mouse button over the image, drag it clockwise or counterclockwise, depending on the direction of rotation.

Figure 4.11: Shortcut to rotate images

Figure 4.12: Image rotated

4.5 Enlarge (Zoom) In InVesalius, there are different ways to enlarge a picture. Can be Maximize the window to the desired orientation, zooming in directly image, or select the region of the image to be enlarged. 4.5.1 Maximizing the windows guidance As we already know, the main window is divided into 4 InVesalius sub-windows: axial, sagittal, coronal and 3D. Each mode can be maximized to occupy the entire area of the main window. Simply click the left mouse button on the icon in the upper right corner the sub window (Figure 4.13). To restore a maximized window to its previous size, just click the icon again.

Figure 4.13: Detail of a subwindow (Notice the icon to maximize the upper right corner) 4.5.2 Enlarging or reducing an image To enlarge or reduce an image, click on the shortcut icon "Zoom" on toolbar (Figure 4.14). Keep the left mouse button on the image and drag the mouse up, if you want a larger view, or down, if you want to reduce it.

Figure 4:14: Zoom shortcut 4.5.3 Enlarging an image area To enlarge a particular area of the image, click on the icon shortcut "Zoom-based selection" in the toolbar (Figure 4.15). Position the mouse pointer at the start position of the selection, click and hold the left mouse button and drag it to the end position of selection, forming a rectangle (Figure 4:16). Once the left button mouse is released, the zoom operation will be applied to the selected region (Figure 4.17).

Figure 4.15: Zoom shortcut based on selection

Figure 4.16: Selected area to zoom

Figure 4.17: Enlarged Image

4.6 Brightness and contrast (Windows) To Improve visualization of the images, we can use the feature window width and window level, popularly known as "brightness and contrast" or "Window" (for radiologists). With this feature, you can define the range of grayscale (window level) and the width of the range (window width) que will be used to display images. The feature can be activated by the shortcut "Contrast" icon in the taskbar tools. See Figure 4.18.

Figure 4:18: Shortcut brightness and contrast To Increase the brightness, hold the left mouse button and drag horizontally to the right. To decrease the brightness, just drag the mouse to the left. The contrast can be changed by dragging the mouse (left button) on the vertical: up to Increase or decrease the contrast down to. To disable the feature, left click on the shortcut icon (Figure 4.18). You can use pre-defined patterns of brightness and contrast. Table 4.1 lists some types of fabric with the respective values of brightness and image contrast. To use the predefined pattern, position the cursor mouse over the image and click the right button to open the menu context on it. When the menu opens, select the entry and Brightness Contrast and then click on the default option, According to the type of fabric, shown in the Figure 4.19.

Figure 4.19: Context menu for selection of brightness and contrast (A) Bone (b) Lung

Figure 4.20: Different types of brightness and contrast

Table 4.1: Values of brightness and contrast to some tissues Brightness Contrast Fabric Standard Exam Amended Amended Manual Abdomen 50 350 Brain 80 40 Emphysema 500 -850 Posterior Fossa Nasal 120 40

Liver 2000 -500 Ischemia - Contrast Fabric Hard 15 32 Ischemia - Contrast Soft Tissue 80 20 Larynx 80 180 Mediastinum 350 25 Hat 2000 300 Pelvis 50 450 Lung Duro 1000 -600 Lung Mole 1600 -600 Sinus 4000 400 Vascular - Hard 240 80 Vascular - Soft 680 160

4.7 Pseudocolor Another resource to Enhance visualization of the images are pseudocolors. They replace the gray levels per color, or reversed by levels of gray. In the Latter case, image regions were previously more than. Clearly if become darker and vice versa. To change the display using the pseudocolor, position the cursor mouse over the image and click the right button to open the menu context on it. When the menu opens, select the enter Pseudocolor and then click the option you want pseudocolor, shown in the Figure 4.21.

Figure 4.21: Pseudo Color Figures 4:22 to 4:28 pseudocolor examples for the various options available.

Figure 4.22: Standard

Figure 4.23: Inverted Image Grey

Figure 4:24: Rainbow

Figure 4:25: Desert

Figure 4:26: Hue

Figure 4:27: Ocean

Figure 4.28: Saturation

4.8 Type of projection You can change the type of 2D projection images to be displayed, beyond the Normal mode, InVesalius has six types of projections can be accessed as follows: Position the mouse cursor over the image and click the right button to open the context menu on it. When the menu opens, select the type of projection entry, then click on the option you want pseudocolor, shown in the Figure 4:29.

Figure 4:29: Menu type projection

4.8.1 Normal Normal mode is the default view, i.e., without any projection, the way In which the image was acquired or previously customized either with or pseudocolor brightness and contrast. Example in Figure 4.30.

Figure 4:30: Normal Projection 4.8.2 MaxiP MaxiP is also known as MIP (Maximum Intensity Projection), Those voxels method selects only have the maximum intensity between those visited as the shown in Figure 4:31. According to the quantity or "Depth" of MaxiP each voxel is visited in order of overlap, For example, to select MaxiP pixel (0, 0) is composed of three slices Necessary to visit the pixel (0, 0) of the slices (1, 2, 3) and select the highest value.

Figure 4.31: Projection MaxiP or MIP The Figure 4:32 shows the number of Images that will make up the MaxiP is Set At the bottom of each image orientation.

Figure 4:32: Select the number of Images that make up the MaxiP or MIP 4.8.3 MinIP Unlike the MaxiP MinIP (Minimun Intensity Projection) selects Only voxels have minimal que internsidade between the visited, we present an example in Figure 4:33. Selecting the number of pictures Which will compose the projection is made in the lower image of each orientation Shown in the Figure 4:32

Figure 4:33: Projection MinIP 4.8.4 MeanIP The technique MeanIP (Mean Intensity Projection) is shown in Figure 4:34 composes the projection perfoming average of visited voxels. The voxels are visited the same way the MaxiP MinIP and methods. Also It is possible defines how many images will make the projection on the bottom of the image each orientation as is shown in figure 4:32.

Figure 4:34: Projection MeanIP 4.8.5 MIDA MIDA technique (Maximum Intensity Difference Accumulation) projects to image taking into Consideration only the voxels have maxima que place. From each screen pixel is simulated lightning toward the volume, each voxel is intersected by each of the rays reaching the end of the volume, each voxel has visited the cumulative value but are taken into account only if the value is greater than the values have visited before. MaxiP The example of, you can select how many pictures will be used to accumulate values. Here an example in Figure 4:35 projection of MIDA.

Figure 4:35: Projection MIDA As the figure shows 4:36, you can reverse the order in which the voxels are visited, but select inverted at the bottom Order option the screen.

Figure 4:36: Projection MIDA in reverse order

4.8.6 Outline MaxiP Composes the 2D projection of the set of images containing the volume using the Date Contour MaxiP. The technique is to visualize contours gifts the projection generated with MaxiP (4.8.2) technique. An example is shown in Figure 4.37.

Figure 4:37: Projection Contour MaxiP 4.8.7 Outline MIDA Composes the 2D projection of the set of images containing the volume using Contour MIDA technique. The technique is to visualize contours present in the projection generated by the MIDA technique (4.8.5.) The example of MIDA is shown. You can reverse the order que the volume is played. We exemplify the Figure 4:38.

Figure 4:38: Projection Contour MIDA

Chapter 5 Segmentation To select a particular type of tissue image, is used segmentation feature, available in InVesalius.

5.1 Threshold (Threshold) Threshold is a technique for image segmentation que Allows you to select the Whose only image pixels intensity is Within the defined threshold user. The threshold is defined by two numbers, initial and end thresholds, Also known as minimum and maximum thresholds. 's a reference for defining the Hounsfield scale (Table 1.1) are used. Segmentation is thrown in the panel on the left side of the interface the InVesalius in item 2. Select region of interest (Figure 5.1).

Figure 5.1: Selection of region of interest Before starting the segmentation, you must configure a mask. The mask is an image with the selected region and superimposed on the color original image. See figure (5.2)

Figure 5.2: Mask (yellow regions) To change the threshold, one can use the bar representing the levels of gray in the image (Figure 5.3.) You can change the initial threshold using the left slider bar. Similarly, the end threshold can be changed via the right control. Also It is possible to enter Their Desired directly into text boxes at the ends of the bar values. With changing values,

automatically the mask will be updated by painting only the pixels with intensity Within the range determined.

Figure 5.3: Selection of pixels with intensity between 226 and 3021 (Bone) Also there are predefined threshold values According to some tissue types, shown in the Figure 5.4. Simply select the Desired tissue and the mask will be automatically updated.

Figure 5.4: Checkbox values predefined threshold Table 5.1 shows the range of gray levels According to the type of fabric or material. Table 5.1: Thresholds for some predefined materials Material Initial Threshold Threshold end Enamel (Adult) 1553 2850 Enamel (Child) 2042 3021 Bone 226 3021 Compact bone (Adult) 662 1988 Compact bone (Child) 586 2198 Spongy Bone (Adult) 148 661 Spongy Bone (Child) 156 585 Custom User Settings User Settings Epithelial tissue (Adult) -718 -177 Epithelial tissue (Child) -766 -202 Fat tissue (Adult) -205 -51 Fat tissue (Child) -212 -72 Muscle Tissue (Adult) -5135 Muscle Tissue (Child) -25 139

Soft Tissue -700 225 Table 5.1 is more suitable for medical CT scanners. tomography In dental, commonly ranges of gray levels are higher and not regular. Thus, it is Necessary to use the threshold bar (Figure 5.3) to adjust Them. If you want to create a new mask, simply click on the shortcut icon This panel, Within the item 2. Select region of interest. See figure 5.5.

Figure 5.5: Shortcut to create new mask Clicking this shortcut, the new window (Figure 5.6) Appears. Select the Desired range of threshold and click OK.

Figure 5.6: Creating a new mask With the segmentation mask in September, it is possible to generate the Corresponding 3D surface images in the study. The surface is composed by a mesh of triangles. The next chapter will bring more details on this type of surface. To start the build, click the Generate surface (figure 5.7) button. If there is already an area previously generated, you can replace it by Young. Simply select, before generation, Overwrite above.

Figure 5.7: Generating surface Button After a while, the surface will be displayed in the preview window 3D InVesalius (Figure 5.8).

Figure 5.8: 3D Surface

5.2 Manual Segmentation (Image Editing) There are situations in which the targeting threshold is not efficient because it is applied to the whole set of images. To apply the segmentation to images insulators, one can use manual segmentation. With it, you can add or deleting a region of the image was segmented by threshold que. However, manual threading requires more knowledge of anatomy by the user. To use it, you need to click Tools Advanced editing (Figure 5.9) to open the editing pane.

Figure 5.9: Advanced Editing Tools The editing pane shown in Figure Appears to 5.10.

Figure 5.10: Editing Panel There are two brush types available for drawing: one in a circle and another squareshaped. To choose the brush, click the triangle selection list to open it and then click on the type chosen. The selected brush appears in the panel shown in the Figure 5.11.

Figure 5:11: Brush type Also you can change the diameter of the brush, shown in the Figure 5.12.

Figure 5.12: Selection of the brush diameter You must select the type of operation to be Performed by the brush. The options are as follows:   

Draw, paint to que the region has not been selected; Delete to remove the que was selected region; Threshold to remove the region Which is outside the threshold and was selected or paint a region that is Within the threshold and was not selected.

Figure 5:13 shows the list of operations of the brush:

Figure 5.13: Selecting the type of operation the brush The Figure shows the case in 5:14 Which some images contain noise Caused by the presence of dental amalgam in patients. Notice the "rays" coming out of the dental arch region. This is because the Also segmentation mask selects part of the noise, They are the same intensity threshold for bone. Figure 15.5 illustrates how the surface is generated from this segmentation.

Figure 5.14: Image with segmented noise threshold

Figure 5.15: Surface generated from noisy image In cases like this, using the editor with the brush on the Delete option, hold the left mouse button while dragging over the area you want to remove (in the shade). Figure 5:17 shows the image of Figure 5:14 after editing.

Figure 5.16: Zoom of the region with noise

Figure 5.17: Image with noise removed

Figure 5.18: Surface created from the image with noise removed Held editing, simply generate the surface from the edited image (Figure 5.18.) How was editing, When You click Create surface is required if you want to generate the surface of the binary method or using the method of smoothing Context aware smoothing (Figure 5:19) to minimize the "steps" on the surface. Other details will be discussed in Chapter 6.

Figure 5.19: Method of creating surface

Chapter 6 Surface (triangle mesh) In InVesalius, the 3D surface is generated based on the segmented model (Obtained from the segmentation of the images.) The method used to generate the surface is the marching cubes algorithm. Briefly, the algorithm transforms the voxels of the images were "stacked" and segmented into the mesh of simple polygons - in this case triangles. The controls available for the configuration of 3D surfaces in InVesalius are in the left pane of the item 3 Within the software. Set the 3D surface, the surface properties option.

Figure 6.1: Setting up a 3D surface

6.1 Creating surfaces You can create a new surface based on an existing segmentation mask. For this, in the left pane, in the Item 3. Configure the 3D surface, click the shortcut shown in Figure 6.2.

Figure 6.2: Shortcut to create a surface When you click this shortcut, a window opens to allow configuration the surface (Figure 6.3) to be created. In addition to being able to determine the generating surface quality, Also there options for filling existing holes and for the selection of the larger region of the surface.

Figure 6.3: Window for surface creation The selection of the larger region can be used, for example, to remove the model or support desk scanner. Figure 6.4 illustrates the case with selected the two options: "Fill holes" and "Keep larger region." (A) Forward (b) Low

Figure 6.4: Surface with selected larger region and holes filled

(A) Forward (b) Low

Figure 6.5: Surface without Selecting the largest region and open holes Have to Figure 6.5 shows the same case without these options selected. Observed support and open the scanner surface. The item creation method surface has The Following options: "Binary", "Context aware smoothing" and "Standard, we can view the sample from the surface in Figure 3 Methods 6.6. The binary method is to match the mask que was targeted being selected the region 1 and the rest 0.'s there are only 2 values, the curves on the surface que the algorithm generates are abrupt or popularly known as "steps". In Context aware smoothing method, the surface is generated from binary INITIALLY, but then runs the algorithm "Context aware smoothing" to smooth the surface and avoid Resulting "Steps" in it. In step 4 figures, to be presented below is required. The

angle in this case is formed between two adjacent triangles Normal, that if it is above the value set in the field angle, the triangle is chosen to be the starting point of the smoothing, the value range is 0 to 1, with 0 and 90 respectively. The maximum distance is the radius of the From the triangles selected in the previous step, Which will be used the boundary smoothing. The minimum weight is how much smoothing is applied in areas outside que Given above are the range. The number of steps is how many times the algorithm will perform. The default method is active Only When manual editing does not exist in the mask, the pixels of the original image are que under the mask is used to generate the surface usually pictures or resonance tomography has several gray levels, the surface is generated with softer curves. (A) Binary (b) Context Aware (c) Standard

Figure 6.6: Surfaces generated by different methods

6.2 Transparency You can view the surface with transparency. For this, first select the surface through the selection list Within the item 3. Configure the 3D surface, the surface Properties option (Figure 6.7).

Figure 6.7: Selection of surface Then, to determine the level of transparency que the surface get selected, drag the slider shown in Figure 6.8. The more to the right track, the higher the transparency applied.

Figure 6.8: Selection of level of transparency Figure 6.9 shows the display of two surfaces: an outer (Green) and one inner (yellow). The outer surface appears with Increased transparency.

Figure 6.9: Surfaces with altered level of transparency

6.3 Color The color of the surface can be changed Also. Select the surface (Review Figure 6.7) and then click the button next to the surface selected. 6:10 The Figure illustrates the button, also located in item 3. Set the 3D surface, the surface properties option.

Figure 6.10: Button to change the color The color selection window opens (Figure 6:11). Select the color Desired and click the OK button.

Figure 6:11: Color Options

6.4 Separating disconnected regions To separate que surface regions are disconnected, it is Necessary click the Advanced Tools option in Item 3. Configure 3D surface. See Figure 6.12.

Figure 6:12: Shortcut to advanced tools The menu with the available options will be displayed, shown in the Figure 6.13.

Figure 6:13: Advanced Tools 6.4.1 Separating the largest surface Separate the largest surface only option automatically selects the disconnected region containing higher volume. To perform the operation, just click the shortcut que Figure 6:14 shows. A new surface is created During operation.

Figure 6:14: Shortcut to greater separation of disjointed region

As an example, Figure 6.15 shows the case before the separation of the larger region.

Figure 6.15: Surfaces disconnected In Figure 6.16, we observe the surface with the most disjointed separate region.

Figure 6:16: Highest separate region 6.4.2 Select the regions of interest Another form of selection is by Select Regions option of interest .... To activate it, the user must click on the button shown in Figure 6.17. Then, just click on the disconnected regions of the surface who want to select.

Figure 6:17: Shortcut for Selecting regions of interest In the example of Figure 6.18 we selected the skull and the right part support the tomograph.

Figure 6:18: Example of selected regions of interest 6.4.3 Separate all disconnected regions Also you can automatically separate all the disjointed regions. Simply click on the button shown in Figure 6.19 Which Represents the Select option all disconnected regions.

Figure 6:19: Shortcut to separate all disconnected regions The figure shows an example 6:20.

Figure 6:20: Example of separation of all disconnected regions

Chapter 7 Measurements The InVesalius Allows to perform linear and angular measurements in 2D (flat axial, coronal and sagittal) and 3D (surfaces). Also It is possible to Volumetric measurements on surfaces.

7.1 Linear Measurement To perform linear measurements, you must enable this feature by clicking the Corresponding shortcut located on the toolbar (Figure 7.1).

Figure 7.1: Shortcut to enable linear measurement The linear measurement is defined between two points. With the feature enabled, click once on the image to set the starting point. Then position the mouse pointer at the end point and click once again. The measurement is performed and the result is automatically displayed on the image or surface. Figure 7.2 shows the 2D linear measurement in the axial direction, and Figure 7.3 shows another linear measure in 3D (surface).

Figure 7.2: Linear Measure on flat image

Figure 7.3: Linear Measurement on surface Note: The linear measurement is given in millimeters (mm).

7.2 Angle Measurement An angular measurement in 2D or on a surface (3d) can be performed clicking the shortcut shown in Figure 7.4.

Figure 7.4: Shortcut for angular measurement To perform angular measurement, it is Necessary to Provide the three points que describe the angle to be measured, the BC. Position the mouse pointer and click once with the left mouse button to determine the first point, A. To enter the second point B (the vertex of the angle or the "center of protractor "), position the mouse pointer and click once again. Repeat the same actions to determine the third point, C. The measurement is performed and automatically, the Resulting measurement is displayed on the image or surface. Figure 7.5 illustrates an angular measurement in a flat image, and figure 7.6 illustrates an angular measurement on the surface.

Figure 7.5: Angle Measure on flat image

Figure 7.6: Angle Measure on surface Note: The angle is measured in degrees.

7.3 Volumetric Measurement Volumetric measurements are made automatically When You create a new surface. They are displayed in 3D Surfaces tab in the Management Data pane in the lower left corner of the screen, the illustrated Figure 7.7.

Figure 7.7: Volumetric Measures Note: The volume measurement is in cubic millimeters Given (Mm3)

Chapter 8 Data Management In the previous chapters, it was shown how to manipulate surfaces, shades for segmentation and measurement. You can display or hide and create or remove these elements by management Data pane, located at the corner bottom left of the screen InVesalius The panel is divided into three tabs: Shades, Surfaces and 3D measurements, shown in the Figure 8.1. Each one of the tabs grouped Corresponding to the data elements to Which They refer.

Figure 8.1: Data Management Within each tab, the panel divided into rows and columns Appears. In each row, the first column listing determines the viewing element que line. This is the icon that represents an active "eye" or disables display of masks, surfaces or measurements. If one of these elements is on display, the icon of corresponding to Figure 8.2 Also it will be visible.

Figure 8.2: Icon That Indicates the visibility of elements

Some operations are possible on the date. For example, to delete the Given, you must first select its name, shown in the Figure 8.3, and then click the Shortcut que the figure 8.4 illustrates.

Figure 8.3: Given selected

Figure 8.4: Delete date To create a new mask, surface or measurement, just click the shortcut shown in Figure 8.5, since the respective tab is open.

Figure 8.5: New date To copy data, just select it and click the shortcut que the figure 8.6 illustrates.

Figure 8.6: Copy date

8.1 Masks In the Name column are shown the color and the name assigned to the mask. Already Threshold column displays the range of values used to create the mask. The Figure 8.1 shows an example.

8.2 3D Surfaces In the Name column are shown the color and the name assigned to the surface. The volume column shows the total volume of surface. Finally, the Transparency column Indicates the level of transparency in use to display the surface. The Figure 8.7 shows an example.

Figure 8.7: Surface Management

8.3 Measurements The Measurements tab Provides the Following information. The Name column displays the color and the name assigned to the measurement. The Location column shows where the measurement was taken (image axial, coronal, sagittal or 3D), and Type Indicates the type of measurement (linear or angular). Finally, the Value column Indicates the measure itself. See figure 8.8.

Figure 8.8: Measurement Management

Chapter 9 Simultaneous display of images and surface Simultaneous viewing of images and surface can be activated by clicking with the left mouse button on the shortcut located on the bottom right of the screen InVesalius. See figure 9.1.

Figure 9.1: Shortcut for simultaneous viewing This feature Allows you to enable or disable the display of images in different orientations (or plans) in the same viewing window of the 3D surface. Simply check or uncheck the option in Corresponding shown in Figure 9.2 menu.

Figure 9.2: Selection of guidelines (plans) showing It is worth noting que guidance, When selected, the check has the Corresponding option. This is illustrated in figure 9.3.

Figure 9.3: Guidance selected for display If the surface is already displayed, the plans of the guidelines will be presented in the Figure 9.4 shown. Otherwise, only plans will be displayed (Figure 9.5).

Figure 9.4: Surface and planes displayed simultaneously

Figure 9.5: Display of plans (on the surface) To disable the display of the plan, simply uncheck the option from the Corresponding menu (Figure 9.3).

Chapter 10 Volume rendering For volume visualization models, has the InVesalius technique called raycasting. Which This is a technique, briefly, is to simulate, for each pixel of the screen, the ray tracing light toward the object. The color of the pixel will be based on color and transparency of each voxel intercepted by the light beam. In InVesalius, there are several pre-defined patterns (presets) to display Certain kinds of fabrics or types of scans (positron in contrast, for example). To access this feature, simply click the shortcut shown in Figure 10.1, located in the lower right corner (next to the display window surfaces) and select one of the available patterns. To disable volume rendering, click the shortcut again Indicated by Figure 10.1 and select the Disabled option.

Figure 10.1: Shortcut to volume rendering

10.1 Standards viewing There are several predefined viewing patterns. Some examples are Following illustrated in the figures.

Figure 10.2: Brilliant

Figure 10.3: Airway II

Figure 10.4: Contrast Medium

Figure 10.5: MIP

10.2 Customization of default Some patterns can be customized (or custom). See figure 10.6, Which displays the pattern and some graphics setting controls. With Them is can change the color of a Given its structure and opacity, Determining how and if it is displayed.

Figure 10.6: Adjustments to the default display Soft Skin + II If you wish to hide the structure, you must use the control adjusting the opacity chart keeping low the Corresponding region. On example of Figure 10.6, suppose we want to hide the muscle part, que appears in red. Simply position the mouse pointer on the point in red and with the left mouse button, drag the point downwards, in order to reduce the opacity (Which is equivalent to increase increasing transparency.) Figure 10.7 shows the result. Note: The Alpha value Indicates the opacity of the color and the value Value, the color intensity of the pixel.

Figure 10.7: Standard display Soft Skin + II changed You can add or remove points on the graph adjustment control. For removal, simply click the right mouse button on the point. For add a new point, click the left button on the line graph. Also you can save the Resulting pattern by clicking the shortcut que Figure 10.8 illustrates.

Figure 10.8: Shortcut to save default When you save the default InVesalius displays a window like figure 10.9. Enter a name for the custom template and click OK. The default saved will be available with the other the next time the software is opened.

Figure 10.9: Window to name and save the default

10.3 Customizing standard with Brightness and Contrast You can customize the pattern without using the chart control setting, presented in the previous section. This is done by controlling brightness and Contrast this toolbar. To activate the control, click the shortcut shown in Figure 10.10.

Figure 10:10: Shortcut to Brightness and Contrast With control enabled by dragging the mouse with the left button on the volume window, you can change the values of window width and window level. The same procedure is applied to the slices 2D, seen in section 4.6. Dragging the mouse in the horizontal direction, the value of alterase window level. To the left, it decreases its value, and is right, it Increases its value. Dragging the mouse in the vertical direction, changes the value of window width. Down, Diminishes its value, and is above, it Increases its value. By manipulating these values can be different results display. For example, to add fabric to the view, drag the mouse diagonally from the lower right to the upper left corner the preview window. To remove tissue from the display, do the opposite, ie, drag the mouse diagonally from the upper left corner to the bottom right corner. See figure 10.11. (A) Bone (b) Muscle (c) Skin

Figure 10.11: Adding fabric

10.4 Cut In volume rendering, the cut is used to view the region internal volume. InVesalius The offers a tool for cutting based on the reference plane. With the display pattern selected, click Tools, and then click Plan to cut (Figure 10:12).

Figure 10:12: Enabling plan to cut The representation of the plan to cut Appears next to the volume. For make the cut, hold the left button down over the plan and drag the mouse. To rotate the plane, hold the left button pressed on its edge and move the mouse in the direction Desired. See an example in Figure 10:13. To disable the cut, click Tools again Plan on cutting (Figure 10:12).

Figure 10.13: Image with cutting plane

Chapter 11 Exporting Data With InVesalius, you can export data to other software, file formats like OBJ, STL, among others. The menu contains options for exporting located on the left panel InVesalius Within Item 4. Export the data. If the menu not visible, double-click the left mouse button on the item to expand it. Figure 11.1 shows this menu.

Figure 11.1: Menu for exporting data

11.1 Surface To export the surface, you must select it in the Data menu, those shown in Figure 11.2.

Figure 11.2: Selection surface exporting Then click on the icon que figure 11.3 illustrates.

Figure 11.3: Shortcut to export surface In the window displayed (Figure 11.4), enter the file name and select the Desired format for export. Then click Save (Save).

Figure 11.4: window to export surface The file types that can be exported are listed in the table 11.1:

Table 11.1: File formats exports InVesalius Format Extension Inventor. Iv Polygon File Format. Ply Renderman. Rib Stereolithography (binary format). Stl Stereolithography (ASCII format). Stl VRML. Vrml VTK PolyData. Vtp Wavefront. Obj

11.2 Picture You can export images of any of the guidance display (axial, coronal, sagittal and 3D). To do this, click the left mouse button on the shortcut shown in Figure 11.5 and select the Corresponding sub-window the image you want to export.

Figure 11.5: Menu for exporting image In the window displayed (Figure 11.6), select the file format and click Save the (Save) button.

Figure 11.6: window to export image

Chapter 12 Customization Some customization options are available for the user InVesalius. They are presented below.

12.1 Menu Tool To hide / display the side menu tools, click on the button Figure 12.1 illustrates.

Figure 12.1: Shortcut to show / hide the sidebar tool With the hidden menu, expands the area of the window InVesalius available for displaying images, shown in the Figure 12.2.

Figure 12.2: hidden side menu

12.2 Automatic positioning of volume / surface To automatically adjust the display position of the volume or surface, you can click on the icon shown in Figure 12.3 (located the bottom right of the screen InVesalius) corner and choose one of the options viewing available.

Figure 12.3: Position options for viewing

12.3 Background color of window volume / surface To change the background color of the volume / surface window, click the shortcut the figure 12.4 shows. The shortcut is Also located at the bottom right of the screen InVesalius.

Figure 12.4: Shortcut to background color of the window volume / surface The window for color selection opens, shown in the Figure 12.5. After que, just click on the Desired color and then click OK.

Figure 12.5: Selection background color

Figure 12.6 shows an example of the window background color change.

Figure 12.6: Background color changed

12.4 Show / Hide Text in 2D window To display or hide the texts que Appear in the windows of 2D images, click the shortcut shown in Figure 12.7, located on the toolbar.

Figure 12.7: Shortcut to display or hide text Figures 12.8 and 12.9 Illustrate, respectivamente, the display of texts enabled and disabled.

Figure 12.8: Display text enabled

Figure 12.9: Text display disabled

Authors Manual Paulo Henrique Junqueira Amorim paulo.amorim @ cti.gov.br Thiago Franco de Moraes thiago.moraes @ cti.gov.br Fábio de Souza Azevedo fabio.azevedo @ cti.gov.br Jorge Vicente Lopes da Silva jorge.silva @ cti.gov.br English Translation by Atin Angrish angrish.atin @ gmail.com