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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.
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.
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.
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.
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.
Chapter 4
Image Manipulation (2D)
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).
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 4.13: 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.
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.
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 4:32: 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
Chapter 5 Segmentation
To select a particular type of tissue image, is used segmentation feature, available in
InVesalius.
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 5.18: 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 6.4: Surface with selected larger region and holes filled
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
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).
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.
As an example, Figure 6.15 shows the case before the separation of the larger region.
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.
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.
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.
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.
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).
11.1 Surface
To export the surface, you must select it in the Data menu, those shown in Figure 11.2.
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.
Chapter 12 Customization
Some customization options are available for the user InVesalius. They are presented
below.
Authors Manual
Paulo Henrique Junqueira Amorim
paulo.amorim @ cti.gov.br
Thiago Franco de Moraes
thiago.moraes @ cti.gov.br
Fbio 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