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docs/user_guide_en_source/cap_img.tex
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1 1 \chapter{Image adjustment}
2 2  
3   -InVesalius does not guarantee the correct image order because sometimes these images have wrong information or do not follow the DICOM standard. Therefore, it is recommended to check if a lesion or an anatomical mark is on the correct side. If not, it is possible to use the flip image or swap axes tools. For image alignment, the rotation image tool can be used.
  3 +InVesalius cannot guarantee the correct image order; images may contain incorrect information, or do not follow the DICOM standard. Therefore, it is recommended to check if a lesion or an anatomical mark is on the correct side. If not, it is possible to use the flip image or swap axes tools. For image alignment, the rotation image tool can be used.
4 4  
5   -It is possible to mirror the image, making them flip. To perform that, it is necessary to click in menu, \textbf{Tools}, \textbf{Image}, \textbf{Flip} and click in one of the following options (figure~\ref{fig:menu_img_mirroring_axis_pt}):
  5 +It is possible to mirror the image. To do so, select the \textbf{Tools} menu, click \textbf{Image}, then \textbf{Flip} and click on one of the following options (Figure~\ref{fig:menu_img_mirroring_axis_pt}):
6 6  
7 7 \begin{itemize}
8 8 \item Right - Left
... ... @@ -18,7 +18,7 @@ It is possible to mirror the image, making them flip. To perform that, it is nec
18 18 \end{figure}
19 19  
20 20  
21   -The figure~\ref{fig:mirrored} shows a comparative between the image without being flipped and the flipped image. Due to all image form the volume, if the flip is applied all other orientation are also modified.
  21 +Figure~\ref{fig:mirrored} shows a comparison between the input image and the flipped image. All other orientations are also modified when the image is flipped.
22 22  
23 23 \begin{figure}[!htb]
24 24 \centering
... ... @@ -31,7 +31,7 @@ The figure~\ref{fig:mirrored} shows a comparative between the image without bein
31 31  
32 32 \section{Swap axes}
33 33  
34   -The swap axes tool changes the image orientation, in the case that the image has been wrongly imported. To perform that, it is necessary to click in menu, \textbf{Tools}, \textbf{Image}, \textbf{Swap axes} and click in one of the following options (figure~\ref{fig:menu_invert_axis}):
  34 +The swap axes tool changes the image orientation, in the case that the image has been wrongly imported. To perform this, select the \textbf{Tools} menu, click \textbf{Image}, then \textbf{Swap Axes} and click on one of the following options (Figure~\ref{fig:menu_invert_axis}):
35 35  
36 36 \begin{itemize}
37 37 \item From Right-Left to Anterior-Posterior
... ... @@ -40,7 +40,7 @@ The swap axes tool changes the image orientation, in the case that the image has
40 40 \end{itemize}
41 41  
42 42  
43   -The figures~\ref{fig:invert_axis_axial} e~\ref{fig:invert_axis_axial_inverted}, shows an example of images with inverted axis.
  43 +The Figures~\ref{fig:invert_axis_axial} and~\ref{fig:invert_axis_axial_inverted}, shows an example of an image with inverted axes.
44 44  
45 45 \begin{figure}[!htb]
46 46 \centering
... ... @@ -65,7 +65,7 @@ The figures~\ref{fig:invert_axis_axial} e~\ref{fig:invert_axis_axial_inverted},
65 65  
66 66 \section{Reorient image (Rotate)}
67 67  
68   -If it is necessary to align the image taking in account some reference point, e.g. anatomical marker, it is possible by using the reorient image tool. To open this tool it is necessary to click in menu, \textbf{Tools}, \textbf{Image} and \textbf{Reorient image} (figure~\ref{fig:menu_img_reorient}).
  68 +If it is necessary to align the image with a certain point of reference, e.g. anatomical marker, use the reorient image tool. To open this tool select the \textbf{Tools} menu, click \textbf{Image}, then \textbf{Reorient Image} (Figure~\ref{fig:menu_img_reorient}).
69 69  
70 70 \begin{figure}[!htb]
71 71 \centering
... ... @@ -74,7 +74,8 @@ If it is necessary to align the image taking in account some reference point, e.
74 74 \label{fig:menu_img_reorient}
75 75 \end{figure}
76 76  
77   -When this tool is activated a window is opened(figure~\ref{fig:image_reorient_window}) that shows which orientation and how much degrees the image was rotated.
  77 +When this tool is activated a window is opened (Figure~\ref{fig:image_reorient_window}) showing orientation and by how many degrees the image was rotated.
  78 +
78 79 \begin{figure}[!htb]
79 80 \centering
80 81 \includegraphics[scale=0.4]{image_reorient_window_en.png}
... ... @@ -82,7 +83,7 @@ When this tool is activated a window is opened(figure~\ref{fig:image_reorient_wi
82 83 \label{fig:image_reorient_window}
83 84 \end{figure}
84 85  
85   -Initially, it is necessary to define the rotation point, to perfom that \textbf{keep the left mouse button pressed} between the two lines intersection (figure~\ref{fig:image_reorient_adjust_center}) at one orientation window, e.g. axial, coronal or sagittal, and drag to the desired point.
  86 +To start reorienting the image, define the rotation point by keeping the \textbf{left} mouse button pressed between the two lines intersecting (Figure~\ref{fig:image_reorient_adjust_center}) at one orientation, e.g. axial, coronal or sagittal, and \textbf{drag} to the desired point.
86 87  
87 88 \begin{figure}[!htb]
88 89 \centering
... ... @@ -91,7 +92,7 @@ Initially, it is necessary to define the rotation point, to perfom that \textbf{
91 92 \label{fig:image_reorient_adjust_center}
92 93 \end{figure}
93 94  
94   -To rotate the image it is necessary to \textbf{keep the left mouse button pressed} and \textbf{drag} until the reference point or anatomical marker stays align with one of the lines (figure~\ref{fig:image_reorient_rotated}). After the image is in the desired position, it is necessary to click the button \textbf{Apply}, in the parameter window (figure~\ref{fig:image_reorient_window}). This task can take some seconds, depends on the image size. The figure~\ref{fig:image_reorient_rotated_applied} shows an image with reorient done.
  95 +To rotate the image it is necessary to keep the \textbf{left} mouse button pressed and \textbf{drag} until the reference point or anatomical marker stays aligned with one of the lines (Figure~\ref{fig:image_reorient_rotated}). After the image is in the desired position, click \textbf{Apply} in the parameter window (Figure~\ref{fig:image_reorient_window}). This may take a few moments depending on the image size. Figure~\ref{fig:image_reorient_rotated_applied} shows an image successfully reoriented.
95 96  
96 97 \begin{figure}[!htb]
97 98 \centering
... ...
docs/user_guide_en_source/cap_import.tex
  Diff comments   View file @f2d179c
1 1 \chapter{Image import}
2 2  
3   -InVesalius imports files in DICOM format, including compressed files (lossless JPEG), Analyze (Mayo Clinic) $^\copyright$, NIfTI, PAR/REC, BMP, TIFF, JPEG and PNG formats.
  3 +InVesalius imports files in DICOM format, including compressed files (lossless JPEG), Analyze (Mayo Clinic$^\copyright$), NIfTI, PAR/REC, BMP, TIFF, JPEG and PNG formats.
4 4  
5 5 \section{DICOM}
6 6  
7   -On menu \textbf{File}, click on \textbf{Import DICOM...}. If you prefer, use the shortcut of keyboard \textbf{Ctrl + I}. Import DICOM images can also be triggered by the toolbar icon described in the figure~\ref{fig:import}.
  7 +Under the File menu, click on Import DICOM or use the shortcut Ctrl+I. Additionally, DICOM files can be imported by clicking on the icon shown in Figure~\ref{fig:import}.
8 8  
9 9 \begin{figure}[!htb]
10 10 \centering
... ... @@ -15,11 +15,12 @@ On menu \textbf{File}, click on \textbf{Import DICOM...}. If you prefer, use the
15 15  
16 16 \hspace{.2cm}
17 17  
18   -Then select the directory containing the DICOM files, as in figure~\ref{fig:win_folder}. InVesalius will search for files also in subdirectories of the chosen directory, if they exist.
  18 +Select the directory containing the DICOM files, as in Figure~\ref{fig:win_folder}. InVesalius will search for files also in subdirectories of the chosen directory,
  19 +if they exist.
19 20  
20 21 \newpage
21 22  
22   -Click on \textbf{OK} button.
  23 +Once the directory is selected, click \textbf{OK}.
23 24  
24 25 \begin{figure}[!htb]
25 26 \centering
... ... @@ -30,7 +31,7 @@ Click on \textbf{OK} button.
30 31  
31 32 \hspace{.2cm}
32 33  
33   -While InVesalius search for DICOM files in the directory, the loading progress of the scanned files is displayed, as shown in the figure~\ref{fig:ver_file}.
  34 +While InVesalius search for DICOM files in the directory, the loading progress of the scanned files is displayed, as shown in the Figure~\ref{fig:ver_file}.
34 35  
35 36 \begin{figure}[!htb]
36 37 \centering
... ... @@ -41,7 +42,7 @@ While InVesalius search for DICOM files in the directory, the loading progress o
41 42  
42 43 \newpage
43 44  
44   -If DICOM files are found, a window open (figure~\ref{fig:win_import}) to select the patient and the respective series to be opened. It is also possible to skip images for reconstruction.
  45 +If DICOM files are found, a window open (shown Figure~\ref{fig:win_import}) will open to select the patient and respective series to be opened. It is also possible to skip images for reconstruction.
45 46  
46 47 \begin{figure}[!htb]
47 48 \centering
... ... @@ -52,7 +53,7 @@ If DICOM files are found, a window open (figure~\ref{fig:win_import}) to select
52 53  
53 54 \newpage
54 55  
55   -If you want to import a series with all the images present, click "\textbf{+}" on the side patient's name to expand the series belonging to him. \textbf {Double-click} with left mouse button on the description of the series. See figure~\ref{fig:import_serie}.
  56 +To import a series with all images present, click "\textbf{$+$}" on the patient’s name to expand the corresponding series. Double-click on the description of the series. See Figure~\ref{fig:import_serie}.
56 57  
57 58 \begin{figure}[!htb]
58 59 \centering
... ... @@ -60,8 +61,8 @@ If you want to import a series with all the images present, click "\textbf{+}" o
60 61 \caption{Series selection}
61 62 \label{fig:import_serie}
62 63 \end{figure}
63   -
64   -Some cases in particular when there is no computer with memory and/or satisfactory processing to work with many images in a series, can be it is recommended to skip (skip) some of them. To do this, click \textbf {once} with the \textbf{left} of the mouse over the description of the series (figure~\ref{fig:import_serie}) and select how many images will be skipped (figure~\ref{fig:skip_image}). Click on~\textbf {Import} button.
  64 +
  65 +In some cases, when there is no computer with memory and/or satisfactory processing to work with large numbers of images in a series, it is recommended to skip some of them. To do this, click \textbf{once} with the \textbf{left} mouse button over the description of the series (Figure~\ref{fig:import_serie}) and select how many images will be skipped (Figure~\ref{fig:skip_image}), then click \textbf{Import}.
65 66  
66 67 \begin{figure}[!htb]
67 68 \centering
... ... @@ -70,8 +71,8 @@ Some cases in particular when there is no computer with memory and/or satisfacto
70 71 \label{fig:skip_image}
71 72 \end{figure}
72 73  
73   -If insufficient amount of available memory is detected at the time of loading the images it is recommended reduce the resolution of the slices to work with volumetric and surface visualization, as shown in the \ref{fig:resize_image} window.
74   -The slices will be resized according to the percentage relative to the original resolution. For example, if each slice of the exam contains the dimension of 512 x 512 pixels and the "Percentage of original resolution" is suggested to be 60 \%, each resulting image will be 307 x 307 pixels. If you want to open with the original resolution select the value 100.
  74 +If there is an insufficient amount of available memory at the time of loading the images it is recommended that the resolution of the slices be reduced to work with volumetric and surface visualization, as shown in Figure~\ref{fig:resize_image}.
  75 +The slices will be resized according to the percentage relative to the original resolution. For example, if each slice of the exam the dimension of 512 x 512 pixels and the "Percentage of original resolution" is suggested to be 60 \%, each resulting image will be 307 x 307 pixels. To open with the original pixel resolution, set the percentage to 100.
75 76  
76 77 \begin{figure}[!htb]
77 78 \centering
... ... @@ -80,7 +81,7 @@ The slices will be resized according to the percentage relative to the original
80 81 \label{fig:resize_image}
81 82 \end{figure}
82 83  
83   -If the image was obtained with the gantry tilted it will be necessary to do a correction to avoid deformations on the reconstruction. InVesalius allows the user do this correction. When importing an image with the gantry tilted it will be shown a dialog with the degree of tilt (figure~\ref{fig:gantry_tilt}). It is possible to change this value, but it is not recommended. Click on the \textbf{Ok} button to do the correction. If you click on the \textbf{cancel} button the correction will not be done.
  84 +If the image was obtained with the gantry tilted it will be necessary to correct to avoid distortion of any reconstruction. InVesalius allows the user to do this easily. When importing an image with the gantry tilted a dialog will appear, showing the gantry tilt angle. (Figure~\ref{fig:gantry_tilt}). It is possible to change this value, but it is not recommended. Click on the \textbf{Ok} to do the correction. If you click on the \textbf{cancel} button the correction will not be done.
84 85  
85 86 \begin{figure}[!htb]
86 87 \centering
... ... @@ -89,7 +90,7 @@ If the image was obtained with the gantry tilted it will be necessary to do a co
89 90 \label{fig:gantry_tilt}
90 91 \end{figure}
91 92  
92   -After the previous procedures, a window will be displayed (figure \ref{fig:prog_recons}) with progress reconstruction (when images are stacked and interpolated).
  93 +After the above procedure, a window will be displayed (Figure \ref{fig:prog_recons}) with reconstruction (when images are stacked and interpolated).
93 94  
94 95 \begin{figure}[!htb]
95 96 \centering
... ... @@ -102,7 +103,7 @@ After the previous procedures, a window will be displayed (figure \ref{fig:prog_
102 103  
103 104 \section{Analyze}
104 105  
105   -To import Analyze files, on menu \textbf{File}, click on \textbf{Importar other files...}, then click in the \textbf{Analyze} option as show the figure~\ref{fig:analyze_menu}.
  106 +To import Analyze files, under the \textbf{File} menu, click \textbf{Import other files}, then click in the \textbf{Analyze} option as show the Figure~\ref{fig:analyze_menu}.
106 107  
107 108 \begin{figure}[!htb]
108 109 \centering
... ... @@ -111,7 +112,7 @@ To import Analyze files, on menu \textbf{File}, click on \textbf{Importar other
111 112 \label{fig:analyze_menu}
112 113 \end{figure}
113 114  
114   -Select the file of Analyze format, in extension \textbf{.hdr} and click on \textbf{Open} button (Figure \ref{fig:analyze_import}).
  115 +Select the Analyze file format (\textbf{.hdr}) and click on \textbf{Open} (Figure~\ref{fig:analyze_import}).
115 116  
116 117 \begin{figure}[!htb]
117 118 \centering
... ... @@ -122,7 +123,7 @@ Select the file of Analyze format, in extension \textbf{.hdr} and click on \text
122 123  
123 124 \section{NIfTI}
124 125  
125   -To import NIfTI files, on menu \textbf{File}, click on option \textbf{Import other files...} and then click on \textbf{NIfTI} option as shown figure~\ref{fig:import_nifti_menu_pt}.
  126 +To import NIfTI files, under the \textbf{File} menu, click \textbf{Import other files} and then click \textbf{NIfTI} as shown in Figure~\ref{fig:import_nifti_menu_pt}.
126 127  
127 128  
128 129 \begin{figure}[!htb]
... ... @@ -132,7 +133,7 @@ To import NIfTI files, on menu \textbf{File}, click on option \textbf{Import oth
132 133 \label{fig:import_nifti_menu_pt}
133 134 \end{figure}
134 135  
135   -Select the file of type NIfTI, on \textbf{nii.gz} or \textbf{.nii} extension, click on \textbf{Open} (figure \ref{fig:import_nifti_window_pt}). If the file is in another extension as \textbf{.hdr}, select \textbf{all files(*.*)} option.
  136 +Select the NIfTI file format, (either \textbf{nii.gz} or \textbf{.nii}) then click \textbf{Open} (Figure~\ref{fig:import_nifti_window_pt}). If the file is in another format as \textbf{.hdr}, select \textbf{all files(*.*)} option.
136 137  
137 138 \begin{figure}[!htb]
138 139 \centering
... ... @@ -143,7 +144,7 @@ Select the file of type NIfTI, on \textbf{nii.gz} or \textbf{.nii} extension, cl
143 144  
144 145 \section{PAR/REC}
145 146  
146   -To import PAR/REC file, on main menu, click on \textbf{File}, \textbf{Import other files...} option and then click on \textbf{PAR/REC} as shown the figure \ref{fig:import_parrec_menu_pt}.
  147 +To import PAR/REC file, under the \textbf{File} menu, click \textbf{Import other files}, and then click on \textbf{PAR/REC} as shown in Figure~\ref{fig:import_parrec_menu_pt}.
147 148  
148 149 \begin{figure}[!htb]
149 150 \centering
... ... @@ -152,7 +153,7 @@ To import PAR/REC file, on main menu, click on \textbf{File}, \textbf{Import oth
152 153 \label{fig:import_parrec_menu_pt}
153 154 \end{figure}
154 155  
155   -Select PAR/REC file type, in extension \textbf{.par} and click on \textbf{Open} (figure~\ref{fig:import_parrec_window_pt}). If the file has no extension, select \textbf{all files(*.*)} option.
  156 +Select PAR/REC file type, with the file extension \textbf{.par} and click \textbf{Open} (Figure~\ref{fig:import_parrec_window_pt}). If the file has no extension, select \textbf{all files(*.*)} option.
156 157  
157 158 \begin{figure}[!htb]
158 159 \centering
... ... @@ -163,7 +164,7 @@ Select PAR/REC file type, in extension \textbf{.par} and click on \textbf{Open}
163 164  
164 165 \section{TIFF, JPG, BMP, JPEG or PNG (micro-CT)}
165 166  
166   -TIFF, JPG, BMP, JPEG or PNG file format for reconstruction can be provided with microtomography equipment (micro-CT or $\mu$CT) or others. InVesalius imports files in these formats if pixels present are represented in \textbf{grayscale}.
  167 +TIFF, JPG, BMP, JPEG or PNG file format for microtomography equipment (micro-CT or $\mu$CT) or others. InVesalius imports files in these formats if pixels present are represented in \textbf{grayscale}.
167 168  
168 169 To import, click on menu \textbf{File}, \textbf{Import other files...} and then click on \textbf{TIFF, JPG, BMP, JPEG ou PNG ($\mu$CT)} option as shown the figure~\ref{fig:import_bmp_menu_pt}.
169 170  
... ... @@ -174,9 +175,9 @@ To import, click on menu \textbf{File}, \textbf{Import other files...} and then
174 175 \label{fig:import_bmp_menu_pt}
175 176 \end{figure}
176 177  
177   -Select the directory that contains the files, as shown the figure~\ref{fig:import_bmp_select_folder}. InVesalius will search for files also in subdirectories of the chosen directory, if they exist.
  178 +Select the directory that contains the files, as shown the Figure~\ref{fig:import_bmp_select_folder}. InVesalius will search for files also in subdirectories of the chosen directory, if they exist.
178 179  
179   -Click on \textbf{OK} button.
  180 +Click on \textbf{OK}.
180 181  
181 182 \begin{figure}[!htb]
182 183 \centering
... ... @@ -185,7 +186,7 @@ Click on \textbf{OK} button.
185 186 \label{fig:import_bmp_select_folder}
186 187 \end{figure}
187 188  
188   -While InVesalius looking for TIFF, JPG, BMP, JPEG, or PNG files in the directory, the upload progress of the scanned files is displayed, as illustrated by the \ref{fig:import_bmp_load_pt} figure.
  189 +While InVesalius is looking for TIFF, JPG, BMP, JPEG, or PNG files in the directory, the upload progress of the scanned files is displayed, as illustrated in Figure~\ref{fig:import_bmp_load_pt}.
189 190  
190 191 \begin{figure}[!htb]
191 192 \centering
... ... @@ -194,7 +195,7 @@ While InVesalius looking for TIFF, JPG, BMP, JPEG, or PNG files in the directory
194 195 \label{fig:import_bmp_load_pt}
195 196 \end{figure}
196 197  
197   -If files of type TIFF, JPG, BMP, JPEG or PNG are founded, a window open (figure~\ref{fig:import_bmp_window_pt}) to display the founded files eligible for reconstruction. You can also skip images to rebuild or remove files from the rebuild list. The files are sorted according to the file name, it is recommended to use numbers in their names according to the order you want to get in the rebuild.
  198 +If files in the desired formats are located, a window will open (shown in Figure~\ref{fig:import_bmp_window_pt}) to display the files eligible for reconstruction. Images can also be skipped to remove files from the rebuild list. The files are sorted according to file names. It is recommended that the files are numbered according to the desired rebuild order.
198 199  
199 200 \begin{figure}[!htb]
200 201 \centering
... ... @@ -203,9 +204,10 @@ If files of type TIFF, JPG, BMP, JPEG or PNG are founded, a window open (figure~
203 204 \label{fig:import_bmp_window_pt}
204 205 \end{figure}
205 206  
206   -To delete files that are not of interest, you can select a file by clicking the \textbf{left mouse button} and then pressing the \textbf{delete} key. You can also choose a range of files to delete, so you need to click the \textbf{left mouse button} on the first file in the track, hold down the \textbf{shift} key, click again with the \textbf{button Left mouse button} in the last file of the track and finally press the \textbf{delete} button.
207   -
208   -Like importing DICOM files module, you can skip BMP images for rebuilding. In some cases, particularly where a computer with satisfactory memory and/or processing is not available to work with many images in a series, it may be advisable to skip (skip) some of them. To do this, select how many images to skip (figure~\ref{fig:import_bmp_skip_pt}). Click \textbf{Import} button.
  207 +To delete files that are not of interest, select a file by clicking the left mouse button and then pressing the delete key. You can also choose a
  208 +range of files to delete by clicking the \textbf{left mouse button} on a file, holding down the \textbf{shift} key, clicking again with the mouse button in the last file of the track and finally pressing the \textbf{delete} button.
  209 +
  210 +Similar to when importing DICOM files, you can skip BMP images for re-building. In some cases, particularly where a computer with satisfactory memory and/or processing is unavailable, it may be advisable to skip some of them to retain adequate program functionality. To do this, select how many images to skip (Figure~\ref{fig:import_bmp_skip_pt}), then click \textbf{Import}.
209 211  
210 212 \begin{figure}[!htb]
211 213 \centering
... ... @@ -214,22 +216,22 @@ Like importing DICOM files module, you can skip BMP images for rebuilding. In so
214 216 \label{fig:import_bmp_skip_pt}
215 217 \end{figure}
216 218  
217   -To reconstruct this file type, it is necessary to define a name for the project, to indicate the orientation of the images (axial, coronal or sagittal), voxel spacing ($X$, $Y$ and $Z$) in \textbf{mm} as shown in the figure~\ref{fig:import_bmp_spacing_pt}. The voxel spacing in $X$ is the pixel width of each image, $Y$ the pixel length, and $Z$ represents the distance of each slice (voxel height).
  219 +To reconstruct files of this type, a project name must be defined to indicate the orientation of the images (axial, coronal or sagittal), voxel spacing ($X$, $Y$ and $Z$) in \textbf{mm} as shown in the Figure~\ref{fig:import_bmp_spacing_pt}. The voxel spacing in $X$ is the pixel width of each image, $Y$ the pixel length, and $Z$ represents the distance of each slice (voxel height).
218 220  
219   -If the image set consists of microtomography images, more specifically GE and Brucker equipment, it is possible that InVesalius will read the text file with the acquisition parameters that normally stay in the same folder as the images and automatically insert the spacing . This verification can be done when the values of $X$, $Y$ and $Z$ are different from "1.00000000", otherwise it is necessary to enter the values of the respective spacing.
  221 +If the image set consists of microtomography images, more specifically GE and Brucker equipment, it is possible that InVesalius will read the text file with the acquisition parameters that normally stay in the same folder as the images and automatically insert the spacing. This verification can be done when the values of $X$, $Y$ and $Z$ are different from "1.00000000", otherwise it is necessary to enter the values of the respective spacing.
220 222  
221   -\textbf{Attention, the spacing is a paramount parameter for the correct dimension of the objects in the software. Incorrect spacing will provide incorrect measurements.}
  223 +\textbf{Correct spacing is crucial for correctly importing objects in InVesalius. Incorrect spacing will provide incorrect measurements.}
222 224  
223   -Once you have completed all the parameters, just click the \textbf{Ok} button.
  225 +Once all parameters have been input, click \textbf{OK}.
224 226  
225 227 \begin{figure}[!htb]
226 228 \centering
227 229 \includegraphics[scale=0.5]{import_bmp_spacing_en.png}
228   -\caption{Tela de importação}
  230 +\caption{Import Screen}
229 231 \label{fig:import_bmp_spacing_pt}
230 232 \end{figure}
231 233  
232   -If insufficient memory is available when loading images, it is recommended to reduce the resolution of the slices to work with volumetric and surface visualization, as shown in the \ref{fig:import_bmp_resize_pt} window. The slices will be resized according to the percentage relative to the original resolution. For example, if each slice of the exam contains the dimension of 512 x 512 pixels and the "Percentage of the original resolution" is suggested at 60\%, each resulting image will have 307 x 307 pixels. If you want to open with the original resolution select the value 100.
  234 +If insufficient memory is available when loading images, it is recommended to reduce the resolution of the slices to work with volumetric and surface visualization, as shown in Figure~\ref{fig:import_bmp_resize_pt} window.The slices will be resized according to the percentage relative to the original resolution. For example, if each slice of the exam contains the dimension of $512 x 512$ pixels and the "Percentage of the original resolution" is suggested at 60, each resulting image will have $307 x 307$ pixels. If you want to open with the original resolution set the percentage to $100$.
233 235  
234 236 \begin{figure}[!htb]
235 237 \centering
... ... @@ -238,9 +240,7 @@ If insufficient memory is available when loading images, it is recommended to re
238 240 \label{fig:import_bmp_resize_pt}
239 241 \end{figure}
240 242  
241   -%Após os passos anteriores é necessário aguardar um instante para completar a reconstrução multiplanar conforme mostra a figura~\ref{fig:import_bmp_mpr_pt.png}.
242   -
243   -After the previous steps it is necessary to wait a moment to complete the multiplanar reconstruction as shown in the figure~\ref{fig:import_bmp_mpr_pt.png}.
  243 +After the previous steps, wait a moment for the program to complete the multiplanar reconstruction as shown in Figure~\ref{fig:import_bmp_mpr_pt.png}.
244 244  
245 245 \begin{figure}[!htb]
246 246 \centering
... ...
docs/user_guide_en_source/cap_instal.tex
  Diff comments   View file @f2d179c
... ... @@ -12,7 +12,7 @@ To install InVesalius on MS-Windows, simply run the installer program. When a wi
12 12  
13 13 \newpage
14 14  
15   -A new window will ask you to select the language of the installer. Select the language and click \textbf{OK} button.
  15 +A new window will ask you to select the language of the installer. Select the language and click \textbf{OK}.
16 16  
17 17 \begin{figure}[!htb]
18 18 \centering
... ... @@ -21,8 +21,7 @@ A new window will ask you to select the language of the installer. Select the la
21 21  
22 22 \hspace{.2cm}
23 23  
24   -Window installer appears. Click \textbf{Next}.
25   -
  24 +The Setup installer will appear. Click \textbf{Next}.
26 25  
27 26 \begin{figure}[!htb]
28 27 \centering
... ... @@ -40,7 +39,7 @@ Select \textbf{I accept the agreement} and click on \textbf{Next} button.
40 39  
41 40 \hspace{.2cm}
42 41  
43   -Click on \textbf{Next} button again.
  42 +Select the preferred destination for the InVesalius program files, then click \textbf{Next}.
44 43  
45 44 \begin{figure}[!htb]
46 45 \centering
... ... @@ -75,7 +74,7 @@ Click on \textbf{Install} button.
75 74  
76 75 \hspace{.2cm}
77 76  
78   -While the software is installed, a progress window will appear.
  77 +While the software is being installed, a progress window will appear.
79 78  
80 79 \begin{figure}[!htb]
81 80 \centering
... ... @@ -93,7 +92,7 @@ To run InVesalius after installation, check \textbf{Lauch InVesalius 3.1} and cl
93 92  
94 93 \hspace{.2cm}
95 94  
96   -If this is the first time the software is installed, a window will appear to select the InVesalius language. Select the language you want and click on \textbf{OK} button.
  95 +When being run for the first time, a window will appear to select the InVesalius language. Select the desired language and click \textbf{OK}.
97 96  
98 97 \begin{figure}[!htb]
99 98 \centering
... ... @@ -102,7 +101,7 @@ If this is the first time the software is installed, a window will appear to sel
102 101  
103 102 \newpage
104 103  
105   -While InVesalius is loaded, an opening window like the one in the next figure is displayed.
  104 +While InVesalius is loading, the opening window shown below will be displayed.
106 105  
107 106 \begin{figure}[!htb]
108 107 \centering
... ... @@ -111,7 +110,7 @@ While InVesalius is loaded, an opening window like the one in the next figure is
111 110  
112 111 \hspace{.2cm}
113 112  
114   -Then, the main program window open.
  113 +The main program window will then open, as shown below.
115 114  
116 115 \begin{figure}[!htb]
117 116 \centering
... ... @@ -120,15 +119,14 @@ Then, the main program window open.
120 119  
121 120 \section{Mac Os X}
122 121  
123   -To start the installation on Mac Os X, double-click the installer with the left mouse button.
124   -Then the installer will be initialized.
  122 +To start the installation on Mac OS X, double-click the installer with the left mouse button to begin installation.
125 123  
126 124 \begin{figure}[!htb]
127 125 \centering
128 126 \includegraphics[scale=0.3]{mac2.png}
129 127 \end{figure}
130 128  
131   -Hold down the left button on the InVesalius software icon and drag it to the \textit{Applications}. Both contained in the installer.
  129 +Hold down the left button on the InVesalius software icon and drag it to the Applications folder. Both are contained in the installer.
132 130  
133 131 \begin{figure}[!htb]
134 132 \centering
... ...
docs/user_guide_en_source/cap_manip.tex
  Diff comments   View file @f2d179c
... ... @@ -2,9 +2,7 @@
2 2  
3 3 \section{Multiplanar Reconstruction}
4 4  
5   -When images are imported, InVesalius automatically shows its reconstruction
6   -Multiplanar in the Axial, Sagittal and Coronal orientations, as well as a window for 3D manipulation.
7   -See figure \ref{fig:mpr}.
  5 +When images are imported, InVesalius automatically shows its multiplanar reconstruction in the Axial, Sagittal and Coronal orientations, as well as a window for 3D manipulation, as seen in Figure~\ref{fig:mpr}.
8 6  
9 7 \begin{figure}[!htb]
10 8 \centering
... ... @@ -15,13 +13,9 @@ See figure \ref{fig:mpr}.
15 13  
16 14 \newpage
17 15  
18   -In addition to creating a multiplanar reconstruction, InVesalius segments an image, highlighting, for example, soft tissue bones. The highlight is represented by the application of colors on a segmented structure, i.e., the colors forms a mask over an image highlighting the structure (figure \ref{fig:mpr}). This is discussed in more detail in the following chapters.
  16 +In addition to creating a multiplanar reconstruction, InVesalius segments an image, highlighting for example soft tissue bones. The highlight is represented by the application of colors on a segmented structure so that the colors form a mask over an image highlighting the structure (Figure~\ref{fig:mpr}).This is discussed in more detail in the following chapters.
19 17  
20   -
21   -To hide the mask, use the data manager, located in the lower left corner
22   -of the screen. Just choose the tab \textbf{Masks} and click \textbf{once} using the
23   -\textbf{left} mouse buttom over the eye icon next to \textbf{"Mask 1"}. See figure
24   -\ref{fig:ger_masc}.
  18 +To hide the mask, use the data manager, located in the lower left corner of the screen. Select the \textbf{Masks} tab and click once using the \textbf{left} mouse button over the eye icon next to \textbf{"Mask 1"}, as shown in Figure~\ref{fig:ger_masc}.
25 19  
26 20 \begin{figure}[!htb]
27 21 \centering
... ... @@ -30,8 +24,7 @@ of the screen. Just choose the tab \textbf{Masks} and click \textbf{once} using
30 24 \label{fig:ger_masc}
31 25 \end{figure}
32 26  
33   -The eye icon disappears, and the colors of the segmentation mask are hidden (figure
34   -\ref{fig:mpr_sem_mask}).
  27 +The eye icon disappears, and the colors of the segmentation mask are hidden (Figure~\ref{fig:mpr_sem_mask}).
35 28  
36 29 \begin{figure}[!htb]
37 30 \centering
... ... @@ -42,8 +35,8 @@ The eye icon disappears, and the colors of the segmentation mask are hidden (fig
42 35  
43 36 \subsection{Axial orientation}
44 37  
45   -The axial orientation consists of cuts made transversal in relation to the region of interest, i.e. parallel cuts to the axial plane of the human body.
46   -In figure \ref{fig:axial_corte}, an axial image of the skull region is displayed.
  38 +The axial orientation consists of cuts made transversally to the region of interest, i.e. parallel cuts to the axial plane of the human body.
  39 +In Figure~\ref{fig:axial_corte}, an axial image of the skull region is displayed.
47 40  
48 41 \begin{figure}[!htb]
49 42 \centering
... ... @@ -55,7 +48,7 @@ In figure \ref{fig:axial_corte}, an axial image of the skull region is displayed
55 48 \subsection{Sagittal orientation}
56 49  
57 50 The sagittal orientation consists of cuts made laterally in relation to the region of interest, i.e. parallel cuts to the sagittal plane of the human body, which divides it into the left and right portions.
58   -In figure \ref{fig:sagital_slice}, a sagittal skull image is displayed.
  51 +In Figure~\ref{fig:sagital_slice}, a sagittal skull image is displayed.
59 52  
60 53 \begin{figure}[!htb]
61 54 \centering
... ... @@ -69,7 +62,7 @@ In figure \ref{fig:sagital_slice}, a sagittal skull image is displayed.
69 62 \subsection{Coronal orientation}
70 63  
71 64 The coronal orientation is composed of cuts parallel to the coronal plane, which divides the human body into ventral and dorsal halves.
72   -In figure \ref{fig:coronal_slice} is displayed a skull image in coronal orientation.
  65 +In Figure~\ref{fig:coronal_slice} is displayed a skull image in coronal orientation.
73 66  
74 67 \begin{figure}[!htb]
75 68 \centering
... ... @@ -82,8 +75,7 @@ In figure \ref{fig:coronal_slice} is displayed a skull image in coronal orienta
82 75 \section{Correspondence between the axial, sagittal and coronal orientations}
83 76 \label{sec:corresp_all_orient}
84 77  
85   -To find out the common point of the images in differents orientations, simply activate the "Slices cross intersection" feature with the shortcut icon located on the toolbar.
86   -See figure \ref{fig:cross_icon}.
  78 +To find out the common point of intersection of the images in differents orientations, simply activate the "Slices cross intersection" feature with the shortcut icon located on the toolbar. See Figure~\ref{fig:cross_icon}.
87 79  
88 80 \begin{figure}[!htb]
89 81 \centering
... ... @@ -92,12 +84,11 @@ See figure \ref{fig:cross_icon}.
92 84 \label{fig:cross_icon}
93 85 \end{figure}
94 86  
95   -When the feature is fired, two cross segments that intersect perpendicularly are displayed on each image (figure \ref{fig:cross_all}). The intersection point of each pair of segments represents the common point between differents orientations.
  87 +When the feature is activated, two cross-sections that intersect perpendicularly are displayed on each image (Figure~\ref{fig:cross_all}). The intersection point of each pair of segments represents the common point between differents orientations.
96 88  
97 89 \newpage
98 90  
99   -To modify the point, keep \textbf{pressed} the \textbf{left} mouse button and
100   -\textbf{drag}. Automatically, the corresponding points will be updated in each image.
  91 +To modify the point, hold down the \textbf{left} mouse button and \textbf{drag}. Automatically, the corresponding points will be updated in each image.
101 92  
102 93 \begin{figure}[!htb]
103 94 \centering
... ... @@ -106,13 +97,13 @@ To modify the point, keep \textbf{pressed} the \textbf{left} mouse button and
106 97 \label{fig:cross_all}
107 98 \end{figure}
108 99  
109   -To disable the feature, simply click on the shortcut again (figure \ref{fig:cross_icon}). This feature can be used in conjunction with the slice editor (which will be discussed later).
  100 +To deactivate the feature, simply click on the shortcut again (Figure~\ref{fig:cross_icon}). This feature can be used in conjunction with the slice editor (which will be discussed later).
110 101  
111 102 \section{Interpolation}
112 103  
113   -By default the 2D images visualization are interpolated (figure~\ref{fig:interp}).a, to deactivate this feature, in menu press \textbf{View}, \textbf{Interpolated slices} (figure~\ref{fig:menu_interpoleted_image_pt}). In this way it will be possible to visualize each pixel individually as shown in the figure~\ref{fig:interp}.b.
  104 +By default the 2D images visualization are interpolated (Figure~\ref{fig:interp}).a). To deactivate this feature, select the \textbf{View} menu and select \textbf{Interpolated slices} (Figure~\ref{fig:menu_interpoleted_image_pt}). It will then be possible to visualize each pixel individually as shown in Figure~\ref{fig:interp}.b.
114 105  
115   -\textbf{Note: This interpolation is for visualization purposes only, not directly influencing segmentation or 3D surface generation.}
  106 +\textbf{This interpolation is for visualization purposes only, and does not directly influence segmentation or 3D surface generation.}
116 107  
117 108 \begin{figure}[!htb]
118 109 \centering
... ... @@ -133,8 +124,7 @@ By default the 2D images visualization are interpolated (figure~\ref{fig:interp}
133 124  
134 125 \section{Move}
135 126  
136   -To move an image on the screen, the toolbar's "Move" shortcut icon can be used (figure
137   -\ref{fig:move_icon}). Click on the icon to activate the feature and then with the \textbf{left} mouse button on the image, \textbf{drag} it to the desired direction. The figure \ref{fig:move_img} shows a displaced (moved) image.
  127 +To move an image on the screen, use the Move shortcut icon on the toolbar (Figure~\ref{fig:move_icon}). Click on the icon to activate, then with the \textbf{left} mouse button on the image, \text{drag} it to the desired direction. Figure~\ref{fig:move_img} shows a displaced (moved) image.
138 128  
139 129 \begin{figure}[!htb]
140 130 \centering
... ... @@ -152,7 +142,7 @@ To move an image on the screen, the toolbar's "Move" shortcut icon can be used (
152 142  
153 143 \section{Rotate}
154 144  
155   -The image rotation can be activated by the toolbar's "Rotate" shortcut icon (figure \ref{fig:rot_icon}). To rotate an image, click on the icon and then with the \textbf{left} mouse button press on the image, \textbf{drag} clockwise or anticlockwise, depending on the desired direction of rotation.
  145 +Images can be rotated by using the Rorate shortcut on the toolbar (Figure~\ref{fig:rot_icon}). To rotate an image, click on the icon and then with the \textbf{left} mouse button \textbf{drag} clockwise or anticlockwise as required.
156 146  
157 147 \begin{figure}[!htb]
158 148 \centering
... ... @@ -171,11 +161,11 @@ The image rotation can be activated by the toolbar's "Rotate" shortcut icon (fig
171 161  
172 162 \section{Zoom}
173 163  
174   -In InVesalius, there are different ways to enlarge an image. You can maximize the desired orientation window, apply zoom directly to the image, or select the region of the image to enlarge.
  164 +In InVesalius, there are different ways to enlarge an image. You can maximize the desired orientation window, apply zoom directly to the image, or select the region of the image to enlarge. Each of these methods are detailed below.
175 165  
176 166 \subsection{Maximizing orientation windows}
177 167  
178   -As we already know, the main InVesalius window is divided into 4 subwindows: axial, sagittal, coronal and 3D. Each of these can be maximized to occupy the entire area of the main window. To do this, simply \textbf{left} mouse click on the subwindow icon located in the \textbf{upper right corner} (figure \ref{fig:maximize_window}). To restore a maximized window to its previous size, simply click the icon again.
  168 +The main InVesalius window is divided into 4 sub-windows: axial, sagittal, coronal and 3D. Each of these can be maximized to occupy the entire area of the main window. To do this, simply \textbf{left} mouse click on the subwindow icon located in the \textbf{upper right corner} (Figure~\ref{fig:maximize_window}). To restore a maximized window to its previous size, simply click the icon again.
179 169  
180 170 \begin{figure}[!htb]
181 171 \centering
... ... @@ -184,9 +174,9 @@ As we already know, the main InVesalius window is divided into 4 subwindows: axi
184 174 \label{fig:maximize_window}
185 175 \end{figure}
186 176  
187   -\subsection{Enlarging or reducing an image}
  177 +\subsection{Enlarging or shrinking an image}
188 178  
189   -To enlarging or reducing an image, click on the zoom shortcut icon in the toolbar (figure \ref{fig:zoom_icon}). Hold down the \textbf{left} mouse button on the image and \textbf{drag} the mouse to \textbf{top} if you want to enlarge it, or \textbf{down}, if you want to reduce it.
  179 +To enlarge or shrink an image, click on the zoom shortcut icon in the toolbar (Figure~\ref{fig:zoom_icon}). Hold down the \textbf{left} mouse button on the image and \textbf{drag} the mouse \textbf{up} to enlarge or \textbf{down} to shrink.
190 180  
191 181 \begin{figure}[!htb]
192 182 \centering
... ... @@ -195,16 +185,9 @@ To enlarging or reducing an image, click on the zoom shortcut icon in the toolba
195 185 \label{fig:zoom_icon}
196 186 \end{figure}
197 187  
198   -%\begin{figure}[!htb]
199   -%\centering
200   -%\includegraphics[scale=0.2]{ScreenHunter_76Dec311201_.jpg}
201   -%\caption{Imagem com \textit{Zoom} aplicado}
202   -%\label{fig:zoom_}
203   -%\end{figure}
204   -
205   -\subsection{Enlarging an Image Area}
  188 +\subsection{Enlarging an image area}
206 189  
207   -To enlarging a certain image area, click on the "Zoom based on selection" icon in the toolbar (figure \ref{fig:zoom_icon_loc}). Position the mouse pointer at the start position of the selection, click and hold the \textbf{left} mouse button and \textbf{drag} it to the end selection position, forming a rectangle (figure \ref{fig:zoom_select}). Once the left mouse button is released, the zoom operation will be applied to the selected region (figure \ref{fig:zoom_applied}).
  190 +To enlarging a certain image area, click on the "Zoom based on selection" icon in the toolbar (Figure~\ref{fig:zoom_icon_loc}). Position the mouse pointer at the origin point of the selection, click and hold the \textbf{left} mouse button and \textbf{drag} it to the end selection point to form a rectangle (Figure~\ref{fig:zoom_select}). Once the left mouse button is released, the zoom operation will be applied to the selected region (Figure~\ref{fig:zoom_applied}).
208 191  
209 192 \begin{figure}[!htb]
210 193 \centering
... ... @@ -231,9 +214,9 @@ To enlarging a certain image area, click on the "Zoom based on selection" icon i
231 214 \section{Brightness and contrast (Windows)}
232 215 \label{sec:ww_wl}
233 216  
234   -To improve images visualization, the feature \textit{window width} and \textit{window level} can be used, popularly known as "brightness and contrast" or "window" (for radiologists). With this feature, it is possible to set the range of the gray scale (\textit{window level}) and the width of the scale (\textit{window width}) to be used to display the images.
  217 +To improve image visualization, the \textit{window width} and \textit{window level} features can be used; these are more commonly known as \textit{brightness and contrast} or \textit{window} (for radiologists). With this feature, it is possible to set the range of the gray scale (\textit{window level}) and the width of the scale (\textit{window width}) to be used to display the images.
235 218  
236   -The feature can be triggered by the "Contrast" shortcut icon in the toolbar. See figure \ref{fig:window_level_shortcut}.
  219 +The feature can be activated by the "Brightness and Contrast" shortcut icon in the toolbar. See Figure~\ref{fig:window_level_shortcut}.
237 220  
238 221 \begin{figure}[!htb]
239 222 \centering
... ... @@ -242,11 +225,11 @@ The feature can be triggered by the "Contrast" shortcut icon in the toolbar. See
242 225 \label{fig:window_level_shortcut}
243 226 \end{figure}
244 227  
245   -To increase the brightness, hold down the \textbf{left} mouse button and \textbf{drag} horizontally to the right. To decrease the brightness, simply drag the mouse to the left. The contrast can be changed by dragging the mouse (with the \textbf{left} button pressed) vertically: up to increase, or down to decrease the contrast.
  228 +To increase the brightness, hold down the \textbf{left} mouse button and \textbf{drag} horizontally to the right. To decrease the brightness, simply drag the mouse to the left. The contrast can be changed by dragging the mouse (with the \textbf{left} button pressed) vertically: up to increase, or down to decrease contrast.
246 229  
247   -To disable the feature, click again on the shortcut icon (figure \ref{fig:window_level_shortcut}).
  230 +To deactivate the feature, click again on the shortcut icon (Figure~\ref{fig:window_level_shortcut}).
248 231  
249   -You can use preset brightness and contrast patterns. The table \ref{tab:window_level} lists some tissues types with their respective brightness and contrast values for the image. To use the presets patterns, position the mouse cursor over the image and \textbf{right-click} to open a context menu on it. When the menu opens, select \textbf{Window width and level}, and then click on the preset option, according to the tissue type, as shown in the figure \ref{fig:window_level}.
  232 +Preset brightness and contrast patterns may be used with InVesalius. Table~\ref{tab:window_level} lists some tissue types with their respective brightness and contrast values. To use the presets, position the mouse cursor over an image and \textbf{right-click} to open a context menu, then select \textbf{Window width and level}, and click on the preset option according to the tissue type, as shown in Figure~\ref{fig:window_level}.
250 233  
251 234 \begin{figure}[!htb]
252 235 \centering
... ... @@ -297,9 +280,9 @@ Vasculature - Soft & 680 & 160\\
297 280  
298 281 \section{Pseudo color}
299 282  
300   -Another feature to improve the visualization of the images is the pseudo color. They replace gray levels by color, or by inverted gray levels. In the latter case, previously clear regions of the image become darker and vice versa.
  283 +Another feature to improve the visualization of the images is the pseudo color. This replaces gray levels by color, or by inverted gray levels. In the latter case, previously clear regions of the image become darker and vice versa.
301 284  
302   -To change the view using a pseudo color, position the mouse cursor over the image and \textbf{right-click} to open a context menu on it. When the menu opens, select the entry \textbf{Pseudo color}, and then click on the desired pseudo color option, as shown in the figure \ref{fig:pseudo_color}.
  285 +To change the view using a pseudo color, position the mouse cursor over the image and \textbf{right-click} to open a context menu on it. When the menu opens, select the entry \textbf{Pseudo color}, and then click on the desired pseudo color option, as shown in Figure~\ref{fig:pseudo_color}.
303 286  
304 287 \begin{figure}[p]
305 288 \centering
... ... @@ -308,7 +291,7 @@ To change the view using a pseudo color, position the mouse cursor over the imag
308 291 \label{fig:pseudo_color}
309 292 \end{figure}
310 293  
311   -Figures \ref{fig:image_default} through \ref{fig:image_saturation} exemplify the various pseudo color options available.
  294 +Figures~\ref{fig:image_default}a-g demonstrate the various pseudo color options available.
312 295  
313 296 \begin{figure}[h]
314 297 \centering
... ... @@ -326,7 +309,7 @@ Figures \ref{fig:image_default} through \ref{fig:image_saturation} exemplify the
326 309 \newpage
327 310 \section{Projection type}
328 311  
329   -It is possible to change the projection type of the 2D images, in addition to the normal mode, InVesalius has six types of projections that can be accessed as follows: Place the mouse over the image and \textbf{rigth-click} to open a context menu on it. When the menu opens, select the projection type option, and then click on the desired projection option, as shown in the figure ~\ref{fig:menu_proj}.
  312 +It is possible to change the projection type of the 2D images, in addition to the normal mode, InVesalius has six types of projections that can be accessed as follows: Place the mouse over the image and \textbf{rigth-click} to open a context menu on it. When the menu opens, select the projection type option, and then click on the desired projection option, as shown in the Figure~\ref{fig:menu_proj}.
330 313  
331 314 \begin{figure}[!h]
332 315 \centering
... ... @@ -337,7 +320,7 @@ It is possible to change the projection type of the 2D images, in addition to th
337 320  
338 321 \subsection{Normal}
339 322  
340   -Normal mode is the default view, i.e. without any type of projection, originally when the image was acquired or customized previously with either brightness and contrast or pseudo color. As shown in figure ~\ref{fig:proj_normal}.
  323 +Normal mode is the default view, showing the unmodified image as it was when acquired or customized previously with either brightness and contrast or pseudo color. Normal mode is shown below in Figure~\ref{fig:proj_normal}.
341 324  
342 325 \begin{figure}[!h]
343 326 \centering
... ... @@ -348,7 +331,8 @@ Normal mode is the default view, i.e. without any type of projection, originally
348 331  
349 332 \subsection{MaxIP}
350 333 \label{sec:max_ip}
351   -MaxIP is also known as MIP (\textit{Maximum Intensity Projection}), the method selects only voxels that have maximum intensity among the visited ones as shown in figure ~\ref{fig:proj_maxip}. According to the amount or "depth" of MaxIP each voxel is visited in order of overlap, for example, to select MaxIP of the pixel $(0,0)$ consisting of 3 slices it is necessary to visit the pixel $(0,0)$ of slices $(1,2,3)$ and select the highest value.
  334 +
  335 +MaxIP is also known as MIP (\textit{Maximum Intensity Projection}). MaxIP selects only voxels that have maximum intensity among those visited as shown in Figure~\ref{fig:proj_maxip}. According to the amount of, or "depth" of MaxIP, each voxel is visited in order of overlap, for example, to select MaxIP of the pixel $(0, 0)$ consisting of 3 slices it is necessary to visit pixel $(0, 0)$ of slices $(1, 2, 3)$ and select the highest value.
352 336  
353 337 \begin{figure}[!h]
354 338 \centering
... ... @@ -357,7 +341,7 @@ MaxIP is also known as MIP (\textit{Maximum Intensity Projection}), the method s
357 341 \label{fig:proj_maxip}
358 342 \end{figure}
359 343  
360   -As shown in the figure~\ref{fig:proj_maxip_qtd}, the number of images that will be composed of MaxIP is set at the bottom of each orientation image.
  344 +As shown in Figure~\ref{fig:proj_maxip_qtd}, the number of MaxIP images is set at the bottom of each orientation image.
361 345  
362 346 \begin{figure}[!h]
363 347 \centering
... ... @@ -368,7 +352,7 @@ As shown in the figure~\ref{fig:proj_maxip_qtd}, the number of images that will
368 352  
369 353 \subsection{MinIP}
370 354  
371   -Unlike MaxIP, MinIP (\textit{Minimun Intensity Projection}) selects only the voxels that have minimal internsity among the visited ones, an example is shown in figure~\ref{fig:proj_minIP}. The image number selection that will compose the projection is made at the bottom of each orientation image as shown in figure~\ref{fig:proj_maxip_qtd}.
  355 +Unlike MaxIP, MinIP (\textit{Minimun Intensity Projection}) selects only the voxels that have minimal intensity among those visited, as shown in Figure~\ref{fig:proj_minIP}. The image number selection comprising the projection is made at the bottom of each orientation image as shown in Figure~\ref{fig:proj_maxip_qtd}.
372 356  
373 357 \begin{figure}[!h]
374 358 \centering
... ... @@ -378,7 +362,7 @@ Unlike MaxIP, MinIP (\textit{Minimun Intensity Projection}) selects only the vox
378 362 \end{figure}
379 363  
380 364 \subsection{MeanIP}
381   -The MeanIP (\textit{Mean Intensity Projection}) technique which is shown in the figure~\ref{fig:proj_meanIP} composes the projection by averaging the voxels visited. The voxels are visited in the same way as the MaxIP and MinIP methods. It is also possible to define how many images will compose the projection at the bottom of the image of each orientation as shown in the figure~\ref{fig:proj_maxip_qtd}.
  365 +The MeanIP (\textit{Mean Intensity Projection}) technique which is shown in the Figure~\ref{fig:proj_meanIP} composes the projection by averaging voxels visited in the same way as the MaxIP and MinIP methods. It is also possible to define how many images will compose the projection at the bottom of the image of each orientation as shown in Figure~\ref{fig:proj_maxip_qtd}.
382 366  
383 367 \begin{figure}[!h]
384 368 \centering
... ... @@ -389,7 +373,7 @@ The MeanIP (\textit{Mean Intensity Projection}) technique which is shown in the
389 373  
390 374 \subsection{MIDA}
391 375 \label{sub:mida}
392   -The MIDA (\textit{Maximum Intensity Difference Accumulation}) technique projects an image taking into account only voxels that have local maximum values. From each pixel a ray is simulated towards the volume, each voxel is intercepted by each of these rays reaching the end of the volume, each of these voxels visited has its accumulated value, but are taken into account only if the value is greater than previously visited values. Like MaxIP, you can select how many images are used to accumulate the values. The figure ~\ref{fig:proj_MIDA} shows an example of MIDA projection.
  376 +The MIDA (\textit{Maximum Intensity Difference Accumulation}) technique projects an image taking into account only voxels that have local maximum values. From each pixel a ray is simulated towards the volume, with each voxel being intercepted by each ray reaching the end of the volume. Each of the voxels visited has its accumulated value, but are taken into account only if the value is greater than previously visited values. Like MaxIP, one can select how many images are used to accumulate the values. Figure~\ref{fig:proj_MIDA} shows an example of MIDA projection.
393 377  
394 378 \begin{figure}[!h]
395 379 \centering
... ... @@ -398,7 +382,7 @@ The MIDA (\textit{Maximum Intensity Difference Accumulation}) technique projects
398 382 \label{fig:proj_MIDA}
399 383 \end{figure}
400 384  
401   -As the figure ~\ref{fig:proj_MIDA_inv} shows, it is possible to invert the order that the voxels are visited by selecting the option \textbf{Inverted order} in the lower corner of the screen.
  385 +As Figure~\ref{fig:proj_MIDA_inv} shows, it is possible to invert the order that the voxels are visited by selecting the \textbf{Inverted order} option in the lower corner of the screen.
402 386  
403 387 \begin{figure}[!h]
404 388 \centering
... ... @@ -409,7 +393,7 @@ As the figure ~\ref{fig:proj_MIDA_inv} shows, it is possible to invert the order
409 393  
410 394 \subsection{Contour MaxIP}
411 395  
412   -The technique consists in visualizing contours present in the projection generated with MaxIP technique(\ref{sec:max_ip}). An example is presented in the figure~\ref{fig:proj_contorno_maxip}.
  396 +The Contour MaxIP function consists of visualizing contours present in the projection generated with MaxIP technique(\ref{sec:max_ip}). An example is presented in Figure~\ref{fig:proj_contorno_maxip}.
413 397  
414 398 \begin{figure}[!h]
415 399 \centering
... ... @@ -420,7 +404,7 @@ The technique consists in visualizing contours present in the projection generat
420 404  
421 405 \subsection{Contour MIDA}
422 406  
423   -The technique consists in visualizing contours present in the projection generated with the MIDA technique(\ref{sub:mida}). Like MIDA, you can reverse the order that the volume is visited. We exemplify in the figure~\ref{fig:proj_contorno_mida}.
  407 +The Contour MIDA function consists of visualizing contours present in the projection generated with the MIDA technique(\ref{sub:mida}). Like MIDA, you can reverse the order that the volume is visited, as shown in Figure~\ref{fig:proj_contorno_mida}.
424 408  
425 409 \begin{figure}[!h]
426 410 \centering
... ...
docs/user_guide_en_source/cap_masc.tex
  Diff comments   View file @f2d179c
... ... @@ -3,14 +3,17 @@
3 3  
4 4 \section{Boolean operations}
5 5  
6   -After segmenting it's possible to perform some boolean operations between masks. The boolean operations supported by InVesalius are:\\
7   -\\
8   -\textbf{Union}, perform union between two masks;\\
9   -\textbf{Difference}, perform difference from the first mask to the second one;\\
10   -\textbf{Intersection}, keeps what is common in both masks.\\
11   -\textbf{Exclusive disjunction}, also known as XOR, keeps the regions of the first mask wich are not in the second mask and regions from the second mask which are no in the first mask.\\
  6 +After segmenting, some boolean operations can be performed between masks. The boolean operations supported by InVesalius are:\\
  7 +
  8 +\begin{itemize}
  9 + \item \textbf{Union}, perform union between two masks;
  10 + \item \textbf{Difference}, perform difference from the first mask to the second one;\\
  11 + \item \textbf{Intersection}, keeps what is common in both masks.\\
  12 + \item \textbf{Exclusive disjunction (XOR)}: keeps the regions of the first mask which are not in the second mask and regions from the second mask which are no in the first mask.
  13 +\end{itemize}
  14 +
  15 +To use this tool go to the \textbf{Tools}, menu, select \textbf{Mask}, and then Boolean operations as shown in Figure~\ref{fig:booleano_menu}. Select the first mask, the operation to be performed and the second mask as shown in Figure~\ref{fig:booleano_janela} then click \textbf{OK}.
12 16  
13   -To use this tool go to menu \textbf{Tools}, \textbf{Mask}, \textbf{Boolean operations} as shown in the figure~\ref{fig:booleano_menu}.
14 17  
15 18 \begin{figure}[!htb]
16 19 \centering
... ... @@ -19,7 +22,6 @@ To use this tool go to menu \textbf{Tools}, \textbf{Mask}, \textbf{Boolean opera
19 22 \label{fig:booleano_menu}
20 23 \end{figure}
21 24  
22   -It's necessary to select the select the first mask, the operation to be performed and the second mask as shown in the figure~\ref{fig:booleano_janela}. Then click on the \textbf{Ok} button.
23 25  
24 26 \begin{figure}[!htb]
25 27 \centering
... ... @@ -28,7 +30,7 @@ It's necessary to select the select the first mask, the operation to be performe
28 30 \label{fig:booleano_janela}
29 31 \end{figure}
30 32  
31   -The figure~\ref{fig:op_boolana} shows some examples of utilization of boolean operations tool.
  33 +Figure~\ref{fig:op_boolana} shows some examples of utilization of boolean operations tool.
32 34  
33 35 \begin{figure}[!htb]
34 36 \centering
... ... @@ -50,7 +52,7 @@ The figure~\ref{fig:op_boolana} shows some examples of utilization of boolean op
50 52 \section{Mask cleaning}
51 53 \label{cap:limpeza_mascara}
52 54  
53   -It's possible to clean a mask (figure~\ref{fig:limpeza_mascara}). This is recommended before starting to insert Watershed markers. This tool is located on menu \textbf{Tools}, \textbf{Mask}, \textbf{Clean mask}. Also, it possible to use keyboard shortcut \textbf{CTRL+SHIFT+A}.
  55 +A mask can be cleaned, as shown in Figure~\ref{fig:limpeza_mascara}. This is recommended before inserting Watershed markers. This tool is located on the \textbf{Tools} menu. Select \textbf{Mask}, then \textbf{Clean mask}, or use the shortcut \textbf{CTRL+SHIFT+A}.
54 56  
55 57 \begin{figure}[!htb]
56 58 \centering
... ... @@ -77,11 +79,9 @@ Segmentation may leave some unwanted holes. It's recommended to fill them becaus
77 79 \label{fig:mask_manual_fill_holes_window}
78 80 \end{figure}
79 81  
80   -It's possible to fill hole on a mask slice (\textbf{2D - Actual slice}) or on all slices, selecting the option \textbf{3D - All slices}. It's also possible to configure the connectivity used. It may be $4$ or $8$ to 2D and $6$, $18$ and $26$ to 3D.
  82 +It is possible to fill hole on a mask slice (\textbf{2D - Actual slice}) or on all slices, selecting the option (\textbf{3D - All slices}). The connectivity may also be configured: $4$ or $8$ for 2D and $6$, $18$ and $26$ for 3D.
81 83  
82   -After configuring the desired parameters click with the \textbf{left-button} of the mouse on holes to fill them.
83   -
84   -The figure~\ref{fig:mask_fill_hole}.a shows mask with some holes and other mask with the holes filled (figure~\ref{fig:mask_fill_hole}.b). Click on the \textbf{close} button or close the dialog to deactivate this tool.
  84 +After configuring the desired parameters left-click on holes to fill them. Figure~\ref{fig:mask_fill_hole}.a shows a mask with some holes and other mask with the holes filled (Figure~\ref{fig:mask_fill_hole}.b). Click on the close button or close the dialog to deactivate this tool.
85 85  
86 86 \begin{figure}[!htb]
87 87 \centering
... ... @@ -95,7 +95,7 @@ The figure~\ref{fig:mask_fill_hole}.a shows mask with some holes and other mask
95 95  
96 96 \section{Fill holes automatically}
97 97  
98   -To open this tool go to the menu \textbf{Tools}, \textbf{Mask}, \textbf{Fill holes automatically} (figure~\ref{fig:menu_mask_automatic_fill_holes}). It'll open a dialog to configure the parameters. This tool doesn't require the user to click on holes he desire to fill. This tool will fill the holes based on the \textbf{max hole size parameter} given in number of voxels (figure~\ref{fig:mask_automatic_fill_holes_window}).
  98 +To open this tool go to the \textbf{Tools} menu, select \textbf{Mask} then \textbf{Fill holes automatically} (Figure~\ref{fig:menu_mask_automatic_fill_holes}). This will open a dialog to configure the parameters. This tool doesn’t require the user to click on holes he desire to fill. This tool will fill the holes based on the \textbf{max hole size parameter} given in number of voxels (Figure~\ref{fig:mask_automatic_fill_holes_window}).
99 99  
100 100 \begin{figure}[!htb]
101 101 \centering
... ... @@ -111,15 +111,15 @@ To open this tool go to the menu \textbf{Tools}, \textbf{Mask}, \textbf{Fill hol
111 111 \label{fig:mask_automatic_fill_holes_window}
112 112 \end{figure}
113 113  
114   -It's possible to fill hole on a mask slice (\textbf{2D - Actual slice}) or on all slices, selecting the option \textbf{3D - All slices}. It's also possible to configure the connectivity used. It may be $4$ or $8$ to 2D and $6$, $18$ and $26$ to 3D. In 2D case it's needed to indicate in which orientation window the holes will be filled.
  114 +Holes can also be filled on a mask slice (\textbf{2D - Actual slice}) or on all slices, selecting the option (\textbf{3D - All slices}. The connectivity will thus be $4$ or $8$ to 2D and $6$, $18$ and $26$ to 3D. If 2D, the user must indicate in which orientation window the holes will be filled.
115 115  
116   -After setting the parameters click in \textbf{Apply} button. If the result is not suitable set other hole size value or try other connectivity. Click on \textbf{Close} button to close this tool.
  116 +After setting the parameters click \textbf{Apply}. If the result is not suitable set another hole size value or connectivity. Click \textbf{Close} to close this tool.
117 117  
118 118 \section{Remove parts}
119 119  
120   -After generating a surface is recommended to remove the unwanted disconnected parts from mask. In this way the surface generation will use less RAM and the process will be quicker. To remove the unwanted parts go the menu \textbf{Tools}, \textbf{Mask} e \textbf{Remove Parts} (figure~\ref{fig:menu_mask_remove_part}). A dialog will be shown to configure the parameters of selection (figure~\ref{fig:mask_remove_parts_window}).
  120 +After generating a surface, it is recommended to remove the unwanted disconnected parts from a mask. This way the surface generation will use less RAM and make the process quicker. To remove any unwanted parts, go to the \textbf{Tools} menu, select \textbf{Mask} and then \textbf{Remove Parts} (Figure~\ref{fig:menu_mask_remove_part}). A dialog will be shown to configure the selection parameters (Figure~\ref{fig:mask_remove_parts_window}).
121 121  
122   -It's possible to select disconnected part only on a mask slice (\textbf{2D - Actual slice}) or on all slices, selecting the option \textbf{3D - All slices}. It's also possible to configure the connectivity used. It may be $4$ or $8$ to 2D and $6$, $18$ and $26$ to 3D.
  122 +It’s possible to select disconnected parts only on a mask slice (\textbf{2D - Actual slice}) or on all slices (\textbf{3D - All slices}); users may also configure the connectivity at the same time.
123 123  
124 124 \begin{figure}[!htb]
125 125 \centering
... ... @@ -135,7 +135,7 @@ It's possible to select disconnected part only on a mask slice (\textbf{2D - Act
135 135 \label{fig:mask_remove_parts_window}
136 136 \end{figure}
137 137  
138   -After selecting the desired parameters click with the \textbf{left-button} of the mouse on the region you want to remove. The figure~\ref{fig:mask_removed_part} an example of mask before and after remove a disconnected part. Click on \textbf{Close} button to close this tool.
  138 +After selecting the desired parameters click with the \textbf{left-button} of the mouse on the region you want to remove. Figure~\ref{fig:mask_removed_part} shows an example of a mask before and after the removal of unused parts. Click \textbf{Close} to stop using this tool.
139 139  
140 140 \begin{figure}[!htb]
141 141 \centering
... ... @@ -148,10 +148,9 @@ After selecting the desired parameters click with the \textbf{left-button} of th
148 148  
149 149 \section{Select parts}
150 150  
151   -To open Select parts tool go to menu \textbf{Tools}, \textbf{Mask}, \textbf{Select parts} (figure~\ref{fig:menu_mask_select_part}). A dialog will be shown to configure the parameters which are the name of the new mask and the connectivity ($6$, $18$ or $26$).
152   -
153   -Click with \textbf{left-button} of the mouse on the wanted pixel of the region you want to select. It's possible to select more than one region. The selected region(s) will be shown with a red mask. After selecting all the wanted regions click on the \textbf{Ok} button to create a new mask with regions selected. The figure~\ref{fig:mask_selected_part}.a shows a region selected in red color. The figure~\ref{fig:mask_selected_part}.b shows the selected region in a new mask.
  151 +To open the Select parts tool, access the \textbf{Tools} menu, select \textbf{Mask} then \textbf{Select parts} (Figure~\ref{fig:menu_mask_select_part}). A dialog will be shown to configure the the name of the new mask and the connectivity ($6$, $18$ or $26$).
154 152  
  153 +To select a region, \textbf{left-click} on a pixel; multiple regions can be selected. The selected region(s) will be shown with a red mask. After selecting all the wanted regions, click \textbf{OK} to create a new mask with the selected regions. Figure~\ref{fig:mask_selected_part}.a shows a region selected in red. Figure~\ref{fig:mask_selected_part}.b shows the selected region in a new mask.
155 154  
156 155 \begin{figure}[!htb]
157 156 \centering
... ... @@ -178,7 +177,7 @@ Click with \textbf{left-button} of the mouse on the wanted pixel of the region y
178 177  
179 178 \section{Crop}
180 179  
181   -It's possible to cut part of a mask in order to select an region of interest. This may reduce the amount of information to processed when generating a surface. To open this tool go to the menu \textbf{Tool}, \textbf{Mask}, \textbf{Crop} (figure~\ref{fig:menu_mask_crop}).
  180 +The crop tool allows users to select and use a specific section of image of interest. This may reduce the amount of information needed to be processed when generating a surface. To open, access the \textbf{Tool} menu, then \textbf{Mask} and \textbf{Crop} (Figure~\ref{fig:menu_mask_crop}).
182 181  
183 182 \begin{figure}[!htb]
184 183 \centering
... ... @@ -187,4 +186,4 @@ It's possible to cut part of a mask in order to select an region of interest. Th
187 186 \label{fig:menu_mask_crop}
188 187 \end{figure}
189 188  
190   -It will be shown a bounding boxes in each orientation window.
  189 +A box allowing for the selection of a specific area will then be displayed.
191 190 \ No newline at end of file
... ...
docs/user_guide_en_source/cap_segmen.tex
  Diff comments   View file @f2d179c
1 1 \chapter{Segmentation}
2 2  
3   -To select a certain type of tissue from an image it's used the segmentation feature at InVesalius.
  3 +To select a certain type of tissue from an image it is used the segmentation feature at InVesalius.
4 4  
5 5 \section{Threshold}
6 6  
7   -Limiar é uma técnica de segmentação de imagens que permite selecionar da imagem somente os \textit{pixels} cuja intensidade está dentro de um limiar definido pelo usuário. O limiar é definido por dois números, limiares inicial e final, também conhecidos como \textit{thresholds} mínimo e máximo. Como referência para a definição, é utilizada a escala de Hounsfield (tabela \ref{tab:escala_hounsfield}).
  7 +When using the thresholding segmentation technique, only the pixels whose intensity is inside the threshold range defined by the user are detected. The threshold is defined by two values, the initial (minimum) and final (maximum) threshold.
8 8  
9 9 In thresholding segmentation technique only the \textit{pixels} whose intensity is inside threshold range defined by the user. Threshold is defined by two number, the initial and final threshold, also known as minimum and maximum threshold. ...
10 10  
11   -Thresholding segmentation is located at the InVesalius left-panel, item \textbf{2. Select region of interest} (figure~\ref{fig:region_selection}).
  11 +Thresholding segmentation is located the InVesalius left-panel, item \textbf{2. Select region of interest} (Figure~\ref{fig:region_selection}).
12 12  
13 13 \begin{figure}[!htb]
14 14 \centering
... ... @@ -17,7 +17,7 @@ Thresholding segmentation is located at the InVesalius left-panel, item \textbf{
17 17 \label{fig:region_selection}
18 18 \end{figure}
19 19  
20   -Before starting segment it's necessary to configure a mask. A mask is a image overlayed to exam image where the selected regions are colored. See figure~\ref{fig:region_selection_masc}
  20 +Before starting a segment it is necessary to configure a mask. A mask is a image over to examine an image where the selected regions are colored. (Figure~\ref{fig:region_selection_masc}).
21 21  
22 22 \begin{figure}[!htb]
23 23 \centering
... ... @@ -26,17 +26,18 @@ Before starting segment it's necessary to configure a mask. A mask is a image ov
26 26 \label{fig:region_selection_masc}
27 27 \end{figure}
28 28  
29   -To change the threshold you may use the control that represents the image grayscale (figure~\ref{fig:region_selection_bar}). Move the \textit{left} sliding control to change the initial threshold. Move the \textit{right} sliding control to change the final threshold. It's also possible to to digit the desired threshold values in the text boxes in the left and right side of the thresholding control. Changing the thresholding values, automatically the mask will be updated, showing with a color the \textit{pixel} that are inside the thresholding range.
  29 +To change the threshold, use the image greyscale control (Figure~\ref{fig:region_selection_bar}). Move the \textit{left} sliding control to change the initial threshold. Move the \textbf{right} sliding control to change the final threshold. It is also possible to to input the desired threshold values in the text boxes in
  30 +the left and right side of the thresholding control. The mask will be automatically updated when the thresholding values are changed, showing in color the pixels inside the thresholding range.
30 31  
31 32  
32 33 \begin{figure}[!htb]
33 34 \centering
34 35 \includegraphics[scale=0.75]{segmentation_threshold_bar.png}
35   -\caption{Selecting the \textit{pixels} with intensity between $226$ and $3021$ (Bone)}
  36 +\caption{Selecting \textit{pixels} with intensity between $226$ and $3021$ (Bone)}
36 37 \label{fig:region_selection_bar}
37 38 \end{figure}
38 39  
39   -It's also possible to select some predefined thresholding values based on some type of tissues, like displayed in the figure~\ref{fig:limiar_presets}. Just select the desired tissue and the mask automatically updated.
  40 +It is also possible to select some predefined thresholding values based on some type of tissues, like those displayed in Figure~\ref{fig:limiar_presets}. Just select the desired tissue and the mask will automatically update.
40 41  
41 42 \begin{figure}[!htb]
42 43 \centering
... ... @@ -45,7 +46,7 @@ It's also possible to select some predefined thresholding values based on some t
45 46 \label{fig:limiar_presets}
46 47 \end{figure}
47 48  
48   -The table~\ref{tab:limiar} show thresholding values according to some tissues or materials.
  49 +Table~\ref{tab:limiar} show thresholding values according to some tissues or materials.
49 50  
50 51 \begin{table}[h]
51 52 \centering
... ... @@ -76,9 +77,9 @@ Spongial Bone (Child) & 156 & 585\\
76 77 \end{table}
77 78 \newpage
78 79  
79   -The table~\ref{tab:limiar} is indicated to images obtained from medical tomographs. The range of gray values from images obtained from odontological tomographs are greater and non-regular. Thus, it's necessary to use sliding control (figure~\ref{fig:region_selection_bar}) to adjust the thresholding values.
  80 +Table~\ref{tab:limiar} indicates images obtained from medical tomographs. The range of gray values from images obtained from odontological tomographs are greater and non-regular. Thus, it is necessary to use sliding controls (Figure~\ref{fig:region_selection_bar}) to adjust the thresholding values.
80 81  
81   -If you want to create a new mask click on the button \textbf{Create new mask} inside the item \textbf{2. Select region of interest}. See the figure~\ref{fig:shortcut_new_mask}.
  82 +To create a new mask, click \textbf{Create new mask} (Figure~\ref{fig:shortcut_new_mask}). Then, click \textbf{Select region of interest}.
82 83  
83 84 \begin{figure}[!htb]
84 85 \centering
... ... @@ -87,9 +88,7 @@ If you want to create a new mask click on the button \textbf{Create new mask} in
87 88 \label{fig:shortcut_new_mask}
88 89 \end{figure}
89 90  
90   -Clicando-se nesse atalho, uma nova janela será apresentada (figure \ref{fig:create_new_mask}). Selecione a faixa de limiar desejada e clique em \textbf{OK}.
91   -
92   -After clicking on this button a dialog will be shown (figure~\ref{fig:create_new_mask}). Select the desired threshold and click on \textbf{Ok}.
  91 +After clicking on this button a dialog will be shown (Figure~\ref{fig:create_new_mask}). Select the desired threshold and click on \textbf{Ok}.
93 92  
94 93 \begin{figure}[!htb]
95 94 \centering
... ... @@ -100,9 +99,9 @@ After clicking on this button a dialog will be shown (figure~\ref{fig:create_new
100 99  
101 100 \newpage
102 101  
103   -After the segmentation it's possible to generate a corresponding 3D surface. The surface is formed by triangles. The following chapter will give more details about surfaces.
  102 +After segmentation it is possible to generate a corresponding 3D surface. The surface is formed by triangles. The following chapter will give more details about surfaces.
104 103  
105   -Click on the \textbf{Create surface} button (figure~\ref{fig:generate_surface}) to create a new surface. If there is a surface created previously you may overwrite it with the new one. To do this select the option \textbf{Overwrite last surface} before creating the new surface.
  104 +Click on the \textbf{Create surface} button (Figure~\ref{fig:generate_surface}) to create a new surface. If there is a surface created previously you may overwrite it with the new one. To do this select the option \textbf{Overwrite last surface} before creating the new surface.
106 105  
107 106 \begin{figure}[!htb]
108 107 \centering
... ... @@ -111,7 +110,7 @@ Click on the \textbf{Create surface} button (figure~\ref{fig:generate_surface})
111 110 \label{fig:generate_surface}
112 111 \end{figure}
113 112  
114   -After a few moments the surface will be displayed at the 3D visualization window of InVesalius (figure~\ref{fig:surface}).
  113 +After a few moments the surface will be displayed at the 3D visualization window of InVesalius (Figure~\ref{fig:surface}).
115 114  
116 115 \begin{figure}[!htb]
117 116 \centering
... ... @@ -124,7 +123,7 @@ After a few moments the surface will be displayed at the 3D visualization window
124 123  
125 124 \section{Manual segmentation (Image edition)}
126 125  
127   -Thresholding segmentation may not be efficient in some case since it's applied to the whole image. Manual segmentation may be used o segment only an isolated image region. Manual segmentation turns possible to add or remove some image regions to the segmentation. Manual segmentation requires more knowledge of human anatomy. To use it click on \textbf{Manual edition} (figure~\ref{fig:advanced_edition}) to open the manual segmentation panel.
  126 +Thresholding segmentation may not be efficient in some cases since it is applied to the whole image. Manual segmentation may be used to segment only an isolated region. Manual segmentation also allows users to add or remove some image regions from the segmentation. To use it click on \textbf{Manual edition} (Figure~\ref{fig:advanced_edition}) to open the manual segmentation panel.
128 127  
129 128 \begin{figure}[!htb]
130 129 \centering
... ... @@ -142,7 +141,7 @@ Figure~\ref{fig:edition_slices_ref} show the Manual segmentation panel.
142 141 \label{fig:edition_slices_ref}
143 142 \end{figure}
144 143  
145   -There are two brushes used to segmentation: a circle and a square. Click on triangle icon (see figure~\ref{fig:brush_type}) to and click on the desired brush.
  144 +There are two brushes used for segmentation: a circle and a square. Click on the triangle icon (see Figure~\ref{fig:brush_type}) to show brush types, then click on the desired brush.
146 145  
147 146 \begin{figure}[!htb]
148 147 \centering
... ... @@ -153,7 +152,7 @@ There are two brushes used to segmentation: a circle and a square. Click on tria
153 152  
154 153 \newpage
155 154  
156   -It's also possible to adjust the brush size, like shown in the figure~\ref{fig:select_diameter}.
  155 +Brush sizes can also be adjusted, as shown in Figure~\ref{fig:select_diameter}.
157 156  
158 157 \begin{figure}[!htb]
159 158 \centering
... ... @@ -162,16 +161,17 @@ It's also possible to adjust the brush size, like shown in the figure~\ref{fig:s
162 161 \label{fig:select_diameter}
163 162 \end{figure}
164 163  
165   -It's needed to select the operation to be performed by the brush. These are the options:
  164 +The following are available options when using brushes in InVesalius:
166 165  
167   -\textbf{Draw}: to add a non-selected region to the segmentation;
  166 +\begin{itemize}
  167 + \item \textbf{Draw}: for adding a non-selected region to the segmentation;
168 168  
169   -\textbf{Erase}: to remove a selected region from the segmentation;
  169 + \item \textbf{Erase}: for removal of a non-selected region;
170 170  
171   -\textbf{Threshold}: applies the thresholding locally, adding or removing a
172   -region if in inside or outside of the threshold range.
  171 + \item \textbf{Threshold}: applies the thresholding locally, adding or removing a region inside or outside of the threshold range.
  172 +\end{itemize}
173 173  
174   -Figure~\ref{fig:select_brush_operations} shows the operations.
  174 +Figure~\ref{fig:select_brush_operations} shows the available brush operations.
175 175  
176 176 \begin{figure}[!htb]
177 177 \centering
... ... @@ -180,7 +180,7 @@ Figure~\ref{fig:select_brush_operations} shows the operations.
180 180 \label{fig:select_brush_operations}
181 181 \end{figure}
182 182  
183   -Figure~\ref{fig:noise_amalgaman} shows a image with noises caused by the presence of dental prosthesis. See the rays emerging from the dental arch. The thresholding segments the noise since its intensity is inside of the threshold of bone.
  183 +Figure~\ref{fig:noise_amalgaman} shows a image with noise caused by the presence of a dental prosthesis. Note the rays emerging from the dental arch: the thresholding segments the noise since its intensity is inside of the threshold of bone.
184 184  
185 185 \begin{figure}[!htb]
186 186 \centering
... ... @@ -189,7 +189,7 @@ Figure~\ref{fig:noise_amalgaman} shows a image with noises caused by the presenc
189 189 \label{fig:noise_amalgaman}
190 190 \end{figure}
191 191  
192   -Figure~\ref{fig:surface_amagaman} shows a surface create from that segmentation.
  192 +Figure~\ref{fig:surface_amagaman} shows a surface created from that segmentation.
193 193  
194 194 \begin{figure}[!htb]
195 195 \centering
... ... @@ -205,9 +205,9 @@ Figure~\ref{fig:surface_amagaman} shows a surface create from that segmentation.
205 205 \label{fig:surface_amagaman_zoom}
206 206 \end{figure}
207 207  
208   -In such cases use the manual segmentation with the \textbf{erase} brush. Keep the \textbf{left} mouse button pressed while dragging the brush over region you want to remove (in mask).
  208 +In such cases use the manual segmentation with the \textbf{erase} brush. Keep the \textbf{left} mouse button pressed while dragging the brush over the region to be removed (in mask).
209 209  
210   -Figure\ref{fig:editor_amalgaman} shows the image from figure~\ref{fig:noise_amalgaman} after the edition.
  210 +Figure\ref{fig:editor_amalgaman} shows the image from Figure~\ref{fig:noise_amalgaman} after.
211 211  
212 212 \begin{figure}[!htb]
213 213 \centering
... ... @@ -223,11 +223,7 @@ Figure\ref{fig:editor_amalgaman} shows the image from figure~\ref{fig:noise_amal
223 223 \label{fig:surface_edited_amalgaman}
224 224 \end{figure}
225 225  
226   -Realizada a edição, basta gerar a superfície a partir da imagem editada (figure \ref{fig:surface_edited_amalgaman}). Como houve edição, ao clicar em \textbf{Criar superfície}, será requerido se deseja gerar a superfície a partir do método \textbf{binário} ou utilizando o método de suavização \textbf{Suavização sensível ao contexto} (figure \ref{fig:new_surface_edited}) para minimizar os "degraus" na superfície. Demais detalhes serão discutidos no capítulo \ref{cap_surface}.
227   -%\ref{fig:generate_surface}).
228   -
229   -It's possible to generate a surface after manual segmentation (figure~\ref{fig:surface_edited_amalgaman}). Since it was used the manual segmentation, when you click on \textbf{Create surface} button, a dialog (figure~\ref{fig:new_surface_edited}) will be opened to to select if the surface will be created with the method \textbf{Binary} (blocky aspect) or \textbf{Context aware smoothing} (smoother).
230   -
  226 +A surface can be generated after manual segmentation (Figure~\ref{fig:surface_edited_amalgaman}). Since it was used in the manual segmentation procedure, when clicking on Create surface button, a dialog (Figure~\ref{fig:new_surface_edited}) will be opened to to select if the surface will be created with the method \textbf{Binary} (blocky) or \textbf{Context aware smoothing (smoother)}.
231 227  
232 228 \begin{figure}[!htb]
233 229 \centering
... ... @@ -239,7 +235,7 @@ It's possible to generate a surface after manual segmentation (figure~\ref{fig:s
239 235  
240 236 \section{Watershed}
241 237  
242   -In watershed segmentation the user indicates with marks what is object and what is background. This method treats the image as watershed (hence the name watershed) in which the gray values (intensity) are the altitudes, forming valleys and mountains. The markers are water source. The waters fill the watershed until the waters gather together segmenting, this way, the background from the object. To use Watershed segmentation click on \textbf{Watershed} to open the watershed panel (figure~\ref{fig:watershed_painel}).
  238 +In watershed segmentation the user demarcates objects and background detail. This method treats the image as watershed (hence the name) in which the gray values (intensity) are the altitudes, forming valleys and mountains. The markers are water source. The waters fill the watershed until the waters gather together, thus distinguishing background from object. To use Watershed segmentation click on Watershed to open the watershed panel (Figure~\ref{fig:watershed_painel}).
243 239  
244 240 \begin{figure}[!htb]
245 241 \centering
... ... @@ -248,11 +244,12 @@ In watershed segmentation the user indicates with marks what is object and what
248 244 \label{fig:watershed_painel}
249 245 \end{figure}
250 246  
251   -Before starting to segment with watershed it recommended to clean the mask (see section~\ref{cap:limpeza_mascara}).
  247 +Before segmenting to with Watershed it recommended to clean the mask (see section~\ref{cap:limpeza_mascara}).
  248 +
  249 +To insert a marker (object or background), a brush is used, similar to manual segmenting. You can use a circle or square brush and set its size.
252 250  
253   -To insert a marker (object or background) is used a brush, like when manual segmenting. You can use a circle or square brush and set its size.
  251 +Select brush operations from the following:
254 252  
255   -It necessary to select the brush operation, which are the following:
256 253 \begin{itemize}
257 254 \item \textbf{Object}: to insert object markers;
258 255 \item \textbf{Background}: to insert background markers (not object);
... ... @@ -260,11 +257,11 @@ It necessary to select the brush operation, which are the following:
260 257 \end{itemize}
261 258  
262 259  
263   -The option \textbf{Overwrite mask} is used when the user wants that the result of watershed segmentation overwrites the existent segmentation. The option \textbf{Use WWWL} is used to make watershed take into account the image with the values of \textbf{window width} and \textbf{window level} not the raw one, which may result in better segmentation.
  260 +The option \textbf{Overwrite mask} is used when the user wants the result of watershed segmentation to overwrite the existing segmentation. The option \textbf{Use WWWL} is used to make watershed take into account the image with the values of window width and window level (not the raw image) which may result in better segmentation.
264 261  
265   -Click on the button on the left side of the panel (figure~\ref{fig:watershed_conf}) to access more watershed configurations. This button will open a dialog (figure~\ref{fig:watershed_janela_conf}). The method option allows to choose the Watershed algorithm to be used to segment. It may be the conventional \textbf{Watershed} or \textbf{Watershed IFT}, which is based on the IFT (\textit{Image Forest Transform}) method. In some cases, like brain segmentation, the \textbf{Watershed IFT} may have a better result.
  262 +Click on the button on the left side of the panel (Figure~\ref{fig:watershed_conf}) to access more watershed configurations. This button will open a dialog (Figure~\ref{fig:watershed_janela_conf}). The method option allows to choose the Watershed algorithm to be used to segment. It may be the conventional \textbf{Watershed} or \textbf{Watershed IFT}, which is based on the IFT (\textit{Image Forest Transform}) method. In some cases, like brain segmentation, the \textbf{Watershed IFT} may have a better result.
266 263  
267   -The connectivity option refers to the pixel neighbourhood which may be $4$ or $8$ when in 2D, or $6$, $18$ or $26$ when in 3D. \textbf{Gaussian sigma} is a parameter used in the smoothing algorithm (the image is smoothed before the segmentation to remove the noise and get better results). The greater this value the smoother the smoother the image will be.
  264 +The connectivity option refers to the pixel neighbourhood ($4$ or $8$ when in 2D, or $6$, $18$ or $26$ when in 3D). \textbf{Gaussian sigma} is a parameter used in the smoothing algorithm (the image is smoothed before the segmentation to remove the noise and get better results). The greater this value the smoother the smoother the image will be.
268 265  
269 266 \begin{figure}[!htb]
270 267 \centering
... ... @@ -280,7 +277,9 @@ The connectivity option refers to the pixel neighbourhood which may be $4$ or $8
280 277 \label{fig:watershed_janela_conf}
281 278 \end{figure}
282 279  
283   -Normally, the \textbf{Watershed} is applied only in one slice, not in the whole image. After adding the markers is possible to apply the watershed to the whole image, just click on the button \textbf{Expand watershed to 3D}. Figure~\ref{fig:watershed_2d} shows the result of watershed segmentation in a slice (2D) of brain image. Figure~\ref{fig:watershed_3d} shows the segmentation expanded to the whole image (3D).
  280 +Normally the \textbf{Watershed} is applied only in one slice, not in the whole image. After adding the markers is possible to apply the watershed to the whole image by clicking on the button \textbf{Expand watershed to 3D}. Figure~\ref{fig:watershed_2d} shows the result of watershed segmentation in a slice (2D) of brain image.
  281 +
  282 +Figure~\ref{fig:watershed_3d} shows the segmentation expanded to the whole image (3D).
284 283  
285 284 Figure~\ref{fig:watershed_2d} also shows the object markers (in light green), the background markers (in red) and the segmentation mask (in green) overlaying the selected regions (result).
286 285  
... ... @@ -316,12 +315,10 @@ Region growing tool is accessed in the menu \textbf{Tools}, \textbf{Segmentation
316 315 \label{fig:segmentation_region_growing_dinamic}
317 316 \end{figure}
318 317  
319   -A técnica parte de um pixel inicial que é indicado clicando com o \textbf{botão direito} do mouse, os pixels vizinhos que satisfazem as condições indicadas anteriormente são selecionados. Cada método leva em consideração diferentes condições, a seguir são apresentadas as diferenças entre cada método:
320   -
321   -This segmentation technique starts with a pixel (indicated by the user clicking with the left-button of the mouse). If the neighbour pixels meet some conditions are selected. Iteratively, the selection expands analyzing the neighbourhood of the selected pixels. Each region growing method has a different condition of selection:
  318 +This segmentation technique starts with a pixel (indicated by the user left-clicking with the mouse). The selection expands by analyzing the neighbourhood of the selected pixels and including those of a given set of qualities. Each region growing method has a different condition of selection:
322 319  
323 320 \begin{itemize}
324   - \item \textbf{Dynamic}: In this method uses the value of the pixel clicked by the user. Then every connected pixel inside the lower (min) and the upper (max) range deviation are selected. The option \textbf{Use WWWL} is default and makes region growing taking into account the image with \textbf{window width} and \textbf{window level} applied not the raw one (figure~\ref{fig:segmentation_region_growing_dinamic_parameter}).
  321 + \item \textbf{Dynamic}: Uses the value of the pixel clicked by the user. Then every connected pixel inside the lower (min) and the upper (max) range deviation are selected. The option \textbf{Use WWWL} is default and takes into account the image with \textbf{window width} and \textbf{window level} applied not the raw one (figure~\ref{fig:segmentation_region_growing_dinamic_parameter}).
325 322  
326 323 \begin{figure}[!htb]
327 324 \centering
... ... @@ -330,7 +327,7 @@ This segmentation technique starts with a pixel (indicated by the user clicking
330 327 \label{fig:segmentation_region_growing_dinamic_parameter}
331 328 \end{figure}
332 329  
333   - \item \textbf{Threshold}: This method selects the pixels whose intensity are inside the minimum and maximum threshold (figure~\ref{fig:segmentation_region_growing_limiar}).
  330 + \item \textbf{Threshold}: This method selects the pixels whose intensity are inside the minimum and maximum threshold (Figure~\ref{fig:segmentation_region_growing_limiar}).
334 331  
335 332 \begin{figure}[!htb]
336 333 \centering
... ... @@ -339,7 +336,7 @@ This segmentation technique starts with a pixel (indicated by the user clicking
339 336 \label{fig:segmentation_region_growing_limiar}
340 337 \end{figure}
341 338  
342   - \item \textbf{Confidence}: This method starts by calculating the standard deviation and the mean value of the pixel selected by the user and its neighbourhood. Connected pixels with value inside the range (given by the mean more and less the standard deviation multiplied by the \textbf{Multiplier} parameter). It's calculated the mean and the standard deviation from the selected pixels. Which follows by other expansion step. This process is repeated according to the number of \textbf{Iterations} parameter. The figure~\ref{fig:segmentation_region_growing_confidence_parameter} shows the parameters for this method.
  339 + \item \textbf{Confidence}: This method starts by calculating the standard deviation and the mean value of the pixel selected by the user and its neighbourhood. Connected pixels with value inside the range (given by the mean more and less the standard deviation multiplied by the \textbf{Multiplier} parameter). It then calculates the mean and the standard deviation from the selected pixels, then carries out the expansion. This process is repeated according to the \textbf{Iterations} parameter. Figure~\ref{fig:segmentation_region_growing_confidence_parameter} shows the parameters for this method.
343 340  
344 341 \begin{figure}[!htb]
345 342 \centering
... ...