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| − | '''To create a new image file'''<br />
| + | <div id="CreatingImages"></div> |
| | + | == Creating new images == |
| | + | [[File:RawDialogBox.jpg|350px|thumb|right|Raw dialog box]] |
| | | | |
| − | 1 Do one of the following: <br />
| + | '''To create a new image file:'''<br /> |
| − | If an image file is not already open, select File > Open Image(A) > Create Blank Image.<br /> | + | <ol> |
| − | If an image file is already open, select File > Load Image (B)> Create Blank Image. The Raw dialog box (Figure 29) appears.<br /> | + | <li>Do one of the following: </li> |
| − | 2 In the dialog box, select the image type. <br />
| + | <ul> |
| − | 3 Select the units of measure for each dimension. <br />
| + | <li>If an image file is not already open, select File > Open Image(A) > Create Blank Image.</li> |
| − | 4 Enter the header offset and byte ordering information.<br />
| + | <li>If an image file is already open, select File > Load Image (B)> Create Blank Image. The [[#ImageDialod |Raw dialog box]] appears.</li> |
| − | 5 Click OK. A blank image (Figure 29) appears in an image window.<br />
| + | </ul> |
| − | 6 Use the paint and VOI tools to create an image.<br />
| + | <li>In the dialog box, select the image type. </li> |
| − | 7 Click File > Save image as. The Save dialog box opens.<br />
| + | <li>Select the units of measure for each dimension. </li> |
| − | 8 Type the name of the file in File Name, and select the file type in Files of type.<br />
| + | <li> Enter the header offset and byte ordering information.</li> |
| − | 9 Click OK. MIPAV saves the image under the file type you selected.<br />
| + | <li>Click OK. A blank image appears in an image window.</li> |
| | + | <li>Use the paint and VOI tools to create an image.</li> |
| | + | <li>Click File > Save image as. The Save dialog box opens.</li> |
| | + | <li>Type the name of the file in File Name, and select the file type in Files of type.</li> |
| | + | <li>Click OK. MIPAV saves the image under the file type you selected.</li> |
| | + | </ol> |
| | | | |
| | + | <div id="ImageDialod"></div> |
| | + | |
| | + | == Image dialog box == |
| | {| border="1" cellpadding="5" | | {| border="1" cellpadding="5" |
| − | |+ '''Figure 29. Raw dialog box<br />''' | + | |+ <br />''' |
| − | |-
| + | |
| − | | rowspan="1" colspan="3" |
| + | |
| − | [[Image:RawDialogBox.jpg]]
| + | |
| | |- | | |- |
| | | | | | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Image type</font>'''</span></div>
| + | '''Image type''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Synonymous with data type. The image type determines the number of intensities that can be represented in an image. For example, a Boolean image can display two intensities: 1 and 0. </div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Boolean</font>''</span>-1 bit per pixel (1 on, 0 off)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Unsigned byte</font>''</span>-1 byte per pixel (0, 255)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Unsigned short</font>''</span>-2 bytes per pixel (0, 65535)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Unsigned integer</font>''</span>-4 bytes per pixel (0, 2<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: super"><font color="#000000">32</font></span> -1)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Float</font>''</span>-4 bytes per pixel (-3.4E38, 3.4E38)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">ARGB</font>''</span>-3 bytes per pixel, plus 1 byte; 8 bits per color channel (alpha, red, green, and blue)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Byte</font>''</span>-1 byte per pixel (-128, 127)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Short</font>''</span>-2 bytes per pixel (-32768, 32767)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Integer</font>''</span>-4 bytes per pixel (-2<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">31</font></span>, 2<span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">31</font></span>-1)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Long</font>''</span>-8 bytes per pixel (-9.22E18, 9.22E18)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Double</font>''</span>-8 bytes per pixel (-1.8E308, 1.8E308)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">ARGB U short</font>''</span>-2 bytes per color channel and 2 bytes for alpha channel<br /></font></div>
| + | Synonymous with data type. The image type determines the number of intensities that can be represented in an image. For example, a Boolean image can display two intensities: 1 and 0. See also [[Supported Formats]]. |
| | + | |
| | + | '''Boolean'''-1 bit per pixel (1 on, 0 off) |
| | + | |
| | + | '''Unsigned byte'''-1 byte per pixel (0, 255) |
| | + | |
| | + | '''Unsigned short'''-2 bytes per pixel (0, 65535) |
| | + | |
| | + | '''Unsigned integer'''-4 bytes per pixel (0, 232 -1) |
| | + | |
| | + | '''Float'''-4 bytes per pixel (-3.4E38, 3.4E38) |
| | + | |
| | + | '''ARGB'''-3 bytes per pixel, plus 1 byte; 8 bits per color channel (alpha, red, green, and blue) |
| | + | |
| | + | '''Byte'''-1 byte per pixel (-128, 127) |
| | + | |
| | + | '''Short'''-2 bytes per pixel (-32768, 32767) |
| | + | |
| | + | '''Integer'''-4 bytes per pixel (-231, 231-1) |
| | + | |
| | + | '''Long'''-8 bytes per pixel (-9.22E18, 9.22E18) |
| | + | |
| | + | '''Double'''-8 bytes per pixel (-1.8E308, 1.8E308) |
| | + | |
| | + | '''ARGB U short'''-2 bytes per color channel and 2 bytes for alpha channel |
| | |- | | |- |
| | | | | | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Dimensions and resolutions</font>'''</span></div>
| + | '''Dimensions and resolutions''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Degree of manifolding of a quantity such as space or time. Two-dimensional datasets are composed of one image (the two dimensions are length and width). Generally, three-dimensional datasets are composed of more than one image. The third dimension is generally space. The fourth dimension is generally time. (Either time or space can be the third or fourth dimensions.) Zeros in the text boxes indicate that the dimension is not represented in the image. For example, if the text boxes for the first and second dimensions are filled, and the rest of the text boxes are filled with a zero, the image only has two dimensions. </div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Dimensions</font>''</span></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">1st</font>''</span>-Width (along <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">x</font>''</span> axis)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">2nd</font>''</span>-Length (along <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">y</font>''</span> axis)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">3rd</font>''</span>-Depth (along <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">z</font>''</span> axis)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">4th</font>''</span>-Time (along <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">t</font>''</span> axis)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 6pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">5th</font>''</span>-Fifth dimension<br /></font></div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Resolutions</font>''</span></div> <div class="CellBody">Size of pixel or voxel per dimensions 1 through 5.</div>
| + | Degree of manifolding of a quantity such as space or time. Two-dimensional datasets are composed of one image (the two dimensions are length and width). Generally, three-dimensional datasets are composed of more than one image. The third dimension is generally space. The fourth dimension is generally time. (Either time or space can be the third or fourth dimensions.) Zeros in the text boxes indicate that the dimension is not represented in the image. For example, if the text boxes for the first and second dimensions are filled, and the rest of the text boxes are filled with a zero, the image only has two dimensions. |
| | + | Dimensions |
| | + | |
| | + | 1st-Width (along x axis) |
| | + | |
| | + | 2nd-Length (along y axis) |
| | + | |
| | + | 3rd-Depth (along z axis) |
| | + | |
| | + | 4th-Time (along t axis) |
| | + | |
| | + | 5th-Fifth dimension |
| | + | |
| | + | Resolutions |
| | + | |
| | + | Size of pixel or voxel per dimensions 1 through 5. |
| | |- | | |- |
| | | | | | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Units of measure</font>'''</span></div>
| + | '''Units of measure''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Indicates the unit of measurement for each of the applicable dimensions.</div>
| + | Indicates the unit of measurement for each of the applicable dimensions. |
| | |- | | |- |
| | | | | | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Header offset</font>'''</span></div>
| + | '''Header offset''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Indicates the size of the space reserved at the beginning of the file where specific types of information is kept. This space, which is called the <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">header,</font>''</span> precedes the image data. If you know the length of the header, type it in this box. When MIPAV accesses the file, it skips the header offset and begins to read the image data. Note that not all image file formats have a header.</div>
| + | Indicates the size of the space reserved at the beginning of the file where specific types of information is kept. This space, which is called the header, precedes the image data. If you know the length of the header, type it in this box. When MIPAV accesses the file, it skips the header offset and begins to read the image data. Note that not all image file formats have a header. |
| | |- | | |- |
| | | | | | |
| | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Big endian</font>'''</span></div> | | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Big endian</font>'''</span></div> |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Indicates whether image data is stored in the big endian format. If not, the image data is stored in the little endian format. <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Endianess</font>''</span> refers to the byte ordering of the data. Some computers order the data with the least significant byte (LSB) first followed by the most significant byte (MSB). This byte order is referred as <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">little endian</font>''</span> or Intel byte ordering. Machines that use little-endian byte ordering are VAXes, Intel x86, and Pentium. The reverse is MSB and then LSB, which is referred as <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">big endian</font>''</span> or Motorola byte ordering. Machines that use big-endian byte ordering are IBM System 3D, RISC, and a Motorola 680x0. MIPAV is biendian; it supports both big- and little-endian byte-ordering formats.</div>
| + | Indicates whether image data is stored in the big endian format. If not, the image data is stored in the little endian format. Endianess refers to the byte ordering of the data. Some computers order the data with the least significant byte (LSB) first followed by the most significant byte (MSB). This byte order is referred as little endian or Intel byte ordering. Machines that use little-endian byte ordering are VAXes, Intel x86, and Pentium. The reverse is MSB and then LSB, which is referred as big endian or Motorola byte ordering. Machines that use big-endian byte ordering are IBM System 3D, RISC, and a Motorola 680x0. MIPAV is biendian; it supports both big- and little-endian byte-ordering formats. |
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| | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">OK</font>'''</span></div> | | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">OK</font>'''</span></div> |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Applies the parameters that you specified and creates a blank image.</div>
| + | Applies the parameters that you specified and creates a blank image. |
| | |- | | |- |
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| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Cancel</font>'''</span></div>
| + | '''Cancel''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Disregards any changes you made in this dialog box, closes the dialog box, and does not create a blank image.</div>
| + | >Disregards any changes you made in this dialog box, closes the dialog box, and does not create a blank image. |
| | |- | | |- |
| | | | | | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
| + | '''Help''' |
| | | rowspan="1" colspan="2" | | | | rowspan="1" colspan="2" | |
| − | <div class="CellBody">Displays online help for this dialog box.TBD.</div>
| + | Displays online help for this dialog box. |
| − | |}
| + | |
| − | | + | |
| − | == Delineating volumes of interest (VOIs) ==
| + | |
| − | '''MIPAV''' provides tools that allow you to automatically, semiautomatically, and manually identify and modify volumes of interest (VOIs). <br />
| + | |
| − | '''volume of interest'''-the portion of the image in the dataset on which you want to focus. It may be either one slice or multiple slices throughout the dataset.<br />
| + | |
| − | | + | |
| − | Each VOI can be formed from multiple contours in a single slice or multiple slices. Once an object is segmented and defined by a VOI, statistics of the volume can be calculated.
| + | |
| − | | + | |
| − | MIPAV supports over 32,000 unique VOIs on a single dataset. Additionally, you can move or delete nodes on the VOI and add new points. VOI types include:
| + | |
| − | | + | |
| − | *Point, which is created by using
| + | |
| − | *2D line
| + | |
| − | *Rectangular
| + | |
| − | *3D rectangular
| + | |
| − | *2D elliptical
| + | |
| − | *Polygonal
| + | |
| − | *3D polygonal
| + | |
| − | *Interactive level-set
| + | |
| − | | + | |
| − | === Generating contour VOIs using predefined shapes ===
| + | |
| − | MIPAV includes icons of predefined shapes, such as points, lines, ellipses, or rectangles, that you can use to create VOIs. These icons are on the VOI toolbar.<br />
| + | |
| − | '''To generate contour VOIs using the predefined shapes'''<br />
| + | |
| − | 1 Select one of the contour icons from the VOI toolbar in the expanded MIPAV window. See also Figure 12.<br />
| + | |
| − | 2 Move the pointer to the image window. The pointer changes to a cross-hair shape. Do one of the following:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Points, levelset:</font>'''</span> Position the cursor on the area where the point or levelset should be drawn. Click the mouse button.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Straight lines, rectangles (2D and 3D), ellipsoids:</font>'''</span> Position the cursor on the area where the contour should begin. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Click the mouse button. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> While holding down the mouse button, drag the cursor until the contour is the desired size.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Polylines, polygons:</font>'''</span> Position the cursor over the area where the contour should begin. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Click the mouse button. A point appears. Alternate between moving the mouse and selecting the mouse button to outline the VOI. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> To complete a polyline, double-click the mouse button. To complete a polygon, connect the first and last nodes.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Tip:</font>'''</span> To draw the same shape several times in succession, hold down the Shift key while you select the applicable icon from the VOI toolbar and draw.<br /></font></div>
| + | |
| − | | + | |
| − | === Adding and moving boundary points on VOIs ===
| + | |
| − | | + | |
| − | No matter which method chosen to delineate a VOI, you can add points and change the boundaries of the VOI. For example, suppose you created a VOI on an image with the Rectangle VOI icon. If you notice that a part of the image that should be included in the VOI is not included, the boundary of the rectangle needs to be adjusted to include the missing portion of the image. <br />
| + | |
| − | '''To add a point and change the boundary of the VOI'''<br />
| + | |
| − | 1 [[Image:crosshairBlack.jpg]] Select the VOI. Notice that white points appear at the corners of the VOI and a small cross appears in the middle of the VOI.<br />
| + | |
| − | 2 [[Image:HandPointer.jpg]] Place the cursor on the portion of the VOI you want to adjust. The cursor changes from a cross to.<br />
| + | |
| − | 3 Click once. A white point appears on the line.<br />
| + | |
| − | 4 Select the point and drag it to include the missing part of the image.<br /></font></div>
| + | |
| − | '''Tip:'''Circular VOIs are composed of a continuous series of points around the diameter of the circle. You only need to select one of those points and drag it to enlarge the circle.<br />
| + | |
| − | | + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+ '''Figure 30. Adding a point and adjusting the boundary of a rectangular VOI<br />
| + | |
| − | |-
| + | |
| − | |[[Image:exampleBoundaryRectangularVOI.jpg]]
| + | |
| − | |}
| + | |
| − | | + | |
| − | === Automatically adjusting contour boundaries ===
| + | |
| − | After a contour is drawn, it might be necessary to adjust the boundaries so it more closely matches the VOI region. <br />
| + | |
| − | ''' To adjust contours'''<br />
| + | |
| − | 1 Click a contour. The nodes become visible. <br />
| + | |
| − | 2 Select VOI > Evolve boundary 2D >Active Contour. The Evolve Boundary dialog box opens.<br />
| + | |
| − | 3 Modify the information in the window if necessary. <br />
| + | |
| − | 4 Click OK.<br />
| + | |
| − | A new contour, that more closely outlines the VOI, appears on the image. The old contour also remains.<br />
| + | |
| − | | + | |
| − | [[Image:iconCutSelectedContour.jpg]] To delete an old contour, select the contour, and then select Cut Selected Contour, or press the Del key on the keyboard.
| + | |
| − | | + | |
| − | | + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+ '''Figure 31. Evolve Boundary dialog box'''<br />
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Scale of the Gaussian</font>'''</span></div>
| + | |
| − | |
| + | |
| − | <div class="CellBody">Enter values for X,Y, and Z directions which will be used to correct blurring. The default value is 2.0</div>
| + | |
| − | |
| + | |
| − | [[Image:EvolveBoundary.jpg]]
| + | |
| − | |-
| + | |
| − | |'''Resolution options'''
| + | |
| − | |If this box is checked, the algorithm uses the image resolution to normalize the Z scale.
| + | |
| − | |-
| + | |
| − | |'''Evolve Boundary'''
| + | |
| − | |Replace Original Contour - the original VOI will be replaced with the new one.
| + | |
| − | |-
| + | |
| − | |'''Algorithm parameters'''
| + | |
| − | | Move Boundary - depending on the selected option, the VOI will be moved in 1) any direction, 2) only inward, 3) only outward.<br /> Boundary Iterations- specify the number of iterations needed to calculate the new boundary.<br />
| + | |
| − | Smoothness- enter the number from 0.5 to 2.4 to specify smoothness.
| + | |
| − | |-
| + | |
| − | |'''OK'''
| + | |
| − | |Applies the algorithm according to the specifications in this dialog box.
| + | |
| − | |-
| + | |
| − | |'''Cancel'''
| + | |
| − | |Disregards any changes that you made in this dialog box and closes it.
| + | |
| − | |-
| + | |
| − | |'''Help'''
| + | |
| − | |TBD.
| + | |
| | |} | | |} |
| | | | |
| | == Annotating images with text == | | == Annotating images with text == |
| | + | [[File:AnnotatingWithTexst.jpg|200px|thumb|right|The Annotation dialog box]] |
| | + | [[Image:AnnotataTExtIco.jpg]] You can use the Annotation tool icon located on [[MIPAV toolbars | VOI toolbar]] to place text directly on an image at any position on the image. You can use any font family, or typeface, that is installed on your computer to display the text. |
| | | | |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [[Image:AnnotataTExtIco.jpg]] Another icon on the VOI toolbar is the Annotation tool icon, which you can use to place text directly on an image at any position on the image. You can use any font family, or typeface, that is installed on your computer to display the text.<br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To annotate images with text<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open an image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Click the Annotation tool icon. The Annotation dialog box (Figure 32) opens.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Click the image on which you want the text to appear. The image becomes the active image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Select the font family and style (bold or italic). To select a regular font style, simply specify the font family.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Type the font size of type in the <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">pt.</font>'''</span> box.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 Press Enter. The Annotation dialog box either enlarges or reduces in size depending on the type size you chose (see "Previewing Font Selection" below).<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 7 Click Color to select the color of the text. The color of the type in the Text box changes to the color you have chosen.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 8 Select "Enter text here" and type the text that you want to display on the image in the Text box.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 9 Click OK. The text appears near the top of the image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 10 Click the text and drag it to any position on the image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | + | <div id="AnnotateImages"></div> |
| − | | + | === To annotate images with text:=== |
| | | | |
| − | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> | + | <ol> |
| | + | <li>Open an image.</li> |
| | + | <li>Click the Annotation tool icon. The Annotation dialog box opens.</li> |
| | + | <li>Click the image on which you want the text to appear. The image becomes the active image.</li> |
| | + | <li>Select the font family and style (bold or italic). To select a regular font style, simply specify the font family.</li> |
| | + | <li>Type the font size of type in the '''pt.''' box.</li> |
| | + | <li>Press Enter. The Annotation dialog box either enlarges or reduces in size depending on the type size you chose.</li> |
| | + | <li>Click Color to select the color of the text. The color of the type in the Text box changes to the color you have chosen.</li> |
| | + | <li>Select "Enter text here" and type the text that you want to display on the image in the Text box.</li> |
| | + | <li> Click OK. The text appears near the top of the image.</li> |
| | + | <li> Click the text and drag it to any position on the image.</li> |
| | + | </ol> |
| | | | |
| | + | === Annotation dialog box === |
| | {| border="1" cellpadding="5" | | {| border="1" cellpadding="5" |
| − | |+'''Figure 32. Annotation dialog box'''<br /> | + | |+''' Annotation dialog box'''<br /> |
| | |- | | |- |
| | |'''Font options''' | | |'''Font options''' |
| | |'''Font'''-Specifies the font family, or typeface, for the text. When you select another typeface, "Enter text here" appears in that typeface. | | |'''Font'''-Specifies the font family, or typeface, for the text. When you select another typeface, "Enter text here" appears in that typeface. |
| − | |[[Image:AnnotatingWithTexst.jpg]]
| |
| | |- | | |- |
| | | | | | |
| Line 183: |
Line 161: |
| | |} | | |} |
| | | | |
| − | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000">
| + | ==== Previewing Font Selection ==== |
| − | | + | [[File:AnnotationDialogBox1.jpg|400px|thumb|left|The Annotation dialog box]] |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | <div style="font-style: normal; margin-bottom: 1pt; margin-left: 0pt; margin-right: 0pt; margin-top: 17pt; text-align: center; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Previewing Font Selection<br /></font>'''</div> <div class="CellHeading">The Annotation dialog box allows you to preview the font family, style, size, and color of the text before you click OK and add the text to the image.</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />
| + | |
| − | |[[Image:AnnotationDialogBox1.jpg]]
| + | |
| − | |}<br clear="all" /><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div> | + | |
| − | | + | |
| − | | + | |
| − | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To edit the text <br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Double-click the added text on an image. The Annotation dialog box opens.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Make any changes you want to the text, font family, font style, and color.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Click OK. The changes you made to the text should appear on the image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To delete the text<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Select the added text on an image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Press Del. MIPAV removes the text from the image.<br /></font></div>
| + | |
| − | | + | |
| − | To restore the text to the image, select Edit > Undo VOI. The text reappears on the image.
| + | |
| − | | + | |
| − | == Calculating VOI statistics ==
| + | |
| − | Once a VOI is drawn, you can calculate the number of voxels in the VOI, the volume, and area. You can also calculate the average and standard deviation of the voxel intensity and the center of mass. For 2D images, you can calculate the principal axis and the eccentricity. MIPAV provides two methods for you to obtain VOI statistics:<br />By using VOI properties-This method is fast and simple and provides statistics for the entire VOI. Although it allows you to save the results in a text file, that is an additional step. However, using this method, you can type additional information directly onto the Data page with the statistics.<br />By using the Statistics Generator-Using this method, you can obtain statistics on the entire VOI, on a single slice of the VOI, or by contour and slice. The Statistics Generator also automatically saves the results in either a tab-delimited file or an XML file of your choosing. In addition, it displays statistics in a tabular format.<br />'''Note:''' MIPAV can calculate statistics for only one VOI at a time. In addition, MIPAV calculates the volume and area in a VOI using image pixel (voxel) resolutions.<br />
| + | |
| − | | + | |
| − | === Using VOI properties ===
| + | |
| − | '''To calculate VOI statistics'''<br />
| + | |
| − | 1 Select the desired VOI in the image window.<br />
| + | |
| − | 2 Select VOI > Properties in the MIPAV window. The VOI Statistics dialog box appears.<br />
| + | |
| − | 3 Select the statistics to be calculated in Statistics to Calculate. Click Calculate. The VOI Statistics dialog box remains on the desktop. In a few moments, statistical data appears on the Data page in the Output window.<br />
| + | |
| − | 4 To close the dialog box, click Cancel in the VOI Statistics dialog box when complete.<br />
| + | |
| − | 5 To add information to the statistics, just type it in into the statistics on the Data page.<br />
| + | |
| − | 6 To remove the data, select them first, and then click the Cut icon or select Edit > Cut to cut the selected data. MIPAV removes the selected text from the Output window and copies it to the clipboard for use in other applications.<br />
| + | |
| − | 7 Select the data that you want to copy, and then click Copy or select Edit > Copy to copy the data to another location in the window or to another application (such as a word processor).<br />
| + | |
| − | 8 Click Save or select File > Save messages to save the data and any comments you've added to a text file.<br />
| + | |
| − | 9 Click Clear Messages or select Edit > Clear Messages to clear the window.<br />
| + | |
| − | | + | |
| − | {| border="1" cellpadding="5"
| + | |
| − | |+ '''Figure 33. VOI Statistics dialog box ''' | + | |
| − | |-
| + | |
| − | | rowspan="1" colspan="3" |
| + | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 6pt; margin-right: 6pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> VOI Properties<br /></font>'''</div>
| + | |
| − | |- | + | |
| − | |
| + | |
| − | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 6pt; margin-right: 6pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Name of VOI<br /></font>'''</div>
| + | |
| − | |
| + | |
| − | <div class="CellBody">Shows the name of VOI.</div>
| + | |
| − | |[[Image:VOIStatisticsDialogBox.jpg]]
| + | |
| − | |-
| + | |
| − | |'''Thickness of VOI '''<br />
| + | |
| − | |rowspan="1" colspan="2" |Shows the number which represents how many slices has a selected VOI.
| + | |
| − | |-
| + | |
| − | |'''Color of VOI'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Shows the color that was used to outline the VOI.
| + | |
| − | |-
| + | |
| − | |'''Show contour bounding box'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Highlights the VOI and, when you select the VOI, displays a box that encompasses all of the VOI's borders and lists the measurements and position of each boundary.
| + | |
| − | |-
| + | |
| − | |'''Use additive polarity for VOI''' <br />
| + | |
| − | |rowspan="1" colspan="2" |If selected, put VOI names, such as "polygon1" to indicate VOI location.
| + | |
| − | |-
| + | |
| − | |'''Include for processing'''<br />
| + | |
| − | |rowspan="1" colspan="2" |This option is very helpful if you have a set of VOIs delineated on your image and want to use some of them for masking. See "Using the Include for Processing option".
| + | |
| − | |-
| + | |
| − | |'''Show VOI name '''<br />
| + | |
| − | |rowspan="1" colspan="2" |If selected, shows the name of the chosen VOI. E.g. "polygon1."
| + | |
| − | |-
| + | |
| − | |rowspan="1" colspan="2" |'''Display VOI shading''' <br />
| + | |
| − | |Shades the area inside a chosen VOI. When this option is selected, the '''Opacity slider''' becomes also available, so you can regulate the opacity of the shaded area.
| + | |
| − | |-
| + | |
| − | |rowspan="1" colspan="3" |'''Statistics to calculate'''<br />
| + | |
| − | |-
| + | |
| − | |
| + | |
| − | |Provides a list of statistics. Select the statistics that you want to include in the report.
| + | |
| − | | [[Image:VOIStatisticsOutput.jpg]]
| + | |
| − | |-
| + | |
| − | |'''Select all'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Selects all of the statistics listed in the Statistics to calculate list.
| + | |
| − | |-
| + | |
| − | |'''Clear'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Clears all of the check boxes that you selected in the Statistics to calculate list.
| + | |
| − | |-
| + | |
| − | |''' VOI Tree'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Displays all VOIs delineated on the image in an hierarchical view.
| + | |
| − | |-
| + | |
| − | |'''Tree options'''<br />
| + | |
| − | |rowspan="1" colspan="2" |Frame follows VOI selection - if this option is selected, the current selected VOI appears in a frame in the VOI tree.
| + | |
| − | |-
| + | |
| − | |'''Exclude intensity range''' <br />
| + | |
| − | |rowspan="1" colspan="2" |Allows you to select specific intensity ranges that you want to exclude from the calculation.
| + | |
| − | |-
| + | |
| − | |'''Watershed seed value (0-32K)''' <br />
| + | |
| − | |rowspan="1" colspan="2" |Indicates the basin value used when running the Watershed algorithm on images.
| + | |
| − | |-
| + | |
| − | |'''Apply''' <br />
| + | |
| − | |rowspan="1" colspan="2" |Applies the changes you made in this dialog box and leaves the dialog box open for you to make further changes.
| + | |
| − | |-
| + | |
| − | |'''Cancel''' <br />
| + | |
| − | |rowspan="1" colspan="2" |Disregards any changes you made in this dialog box, closes the dialog box, and does not run a statistics report.
| + | |
| − | |-
| + | |
| − | |'''Calculate''' <br />
| + | |
| − | |rowspan="1" colspan="2" |Calculates the statistics requested in this dialog box and displays them in the Data page of the Output window.
| + | |
| − | |}
| + | |
| − | <br />
| + | |
| − | | + | |
| − | '''Using the Include for Processing option'''<br />
| + | |
| − | | + | |
| − | The Include for Processing option is very helpful if you have a set of VOIs delineated on your image and want to use some of them for masking. In that case, select the VOI(s) of interest, then activate the Include for Processing option, and after that, call one of the mask tools, e.g. the Quick AND VOI mask operation. The tool will apply on the selected VOI(s). In case when the Include for Processing option has not been activated, then the Quick AND VOI mask operation will apply on the whole image and darken it. See Figure 34 (a) and (b).
| + | |
| − | | + | |
| − | | + | |
| − | '''Figure 34. Using the Include for processing option for the Quick AND VOI mask operation.''' (a) The Include for Processing option is activated and (b) the Include for Processing option is disabled.<br />
| + | |
| − | | + | |
| − | [[Image:VOIProtertiesIncludeForProcessing.jpg]]
| + | |
| − | <br />
| + | |
| − | | + | |
| − | === Using the Statistics Generator ===
| + | |
| − | If you plan either to use a database or spreadsheet to keep track of VOI statistics or to obtain them in an XML format, use the Statistics Generator. As mentioned earlier, the Statistics Generator can provide statistics on an entire VOI(s) or a particular slice or by contour and slice.<br />
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| − | | + | |
| − | Using the Statistics Generator involves three tasks:
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| − | #Selecting VOI and save options<br />
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| − | #Selecting statistics options<br />
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| − | #Reviewing the statistics<br />
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| − | ==== Selecting VOI and save options ====
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| − | The first task is to select the VOIs on which you want to obtain statistics and select the file in which the resulting statistics should be saved.<br /><
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| − | '''To Calculate Statistics on VOI Groups'' <br />
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| − | 1 Delineate or select the VOI(s) on the image.<br />
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| − | 2 Select VOI > Statistics Generator in the MIPAV window. The Calculate Statistics on VOI Groups window appears (Figure 35). This window displays all of the VOIs on the image in the VOI group list on the left.<br />
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| − | '''Figure 35. Calculate Statistics on VOI Groups window'''<br />
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| − | [[Image:CalculateStatisticsOnVOIGroups.jpg]]
| + | The Annotation dialog box allows you to preview the font family, style, size, and color of the text before you click OK and add the text to the image. |
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| | + | === To edit the text === |
| | + | <ol> |
| | + | <li> Double-click the added text on an image. The Annotation dialog box opens.</li> |
| | + | <li>Make any changes you want to the text, font family, font style, and color.</li> |
| | + | <li>Click OK. The changes you made to the text should appear on the image.</li> |
| | + | </ol> |
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| − | <br /> | + | === To delete the text === |
| − | 3 Select the VOI on which you want to obtain statistics.<br />
| + | <ol> |
| − | 4 Press Send Selection Right. The name of the VOI appears in the VOI group list on the right.<br />
| + | <li>Select the added text on an image.</li> |
| − | 5 Use Browse to choose a file name in the VOI Statistic File Destination box.<br />
| + | <li>Press Del. MIPAV removes the text from the image.</li> |
| − | 6 Select either one of the two formats in the Output Format group: Tab delimited or XML.<br />
| + | </ol> |
| − | 7 Click Statistics Options. The Statistics Options page opens.<br />
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| − | 8 Proceed to the next task: Selecting statistics options.<br />
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| − | ==== Selecting statistics options ====
| + | To restore the text to the image, select Edit > Undo VOI. The text reappears on the image. |
| − | The Statistics Options page (Figure 36) provides a list of statistics from which you can select and the options to obtain statistics by slice, by contour and slice, or by the total VOI.<br />
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| − | '''To select statistics to perform on VOIs'''<br />
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| − | '''Figure 36. Statistics Options page<br />'''
| + | == See also: == |
| − | [[Image:StatisticsOptionsVOIStatistics.jpg]] | + | *[[Saving and printing images]] |
| | + | *[[Delineating volumes of interest (VOIs)| Volumes of Interest]] |
| | + | **[[Delineating volumes of interest (VOIs)]] |
| | + | **[[Calculating VOI statistics]] |
| | + | **[[Reviewing VOI statistics]] |
| | + | **[[Reviewing VOI statistics|Generating graphs (intensity profiles)]] |
| | + | *[[ImageJ | Working with ImageJ]] |
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| − | 1 Do either of the following in the Statistics to calculate group:<br />
| + | [[Category:Help]] |
| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Select one or more of the listed types of statistics.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Click Select all to obtain all of the statistic types.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Select one of the following options in the Statistics options group:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> By contour & slice<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> By slice only<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> By total VOI (the default selection)<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Select Show all totals if you want to record the totals for each type of statistic.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Click Calculate.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 5 Select Logging. The Logging page Figure 37) appears.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 Proceed to the next task: "Reviewing the statistics".<br />
| + | [[Category:Getting started]] |
| − | [[Reviewing the statistics]] | + | |
The Annotation dialog box allows you to preview the font family, style, size, and color of the text before you click OK and add the text to the image.
To restore the text to the image, select Edit > Undo VOI. The text reappears on the image.
You can use the Annotation tool icon located on VOI toolbar to place text directly on an image at any position on the image. You can use any font family, or typeface, that is installed on your computer to display the text.
