Difference between revisions of "Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs"
(Created page with '<br /> === Changing image brightness and contrast using LUTs === <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; m...') |
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To do this, complete the following steps: | To do this, complete the following steps: | ||
− | <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 [[Image:iconQuickLUT.jpg]] (Quick LUT) in the MIPAV window. <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 Move the cursor to the image window and draw a box around an area that has the highest and lowest intensities you want the image to display. These values are used to remap the image data to the LUT. The net effect is increased contrast in the area of interest ( | + | <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 [[Image:iconQuickLUT.jpg]] (Quick LUT) in the MIPAV window. <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 Move the cursor to the image window and draw a box around an area that has the highest and lowest intensities you want the image to display. These values are used to remap the image data to the LUT. The net effect is increased contrast in the area of interest (Figure 14). |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 14. An image before and after applying Quick LUT<br /></font>'''</div> |
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[[Image:exampleImagesBeforeDuringAfterQuickLUT.jpg]] | [[Image:exampleImagesBeforeDuringAfterQuickLUT.jpg]] | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 15. Histogram dialog box<br /></font>'''</div> |
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[[Image:dialogboxHistogram.jpg]] | [[Image:dialogboxHistogram.jpg]] | ||
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− | <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: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If there are no VOIs on the image, the Look-up Table window (Figure 16) 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"> 4 Choose 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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Whole image</font>''</span>-To generate a histogram for the whole image <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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">VOI region(s)</font>''</span>-To generate a histogram for the VOI region 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"> 5 Click OK. A progress message appears briefly. After a few moments, the Look-up Table window 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: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If there are no VOIs on the image, the Look-up Table window (Figure 16) 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"> 4 Choose 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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Whole image</font>''</span>-To generate a histogram for the whole image <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-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">VOI region(s)</font>''</span>-To generate a histogram for the VOI region 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"> 5 Click OK. A progress message appears briefly. After a few moments, the Look-up Table window appears (Figure 16).<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"> |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 16. Look-up Table window <br /></font>'''</div> |
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<div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Open LUT</font>''</span>-Opens a previously saved LUT file. LUT files have a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">.LUT</font>''</span> extension.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Save LUT</font>''</span>-Saves the LUT displayed in this window in a LUT file.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Open Transfer Functions</font>''</span>-Opens a previously saved transfer function. Transfer function files have a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">.FUN</font>''</span> extension.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Save Transfer Functions</font>''</span>-Saves the transfer function displayed in this window to a file.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Close LUT</font>''</span>-Closes the LUT window.</div> | <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Open LUT</font>''</span>-Opens a previously saved LUT file. LUT files have a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">.LUT</font>''</span> extension.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Save LUT</font>''</span>-Saves the LUT displayed in this window in a LUT file.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Open Transfer Functions</font>''</span>-Opens a previously saved transfer function. Transfer function files have a <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">.FUN</font>''</span> extension.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Save Transfer Functions</font>''</span>-Saves the transfer function displayed in this window to a file.</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">Close LUT</font>''</span>-Closes the LUT window.</div> | ||
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[[Image:windowLookupTable.jpg]] | [[Image:windowLookupTable.jpg]] | ||
− | + | <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><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><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><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><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><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> | |
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">LUT toolbar</font>'''</span></div> | <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">LUT toolbar</font>'''</span></div> | ||
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− | <div class="CellBody">Provides tools that allow you to manipulate the displayed image. Refer to | + | <div class="CellBody">Provides tools that allow you to manipulate the displayed image. Refer to Figure 19.</div> |
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The toolbar allows you to manipulate the displayed image. You can apply pseudocolor LUTs, adjust the image contrast with the transfer function, and apply preset window and level settings for CT slices. You can also edit the red, blue, green, and alpha channels of a LUT. | The toolbar allows you to manipulate the displayed image. You can apply pseudocolor LUTs, adjust the image contrast with the transfer function, and apply preset window and level settings for CT slices. You can also edit the red, blue, green, and alpha channels of a LUT. | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">look-up table (LUT)</font>'''</span>-Indicates the intensity of each voxel in the image and, in MIPAV, allows you to remap the original intensities to other intensities.<br /><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"><br />transfer function</font>'''</span>-Reflects the relationship between the original image intensity values and how they are mapped into the LUT. The line in the LUT represents the transfer function.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">Note:</font>'''</span> You can generate a histogram for two image datasets that are loaded together. In this case, the Look-up Table window ( | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">look-up table (LUT)</font>'''</span>-Indicates the intensity of each voxel in the image and, in MIPAV, allows you to remap the original intensities to other intensities.<br /><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000"><br />transfer function</font>'''</span>-Reflects the relationship between the original image intensity values and how they are mapped into the LUT. The line in the LUT represents the transfer function.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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">Note:</font>'''</span> You can generate a histogram for two image datasets that are loaded together. In this case, the Look-up Table window (Figure 17) shows two tabs-one for Image A and one for Image B.<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"> |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 17. Look-up Table window showing Image A and B histograms<br /></font>'''</div> |
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[[Image:windowLUTAlphablending2images.jpg]] | [[Image:windowLUTAlphablending2images.jpg]] | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 18. Change Number of Colors dialog box<br /></font>'''</div> |
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[[Image:ZeroBasedILUTChangeNumberofColors.jpg]] | [[Image:ZeroBasedILUTChangeNumberofColors.jpg]] | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 19. LUT toolbar<br /></font>'''</div> |
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[[Image:toolbarLUT.jpg]] | [[Image:toolbarLUT.jpg]] | ||
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The grayscale intensity values in the image dataset are remapped to color intensity values. | The grayscale intensity values in the image dataset are remapped to color intensity values. | ||
− | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To invert intensities</font>'''</span><br /></font>'''</div><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"> To invert the intensities so that a negative of the dataset appears, click [[Image:buttonInvertLUT.jpg]] , the Invert LUT icon. The Invert LUT icon is in both the Look-up Table window ( | + | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To invert intensities</font>'''</span><br /></font>'''</div><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"> To invert the intensities so that a negative of the dataset appears, click [[Image:buttonInvertLUT.jpg]] , the Invert LUT icon. The Invert LUT icon is in both the Look-up Table window (Figure 16) and the MIPAV window. Figure 19 shows the location of this icon in the Look-up Table window.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To apply CT level presets to images</font>'''</span><br /></font>'''</div> |
There are six CT window and level presets: abdomen, head, lung, mediastinum, spine, and vertebrae. To apply a preset level to the image, complete the following steps: | There are six CT window and level presets: abdomen, head, lung, mediastinum, spine, and vertebrae. To apply a preset level to the image, complete the following steps: | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 20. CT Presets dialog box<br /></font>'''</div> |
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[[Image:dialogboxCTPresets.jpg]] | [[Image:dialogboxCTPresets.jpg]] | ||
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==== Adjusting contrast using the transfer function ==== | ==== Adjusting contrast using the transfer function ==== | ||
− | <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"> The transfer function reflects the relationship between the original image intensity values and how they are mapped into the LUT. An example of how adjusting the transfer function affects the display of an image appears in Figure 16. In this example, the top image is generated by applying the linear transfer function (slope = 1) to produce display values that are evenly distributed over the range of the LUT (see | + | <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"> The transfer function reflects the relationship between the original image intensity values and how they are mapped into the LUT. An example of how adjusting the transfer function affects the display of an image appears in Figure 16. In this example, the top image is generated by applying the linear transfer function (slope = 1) to produce display values that are evenly distributed over the range of the LUT (see Figure 21A). This results, in this case, in a low-contrast image (see Figure 21B). The contrast of the image can be improved by adjusting the transfer function in a manner shown in Figure 21A (e.g., changing a low-contrast image into a high-contrast image). The image scalar values between -175 and 275 are remapped as a function of the modified transfer function and distributed across the full LUT range. The values above 275 are remapped to white and the values below -175 are remapped to black. The effect can be readily seen in Figure 21B.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To modify transfer functions</font>'''</span><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. The image appears in the default image window.<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 [[Image:iconLookupTable.jpg]] , the Displays Look-up Table (LUT) icon. The Look-up Table 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"> 3 Click the transfer function. A new node may appear.<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 Drag the node to the new location.<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: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> You can also adjust the transfer function for the alpha, red, green, and blue channels in an image. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 4pt; 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="#0000ff"> <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000"><br clear="all" /> |
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[[Image:MIPAV_VisualizationTools46.gif]] | [[Image:MIPAV_VisualizationTools46.gif]] | ||
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{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 21. An image before and after modifying the transfer function<br /></font>'''</div> |
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[[Image:exampleTransferFunctionSample.jpg]] | [[Image:exampleTransferFunctionSample.jpg]] | ||
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− | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To save transfer functions</font>'''</span><br /></font>'''</div><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"> To save a transfer function to a file, complete the following steps:<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 In the Look-up Table dialog box, select File > Save Transfer Functions ( | + | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To save transfer functions</font>'''</span><br /></font>'''</div><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"> To save a transfer function to a file, complete the following steps:<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 In the Look-up Table dialog box, select File > Save Transfer Functions (Figure 22) or press Ctrl S. The Save dialog box (Figure 23) appears.<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"> |
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 22. Open and Save commands in the File menu<br /></font>'''</div> |
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[[Image:menuFileLUTwindow.jpg]] | [[Image:menuFileLUTwindow.jpg]] | ||
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{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 23. Save dialog box<br /></font>'''</div> |
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[[Image:dialogboxSaveTransferFunction.jpg]] | [[Image:dialogboxSaveTransferFunction.jpg]] | ||
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− | <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 Save. The program saves the transfer function under the name you specified.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To apply previously saved transfer functions</font>'''</span><br /></font>'''</div><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"> To open a transfer function file and apply it to an image, complete the following steps:<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 File > Open Transfer Functions in the Look-up Table window. The Open dialog box 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"> 2 Select the desired file. LUT files have a <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">.fun</font></span> extension. <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 Open. The program applies the transfer functions file to the current image.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To save LUTs for later use</font>'''</span><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 File > Save LUT in the Look-up Table window, or press Ctrl S. The Save dialog 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"> 3 Click Save. The program saves the transfer function under the name you specified.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To apply previously saved transfer functions</font>'''</span><br /></font>'''</div><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"> To open a transfer function file and apply it to an image, complete the following steps:<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 File > Open Transfer Functions in the Look-up Table window. The Open dialog box 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"> 2 Select the desired file. LUT files have a <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">.fun</font></span> extension. <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 Open. The program applies the transfer functions file to the current image.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To save LUTs for later use</font>'''</span><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 File > Save LUT in the Look-up Table window, or press Ctrl S. The Save dialog box (Figure 24) appears.<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"> |
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
|+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 128. Save dialog box <br /></font>'''</div> | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 128. Save dialog box <br /></font>'''</div> | ||
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[[Image:dialogboxSaveLUT.jpg]] | [[Image:dialogboxSaveLUT.jpg]] | ||
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 25. Open dialog box<br /></font>'''</div> |
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[[Image:dialogboxopenLut.jpg]] | [[Image:dialogboxopenLut.jpg]] | ||
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− | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To open, save, and apply frequently used LUTs</font>'''</span><br /></font>'''</div><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"> For a LUT that you defined and expect to use frequently, MIPAV provides a simple method for saving, opening, and applying it without needing to use the commands on the File menu. You use two icons on the toolbar in the Look-up Table window:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [[Image:buttonSaveUserDefinedLUT.jpg]] , the Save User-Defined LUT icon, allows you to save the LUT.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [[Image:buttonOpenUserDefinedLUT.jpg]] , the Open User-Defined LUT icon, provides a very quick way of opening and applying the user-defined LUT<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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"><br clear="all" /> {| align="left" | [[Image:MIPAV_VisualizationTools59.gif]] |} <br clear="all" />Recommendation:</font>'''</span> Because these icons only apply to one user-defined LUT, it is recommended that you select the LUT that is used most frequently.<br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 8pt; 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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To reset original LUTs to images</font>'''</span><br /></font>'''</div><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"> Click [[Image:buttonGrayLut.jpg]] , the Grayscale icon in the Look-up Table window (refer to Figure 16 and Figure 19). Alternatively, you can click [[Image:iconResetLUT.jpg]] , the Reset LUT icon, in the MIPAV window.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To adjust the threshold</font>'''</span><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. The image appears in the default image window.<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 [[Image:iconLookupTable.jpg]] , the Displays Look-up Table (LUT) icon. The Look-up Table 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"> 3 Click [[Image:buttonDualThresholdFunction.jpg]] , the Dual threshold function icon. The Threshold icon becomes active and the transfer function of the histogram changes.<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 Algorithms > Threshold. The Threshold dialog box ( | + | <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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To open, save, and apply frequently used LUTs</font>'''</span><br /></font>'''</div><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"> For a LUT that you defined and expect to use frequently, MIPAV provides a simple method for saving, opening, and applying it without needing to use the commands on the File menu. You use two icons on the toolbar in the Look-up Table window:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [[Image:buttonSaveUserDefinedLUT.jpg]] , the Save User-Defined LUT icon, allows you to save the LUT.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: -24pt; text-transform: none; vertical-align: baseline"><font color="#000000"> [[Image:buttonOpenUserDefinedLUT.jpg]] , the Open User-Defined LUT icon, provides a very quick way of opening and applying the user-defined LUT<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; 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"><br clear="all" /> {| align="left" | [[Image:MIPAV_VisualizationTools59.gif]] |} <br clear="all" />Recommendation:</font>'''</span> Because these icons only apply to one user-defined LUT, it is recommended that you select the LUT that is used most frequently.<br /></font></div><div style="font-style: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 8pt; 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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To reset original LUTs to images</font>'''</span><br /></font>'''</div><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"> Click [[Image:buttonGrayLut.jpg]] , the Grayscale icon in the Look-up Table window (refer to Figure 16 and Figure 19). Alternatively, you can click [[Image:iconResetLUT.jpg]] , the Reset LUT icon, in the MIPAV window.<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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To adjust the threshold</font>'''</span><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. The image appears in the default image window.<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 [[Image:iconLookupTable.jpg]] , the Displays Look-up Table (LUT) icon. The Look-up Table 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"> 3 Click [[Image:buttonDualThresholdFunction.jpg]] , the Dual threshold function icon. The Threshold icon becomes active and the transfer function of the histogram changes.<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 Algorithms > Threshold. The Threshold dialog box (Figure 26) opens.<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"> |
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 26. Threshold dialog box <br /></font>'''</div> |
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<div class="CellBody">Threshold limit for the lowest image intensities.</div> | <div class="CellBody">Threshold limit for the lowest image intensities.</div> | ||
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<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 Complete the dialog box.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" /> | <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 Complete the dialog box.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 5pt; margin-left: 0pt; margin-right: 0pt; margin-top: 5pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" /> | ||
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[[Image:MIPAV_VisualizationTools68.gif]] | [[Image:MIPAV_VisualizationTools68.gif]] |
Revision as of 15:57, 13 February 2012
Changing image brightness and contrast using LUTs
To adjust the LUT, you open the Look-up Table window to modify the LUT's values and transfer function. However, you can use the Quick LUT icon to modify the LUT without opening the Look-up Table window. Quick LUT allows you to easily choose the highest and lowest values for the intensity levels in a user- defined area.
To do this, complete the following steps:
To generate a histogram, and view the LUT, complete the following steps:
File
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Open LUT-Opens a previously saved LUT file. LUT files have a .LUT extension. Save LUT-Saves the LUT displayed in this window in a LUT file. Open Transfer Functions-Opens a previously saved transfer function. Transfer function files have a .FUN extension. Save Transfer Functions-Saves the transfer function displayed in this window to a file. Close LUT-Closes the LUT window.
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Utilities
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Change number of colors-Allows you to change the number of colors displayed in the image. Valid values are 2 to 256.
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CT function-Allows you to select a preset LUT that is appropriate for the image content. Values are abdomen, head, lung, mediastinum, spine, and vertebrae. Invert LUT-Creates a negative of the image. Reset histogram and LUT A-Returns image A to its original values. Reset histogram and LUT B-Returns image B to its original values. This command is only available if two images are open.
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LUT toolbar
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Provides tools that allow you to manipulate the displayed image. Refer to Figure 19.
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Update (real-time)
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Changes the image as you make changes to the LUT, which allows you to see the effect of your changes immediately on the image.
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Log scale (histogram)
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Displays the image's histogram count in log scale along the Y axis.
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Interpolate image
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Displays image using interpolation, which reduces pixilated image to appear more smooth. Caution: Depending on the memory resources of your workstation, interpolation can be very lengthy.
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Number of colors
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Allows you to change the number of colors displayed in the image.
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LUT
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Displays the image intensities.
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The Look-up Table window consists of three sections: a menu bar, a toolbar, and one or more pages containing histograms. A tab appears for each image that is opened in the image window. For example, if only one image is in the image window, then only the Image A tab appears. If you generated the histogram for an image window that contains two images, a tab for Image A and a tab for Image B appear. Each of these tabbed pages contain a histogram for the applicable image. If you generated the histogram for a VOI, the window does not display a tab and only the applicable icons and buttons in the toolbar appear.
The toolbar allows you to manipulate the displayed image. You can apply pseudocolor LUTs, adjust the image contrast with the transfer function, and apply preset window and level settings for CT slices. You can also edit the red, blue, green, and alpha channels of a LUT.
transfer function-Reflects the relationship between the original image intensity values and how they are mapped into the LUT. The line in the LUT represents the transfer function.
When you modify the LUT, be sure to select the Update (real time) check box. The image in the image window is then updated in real time.
Applying predefined LUTs to images
To apply a pseudocolor LUT, click one of the following icons:
The grayscale intensity values in the image dataset are remapped to color intensity values.
There are six CT window and level presets: abdomen, head, lung, mediastinum, spine, and vertebrae. To apply a preset level to the image, complete the following steps:
Adjusting contrast using the transfer function
Example: You might want to use these icons to highlight certain intensities in a particular color.
{| align="left" | File:MIPAV VisualizationTools59.gif |}
Recommendation: Because these icons only apply to one user-defined LUT, it is recommended that you select the LUT that is used most frequently.
Set lower limits between (1.0-3774.0)
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Threshold limit for the lowest image intensities.
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Set threshold between (1258.3334-3774.0)
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Threshold limit for the highest image intensities.
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Produce binary image
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Produces a binary image (Boolean).
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Set values outside of limits to
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Specifies the intensity value to assign to values outside the threshold limits.
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New image
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Shows the results of the algorithm in a new image window
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Replace image
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Replaces the current active image with the results of the algorithm.
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Whole image
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Applies the algorithm to the whole image.
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VOI regions
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Applies the algorithm to the volumes (regions) delineated by the VOIs.
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OK
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Applies the changes you made in this dialog box and closes the dialog box.
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Cancel
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Disregards any changes you made in this dialog box, closes the dialog box, and does not change the threshold.
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Help
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Displays online help for this dialog box.
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Note: You can choose to generate a binary image (Boolean) by selecting the Produce binary Image check box. Alternatively, you can clear the binary option and enter a threshold value. If you still want to generate a Boolean image, select the check box again. Note that, if you generate a Boolean image, MIPAV does not allow you to reapply the threshold or to generate either a histogram or LUT for a Boolean image.
Visualizing Images: Displaying images using the animate view