Difference between revisions of "Visualizing Images: Displaying images using the default view:Changing image brightness and contrast using LUTs"
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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" /> | + | <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" /> [[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"> |
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Revision as of 16:04, 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.
To change the number of intensities displayed in the LUT</font></span></font></div>
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.
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