Correcting image spacing and Generating graphs: Difference between pages

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The Correct Image Spacing command on the Utilities menu corrects images in which slice thickness and slice spacing are unequal, which may distort images. To understand how this problem can occur, the following section presents some background information.<br />
MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"<br />


<div id="UnderstandingContiguousPlanes"><div>
=== Generating contour VOI graphs ===
== Understanding contiguous planes' effect on image scanning ==
Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs. <br />
Image scanning is usually done in contiguous planes. For example, if the first slice is centered at position 5.0 and the slices are 2 mm thick, the second slice is centered at 7.0. In such a case, the slice thickness, 2, and the slice spacing, 2, are equal. There are, however, two scenarios when the slice spacing does not equal the slice thickness:<br />
* '''Slice spacing is less than the slice thickness''' -In this case, although the images are, for example, 2 mm thick, they are spaced only 1 mm apart (Figure 13). This scenario arises when the ZIP x 2 feature is used during MRI scanning, which enables the acquisition of slices only 1 mm apart but uses signals from a 2-mm slab to increase the signal-to-noise ratio.<br />
* '''Slice spacing is greater than the slice thickness''' -This scenario (Figure 13), which is more common than the first, occurs when the operator chooses to acquire images at intervals greater than the slice thickness (i.e., there is a gap between successive image slices) in order to cover a deeper field of view.<br />


MIPAV assumes that successive images are contiguous. So, for example, if users chose the triplanar view to display an image that had slice spacing larger than slice thickness, the image would appear shortened in the out-of-plane direction. The Correct Image Spacing utility corrects both situations in which the slice thickness and spacing are not equal. Once the correction is applied, the slice thickness and slice spacing for the given image dataset are the same.
'''To generate 2D contour VOI graphs'''<br />
 
<div id="UnderstandingImageSpacing"><div>
== Understanding how MIPAV solves the image spacing problem ==
When the spacing between slices is ''less'' than the slice thickness, the Correct Image Spacing utility assigns the slice spacing to the slice thickness (refer to Figure 13 for triplanar views before and after correction). When the slice spacing is ''larger'' than the slice thickness (refer to Figure 13 for triplanar views before and after correction), the utility inserts blank slices between the existing images. <br />
 
Since all slices within an image volume must have the same slice thickness, in many cases more than one slice must be inserted and the original images must be repeated so that a new value can be found for the slice thickness that fits evenly into the original slice spacing. Since there are an infinite number of combinations of slice spacing and thickness, not all could be handled. Table 2 displays the most common combinations and the algorithms MIPAV uses for handling them.
 
''T'' = Original slice thickness<br />
''S'' = Original space between slices<br /
''G'' = Gap = ''S'' - ''T''<br />
''M'' = Number of original images<br />
''O'' = Original image set origin<br />
''N'' = New slice thickness<br />
 
To use the Correct Image Spacing utility, DICOM images must first be saved in XML format. The following DICOM tags (Figure 13) are used:
(0018, 0050) Slice Thickness<br />
(0018, 0088) Spacing Between Slices<br />
 
You can also find this information listed in the Essential Image Information section of the image header (Figure 13) as Pixel resolution 2 (i.e., slice thickness) and Slice Spacing.
 
<div id="ViewImageAttributes"><div>
<div id="ImageAttributes"><div>
=== To view and edit image attributes ===
1 Open an image.<br />
1 Open an image.<br />
2 Select one of the tabs - Image Attributes &gt; General, or Image Attributes &gt;Orientation/Origin, or Image Attributes &gt; Transformation matrix.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br />
3 In the Transformation matrix tab find values for Pixel resolution 2 and Slice Spacing, or find the values of the DICOM tags Slice Thickness and Spacing Between Slices.<br />
 
[[File:ImageAttributesDialogBox.jpg |frame|center|Image Attributes dialog box]]
 
 
 
<div id="SaveDicomXml"><div>
 
=== To save DICOM images as XML files ===
 
The Correct Image Spacing utility works only on XML files.<br />
1 Open the DICOM image.<br />
2 Select File &gt; Save Image as in the MIPAV window. The Open dialog box appears.<br />
3 Type the name for the file including the XML extension in File Name.<br />
4 The Select DICOM tags to convert to XML dialog box opens.<br />
5 In the left dialog box window, select tags which you would like to convert to XML. Use the CTRL right mouse button combination of keys to select multiple tags. Then, use the arrows to move selected tags to the right window. See Figure 14 for more information.<br />
6 Press Save to save the file.<br />




{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Figure 14. Saving a DICOM image as an XML file'''
|+ '''Figure 10. Contour VOI Graph window '''
|-
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[[Image:windowContourVOIGraph.jpg]]
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></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">Open Graph</font>'''</span>-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </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">Save Graph</font>'''</span>-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</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">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</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">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</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">Edit</font>'''</span></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">Delete Function</font>'''</span>-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.</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">Copy Function</font>'''</span>-Copies a function that is currently displayed in the window.</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">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</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">Views</font>'''</span></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">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</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">Reset Range to Default</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span></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">Reset Graph to Original</font>'''</span>-<span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">[TBD]</font>'''</span>. </div>
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[[Image:SelectDICOMTAGS.jpg]]
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></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">Help Topics</font>'''</span>-Displays online help topics.</div>
|}
|}


<div id="SaveOtherXml"><div>
<br />
=== To save other images as XML files ===
3 Select the VOI. <br />
The Correct Image Spacing utility works only on XML files.<br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
1 Open the image that has spacing problems if you have not already done so.<br />
*To Next Slice<br />
2 Select File &gt; Save Image as in the MIPAV window. The Open dialog box appears.<br />
*To Previous Slice<br />
3 Type the name for the file including the XML extension in File Name.<br />
*To All Slices<br />
4 Select Medical, which includes XML files, in Files of Type.<br />
4 Do one of the following:<br />
5 Click OK. The Save Range of Slices dialog box appears. Complete the dialog box and press OK. See Figure 15.<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window. <br />
6 The program saves the image as an XML file.<br />
*Right click on the VOI and then select Graph &gt; Boundary Intensity.<br />
*The Contour VOI Graph window (Figure 10) opens.<br />


'''To generate 3D contour VOI graphs'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window. <br />
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
*Select VOI &gt; Graph &gt; Boundary Intensity in the MIPAV window.<br />
*Right-click on the VOI and then select Graph &gt; Boundary Intensity. <br />
The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary. <br />
=== Generating intensity graphs ===
Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).<br />
'''To generate 2D intensity graphs'''<br />
1 Open an image.<br />
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.<br /><
3 Select the VOI. <br />
As an option, copy the VOI to other slices in the dataset by selecting VOI &gt; Propagate and one of the following commands:<br />
*To Next Slice<br />
*To Previous Slice<br />
*To All Slices<br />
4 Do one of the following:<br />
Select VOI &gt; Graph in the MIPAV window and either of the following:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the VOI region. <br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
Right-click on the VOI and then select Graph and one of the following commands:<br />
* ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
* ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
* ''2.5D Total Intensity with Threshold'' -TBD. <br />
* ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.


{| border="1" cellpadding="5"
{| border="1" cellpadding="5"
|+ '''Figure 15. The Save Range of Slices dialog box options '''
|+ '''Figure 11. Intensity Graph window '''
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<div class="CellBody">General Options</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">Save image slices to separate files</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File</font>'''</span></div>
|
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<div class="CellBody">If checked, allows to save the image slices as separate files. The slices will be saved as files with the file name contains the name of the original image followed by the slice number specified by a user, e.g. <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">patientX001</font></span>. Here <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">patientX</font></span> is the name of the original image and <span style="font-style: normal; font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline"><font color="#000000">001</font></span> is the number of the slice. Refer to [MIPAV_Utilities.html#1169544 "Understanding contiguous planes' effect on image scanning" on page 423].</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Open Graph</font>'''</span>-Opens a PLT file that contains graph data.</div> <div class="CellBody">When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears. </div>
| rowspan="2" colspan="1" |
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[[Image:SaveRangeofSlicesa.jpg]]
[[Image:VOIGRaphMOdifyPointsVis.jpg]]
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<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">First File Starting Number</font>'''</span></div> <div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">File Name Number of Digits</font>'''</span></div>
<div class="CellBody"> </div>
|
|
<div class="CellBody">Set the start counter number and how many digits will appear in the counter number. </div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Save Graph</font>'''</span>-Saves the graph data in a PLT file. </div> <div class="CellBody">When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.</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">Choose Range of Slices to Save</font>'''</span></div>
|-
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<div class="CellBody">First Slice</div>
<div class="CellBody"> </div>
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| rowspan="1" colspan="2" |
<div class="CellBody">Specify the number of the first slice.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Print Graph</font>'''</span>-Allows you to print the graph. When you select this command or press <br />Ctrl P, the Print dialog box opens.</div>
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<div class="CellBody">Last Slice</div>
<div class="CellBody"> </div>
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| rowspan="1" colspan="2" |
<div class="CellBody">Specify the number of the last slice.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Close Graph</font>'''</span>-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.</div>
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<div class="CellBody">Choose Range of Time Periods to Save</div>
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<div class="CellBody">First Time period</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Edit</font>'''</span></div>
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<div class="CellBody">Specify the first time period.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Delete Function</font>'''</span>-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.</div>
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<div class="CellBody">Last Time Period</div>
<div class="CellBody"> </div>
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<div class="CellBody">Specify the last time period.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Paste Function</font>'''</span>-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.</div>
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<div class="CellBody">TIFF options</div>
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<div class="CellBody">Save with packed bit compression</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Views</font>'''</span></div>
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<div class="CellBody">Packed bit compression uses a single control byte to indicate how the next byte or series of bytes will be used. The high bit in the control byte indicates if the following byte or bytes should be a used as a series or should be used as individual bytes. The remaining 7 bits indicate the number of bytes that are indicated in the control byte.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Modify Graph Features</font>'''</span>-Allows you to customize the appearance of the graph.</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">OK</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Applies the changes you made in this dialog box, saves the image as a range of slices, and closes the dialog box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Range to Default</font>'''</span>-TBD.</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">Cancel</font>'''</span></div>
<div class="CellBody"> </div>
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<div class="CellBody">Disregards any changes you made in this dialog box, closes the dialog box, and does not save the image as a range of slices.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Reset Graph to Original</font>'''</span>-TBD.</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">Help</font>'''</span></div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help</font>'''</span></div>
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<div class="CellBody">Displays online help for this dialog box.</div>
<div class="CellBody"><span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Help Topics</font>'''</span>-Displays online help topics.</div>
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<div id="CorrectImageSpacing"><div>
'''To generate 3D intensity graphs of all slices in a dataset at a specific point'''<br />
=== To correct image spacing ===
1 Open an image.<br />
2 Draw a point VOI on the image (Figure 12).<br />
3 Select the VOI.<br />
4 Do one of the following:<br />
*Select the Propagate VOI to all slices icon.<br />
*Select VOI &gt; Propagate &gt; To All Slices. <br />
*Right-click on the VOI, then select Propagate &gt; To All Slices (Figure 12).<br />
5 Right-click on the VOI and select Show VOI Graph (Figure 12).<br />
 
{| border="1" cellpadding="5"
|+ '''Figure 12. Point VOI'''
|-
|
<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 clear="all" />


1 Open the image that contains spacing problems. <br />
{|
<br clear="all" />To determine whether images contain spacing problems, remember to view them using the triplanar view or to view the header file.<br />
|
2 Save the image as an XML file.<br />
[[Image:PointVOIPropagate.jpg]]
3 Select Utility &gt; Correct Image Spacing. <br />
|}
*If the image file does have spacing problems, then the program runs the utility. <br />
 
*If the image spacing is correct, the program displays a message indicating that the spacing is correct.<br />
'''To generate 3D intensity graphs of specific areas'''<br />
1 Open an image.<br />
2 Delineate a VOI on the image using the 3D rectangular VOI icon.<br />
3 Select the VOI. Then, do one of the following:<br />
*a Select VOI &gt; Graph and either of the following in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
*b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:<br />
** ''2.5D Total Intensity'' -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.<br />
** ''2.5D Average Intensity'' -To generate a graph of the average of the intensity values of the VOI region.<br />
** ''2.5D Total Intensity with Threshold'' -TBD.<br />
** ''2.5D Average Intensity with Threshold'' -TBD.<br />
The Intensity Graph window (Figure 11) opens.<br />


[[Cropping images]]


[[Category:Help]]
[[Customizing the appearance of graphs - Modify graph dialog box]]

Revision as of 20:22, 21 February 2012

MIPAV allows you to generate intensity profiles, or contour VOI graphs, for VOI contours. For delineated VOIs, you can generate 2D, 3D, or 4D intensity graphs. You can also generate a 3D intensity graph at a specific point across all slices in a dataset. For information on how to contour a VOI, refer to Chapter 1, "Segmenting Images Using Contours and Masks,"

Generating contour VOI graphs

Contour VOI graphs display the intensity values of the selected contour's boundary in the Contour VOI Graph window (Figure 10). You can generate either 2D or 3D contour VOI graphs.

To generate 2D contour VOI graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.


Figure 10. Contour VOI Graph window

WindowContourVOIGraph.jpg

File
Open Graph-Opens a PLT file that contains graph data. When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.
Save Graph-Saves the graph data in a PLT file. When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete a specific function. However, you cannot delete a function if it is the only function displayed in the window.
Copy Function-Copies a function that is currently displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-[TBD]
Reset Graph to Original-[TBD].
Help
Help Topics-Displays online help topics.


3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right click on the VOI and then select Graph > Boundary Intensity.
  • The Contour VOI Graph window (Figure 10) opens.

To generate 3D contour VOI graphs
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon, in the MIPAV window.
3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:

  • Select VOI > Graph > Boundary Intensity in the MIPAV window.
  • Right-click on the VOI and then select Graph > Boundary Intensity.

The Contour VOI Graph window (Figure 10) opens. This window displays a graph of the intensity values of the selected contour's boundary.

Generating intensity graphs

Intensity profiles, or graphs, present information on the intensity values of the VOI region in an image. The intensity graph appears in the Intensity Graph window (Figure 11).

To generate 2D intensity graphs
1 Open an image.
2 Delineate a 2D VOI on the image using one of the 2D icons in the MIPAV window.
< 3 Select the VOI.
As an option, copy the VOI to other slices in the dataset by selecting VOI > Propagate and one of the following commands:

  • To Next Slice
  • To Previous Slice
  • To All Slices

4 Do one of the following:
Select VOI > Graph in the MIPAV window and either of the following:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the VOI region.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.

Right-click on the VOI and then select Graph and one of the following commands:

  • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
  • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • 2.5D Total Intensity with Threshold -TBD.
  • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.

Figure 11. Intensity Graph window
File
Open Graph-Opens a PLT file that contains graph data.
When you select this command or press Ctrl O on the keyboard, the Open Graph Data dialog box appears.

VOIGRaphMOdifyPointsVis.jpg

Save Graph-Saves the graph data in a PLT file.
When you select this command or when you press Ctrl S on the keyboard, the Save dialog box opens.
Print Graph-Allows you to print the graph. When you select this command or press
Ctrl P, the Print dialog box opens.
Close Graph-Closes the Intensity Graph window. To close the window, you can also press Ctrl X on the keyboard.
Edit
Delete Function-Allows you to delete the function that you select. However, you cannot delete a function if it is the only function displayed in the window.
Paste Function-Pastes a previously copied function into the window. The pasted function has a different color than the first function displayed in the window.
Views
Modify Graph Features-Allows you to customize the appearance of the graph.
Reset Range to Default-TBD.
Reset Graph to Original-TBD.
Help
Help Topics-Displays online help topics.

To generate 3D intensity graphs of all slices in a dataset at a specific point
1 Open an image.
2 Draw a point VOI on the image (Figure 12).
3 Select the VOI.
4 Do one of the following:

  • Select the Propagate VOI to all slices icon.
  • Select VOI > Propagate > To All Slices.
  • Right-click on the VOI, then select Propagate > To All Slices (Figure 12).

5 Right-click on the VOI and select Show VOI Graph (Figure 12).

Figure 12. Point VOI


PointVOIPropagate.jpg

To generate 3D intensity graphs of specific areas
1 Open an image.
2 Delineate a VOI on the image using the 3D rectangular VOI icon.
3 Select the VOI. Then, do one of the following:

  • a Select VOI > Graph and either of the following in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
  • b Right-click the VOI, and then select Graph and one of the following commands in the MIPAV window:
    • 2.5D Total Intensity -To generate a graph of the sum of the intensity values of the area delineated by the VOI per slice.
    • 2.5D Average Intensity -To generate a graph of the average of the intensity values of the VOI region.
    • 2.5D Total Intensity with Threshold -TBD.
    • 2.5D Average Intensity with Threshold -TBD.

The Intensity Graph window (Figure 11) opens.


Customizing the appearance of graphs - Modify graph dialog box

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