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| − | | + | 1 Select a segmented image that was produced in task 5.<br /> |
| − | <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: 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 a segmented image that was produced in task 5.<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 VOI > Statistics Generator in the main MIPAV window. The Calculate Statistics on VOI Groups window opens and displays the VOI Selection page ([TechGuide_MappingBrainsTalairach.html#1222067 Figure 55 on page 49]).<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"> The VOI group list on the left of the window lists all of the VOIs that are in 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"> 3 Make sure that the path and file name listed in VOI Statistic File Destination is correct. The path indicates where MIPAV should place the statistics file; the file name is the name of the statistics file.<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"> To change the path and file name, do either 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"> Click Browse to navigate to the correct directory and file name.<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"> Type the correct path and file name over the current path and file name.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Select the VOIs in the VOI group list on which you want to generate statistics ([TechGuide_MappingBrainsTalairach.html#1222067 Figure 55]).<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 the right arrow. MIPAV moves the selected VOIs to the list on the right ([TechGuide_MappingBrainsTalairach.html#1222067 Figure 55]).<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 Select the Statistics Options tab. The Statistics Options page ([TechGuide_MappingBrainsTalairach.html#1222077 Figure 56 on page 49]) 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"> 7 Select the statistics that you want to be generated in Statistics to Calculate list. <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"> To select all of the statistics, click Select 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"> 8 Select Exclude pixels from calculation.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 9 Change the value of Exclude Pixels from Between to Outside.<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">
| + | 2 Select VOI > Statistics Generator in the main MIPAV window. The Calculate Statistics on VOI Groups window opens and displays the VOI Selection page (Figure 1).<br />The VOI group list on the left of the window lists all of the VOIs that are in the image.<br /> |
| | + | 3 Make sure that the path and file name listed in VOI Statistic File Destination is correct. The path indicates where MIPAV should place the statistics file; the file name is the name of the statistics file.<br /> To change the path and file name, do either of the following:<br /> |
| | + | *Click Browse to navigate to the correct directory and file name.<br /> |
| | + | *Type the correct path and file name over the current path and file name.<br /> |
| | + | 4 Select the VOIs in the VOI group list on which you want to generate statistics (Figure 1).<br /> |
| | + | 5 Click the right arrow. MIPAV moves the selected VOIs to the list on the right (Figure 1).<br /> |
| | + | 6 Select the Statistics Options tab. The Statistics Options page (Figure 2) opens.<br /> |
| | + | 7 Select the statistics that you want to be generated in Statistics to Calculate list. <br /> |
| | + | 8 Select Exclude pixels from calculation.<br /> |
| | + | 9 Change the value of Exclude Pixels from Between to Outside.<br /> |
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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 55. Calculate Statistics on VOI Groups window showing four VOIs that were moved to the right list<br /></font>'''</div> | + | |+ '''Figure 1. Calculate Statistics on VOI Groups window showing four VOIs that were moved to the right list''' |
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| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />{| align="center"
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| | [[Image:exampleTalairachStatisticsOneVOI.jpg]] | | [[Image:exampleTalairachStatisticsOneVOI.jpg]] |
| − | |}<br clear="all" /><br /></font></div>
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| | |} | | |} |
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| − | <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 /> |
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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 56. Statistics Options page in the Calculate Statistics on VOI Groups window<br /></font>'''</div> | + | |+ '''Figure 2. Statistics Options page in the Calculate Statistics on VOI Groups window''' |
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| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />{| align="center"
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| | [[Image:exampleTalairachStatisticsOptionsPage.jpg]] | | [[Image:exampleTalairachStatisticsOptionsPage.jpg]] |
| − | |}<br clear="all" /><br /></font></div>
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| | |} | | |} |
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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"> 10 Insert the range of pixels that you want to exclude in the boxes. <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"> To check the intensity level of the pixels in the image, click on any point within one of the VOIs ([TechGuide_MappingBrainsTalairach.html#1257324 Figure 57]). MIPAV displays the intensity level at that point on the left bottom of the MIPAV main window.<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 /> To check the intensity level of the pixels in the image, click on any point within one of the VOIs (Figure 3). MIPAV displays the intensity level at that point on the left bottom of the MIPAV main window.<br /> |
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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 57. Finding the intensity level <br /></font>'''</div> | + | |+ '''Figure 3. Finding the intensity level''' |
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| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />{| align="center"
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| | [[Image:exampleTalairachIntensityLevel.gif]] | | [[Image:exampleTalairachIntensityLevel.gif]] |
| − | |}<br clear="all" /><br /></font></div>
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| | |} | | |} |
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| − | <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="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Example:</font>'''</span> If the intensity level of the gray matter is 2, exclude pixels outside the range 1.5-2.5 or 1.9-2.1.<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"> 11 Click Calculate.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> The Logging page ([TechGuide_MappingBrainsTalairach.html#1222087 Figure 58 on page 51]) opens showing a table of the statistics.<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> If a message appears asking you whether to overwrite the file, refer to [TechGuide_MappingBrainsTalairach.html#1222092 "Overwriting the VOI Statistics File" on page 51].<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 />'''Example:''' If the intensity level of the gray matter is 2, exclude pixels outside the range 1.5-2.5 or 1.9-2.1.<br /> |
| | + | The Logging page (Figure 4) opens showing a table of the statistics.<br /> |
| | + | '''Note:'''If a message appears asking you whether to overwrite the file, refer to "Overwriting the VOI Statistics File".<br /> |
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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 58. Logging page in the Calculate Statistics on VOI Groups window showing a table of the generated statistics<br /></font>'''</div> | + | |+ '''Figure 4. Logging page in the Calculate Statistics on VOI Groups window showing a table of the generated statistics''' |
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| − | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 1pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br clear="all" />{| align="center"
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| | [[Image:exampleTalairachStatisticsContours.jpg]] | | [[Image:exampleTalairachStatisticsContours.jpg]] |
| − | |}<br clear="all" /><br /></font></div>
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| − | <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: 1pt; margin-left: 0pt; margin-right: 0pt; margin-top: 17pt; text-align: center; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Overwriting the VOI Statistics File<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> If statistics were written to the statistics file in the past, a message may appear asking whether to overwrite the previous statistics table.<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 clear="all" />{| align="center"
| + | '''Overwriting the VOI Statistics File''' If statistics were written to the statistics file in the past, a message may appear asking whether to overwrite the previous statistics table.<br /> |
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| | [[Image:messageTalairachOverwriteStatisticsFile.jpg]] | | [[Image:messageTalairachOverwriteStatisticsFile.jpg]] |
| − | |}<br clear="all" /><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To overwrite the file</font>'''</span>, click Overwrite.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To cancel</font>'''</span>, click Cancel, and change the file name in VOI Statistic File Destination on the VOI Selection page.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To always overwrite the statistics file</font>'''</span>, either select Options > Overwrite file automatically or press Alt O.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">To clear the Logging page</font>'''</span>, either select Options > Clear Log Window or press Alt C.<br /></font></div> | + | |- |
| | + | |rowspan "1" colspan "2"| |
| | + | '''To overwrite the file''', click Overwrite.<br /> |
| | + | '''To cancel''', click Cancel, and change the file name in VOI Statistic File Destination on the VOI Selection page.<br /> |
| | + | '''To always overwrite the statistics file''', either select Options > Overwrite file automatically or press Alt O.<br /> |
| | + | '''To clear the Logging page''', either select Options > Clear Log Window or press Alt C.<br /> |
| | |} | | |} |
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| | [[Viewing the Talairach grid on Talairach images]] | | [[Viewing the Talairach grid on Talairach images]] |
1 Select a segmented image that was produced in task 5.
2 Select VOI > Statistics Generator in the main MIPAV window. The Calculate Statistics on VOI Groups window opens and displays the VOI Selection page (Figure 1).
The VOI group list on the left of the window lists all of the VOIs that are in the image.
3 Make sure that the path and file name listed in VOI Statistic File Destination is correct. The path indicates where MIPAV should place the statistics file; the file name is the name of the statistics file.
To change the path and file name, do either of the following:
4 Select the VOIs in the VOI group list on which you want to generate statistics (Figure 1).
5 Click the right arrow. MIPAV moves the selected VOIs to the list on the right (Figure 1).
6 Select the Statistics Options tab. The Statistics Options page (Figure 2) opens.
7 Select the statistics that you want to be generated in Statistics to Calculate list.
8 Select Exclude pixels from calculation.
9 Change the value of Exclude Pixels from Between to Outside.
