Difference between revisions of "Correcting image spacing"
(→Understanding contiguous planes' effect on image scanning) |
(→Understanding how MIPAV solves the image spacing problem) |
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==== Understanding how MIPAV solves the image spacing problem ==== | ==== Understanding how MIPAV solves the image spacing problem ==== | ||
− | <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"> When the spacing between slices is <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">less</font>''</span> than the slice thickness, the Correct Image Spacing utility assigns the slice spacing to the slice thickness (refer to [MIPAV_Utilities.html#1169929 Figure 233 on page 427] for triplanar views before and after correction). When the slice spacing is <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">larger</font>''</span> than the slice thickness (refer to | + | <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"> When the spacing between slices is <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">less</font>''</span> than the slice thickness, the Correct Image Spacing utility assigns the slice spacing to the slice thickness (refer to [MIPAV_Utilities.html#1169929 Figure 233 on page 427] for triplanar views before and after correction). When the slice spacing is <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">larger</font>''</span> 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 /></font></div> |
− | 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. | + | 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. |
<div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">T</font>''</span> = Original slice thickness<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">S</font>''</span> = Original space between slices<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">G</font>''</span> = Gap = <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">S</font>''</span> - <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">T</font>''</span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">M</font>''</span> = Number of original images<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">O</font>''</span> = Original image set origin<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">N</font>''</span> = New slice thickness<br /></font></div> | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">T</font>''</span> = Original slice thickness<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">S</font>''</span> = Original space between slices<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">G</font>''</span> = Gap = <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">S</font>''</span> - <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">T</font>''</span><br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">M</font>''</span> = Number of original images<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">O</font>''</span> = Original image set origin<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 24pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: 0pt; 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">N</font>''</span> = New slice thickness<br /></font></div> | ||
− | To use the Correct Image Spacing utility, DICOM images must first be saved in XML format. The following DICOM tags ( | + | To use the Correct Image Spacing utility, DICOM images must first be saved in XML format. The following DICOM tags (Figure 13) are used: |
<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"> (0018, 0050) Slice Thickness<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"> (0018, 0088) Spacing Between Slices<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"> (0018, 0050) Slice Thickness<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"> (0018, 0088) Spacing Between Slices<br /></font></div> | ||
− | You can also find this information listed in the Essential Image Information section of the image header ( | + | 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 style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To view image attributes<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open an image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Select Image > Attributes > View Header. The Header dialog box ( | + | <div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To view image attributes<br /></font>'''</div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open an image.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Select Image > Attributes > View Header. The Header dialog box (Figure 13) 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 Find the tags under Essential Image Information to find the values for Pixel resolution 2 and Slice Spacing, or find the values of the DICOM tags Slice Thickness and Spacing Between Slices.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 600pt; 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"> . |
{| border="1" cellpadding="5" | {| border="1" cellpadding="5" | ||
− | |+ <div class="TableTitle">Table | + | |+ <div class="TableTitle">Table 2. Solutions for correct image spacing </div> |
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<div class="CellBody">don't handle, give message</div> | <div class="CellBody">don't handle, give message</div> | ||
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− | <div class="CellBody"> | + | <div class="CellBody"> </div> |
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− | <div class="CellBody"> | + | <div class="CellBody"> </div> |
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| rowspan="1" colspan="2" | | | rowspan="1" colspan="2" | | ||
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<div class="CellBody">Â </div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">G</font>''</span> = Gap = <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">S</font>''</span> - <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">T</font>''</span></div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">M</font>''</span> = Number of original images</div> | <div class="CellBody">Â </div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">G</font>''</span> = Gap = <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">S</font>''</span> - <span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">T</font>''</span></div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">M</font>''</span> = Number of original images</div> | ||
| rowspan="1" colspan="2" | | | rowspan="1" colspan="2" | | ||
− | <div class="CellBody"> | + | <div class="CellBody"> </div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">O</font>''</span> = Original image set origin</div> <div class="CellBody"><span style="font-weight: normal; text-decoration: none; text-transform: none; vertical-align: baseline">''<font color="#000000">N = </font>''</span>New slice thickness</div> |
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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 233. Views of the Header dialog box showing the tags listed under (A) Essential Image Information and (B) the DICOM tags in a later section of the header <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 233. Views of the Header dialog box showing the tags listed under (A) Essential Image Information and (B) the DICOM tags in a later section of the header <br /></font>'''</div> | ||
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[[Image:dialogboxViewHeaderDICOMtags.jpg]] | [[Image:dialogboxViewHeaderDICOMtags.jpg]] | ||
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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; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To save DICOM images as XML files<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"> The Correct Image Spacing utility works only on XML files.<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 the DICOM 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 Select File > Save Image as in the MIPAV 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"> 3 Type the name for the file including the XML extension in 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 The Select DICOM tags to convert to XML 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"> 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 | + | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To save DICOM images as XML files<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"> The Correct Image Spacing utility works only on XML files.<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 the DICOM 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 Select File > Save Image as in the MIPAV 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"> 3 Type the name for the file including the XML extension in 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 The Select DICOM tags to convert to XML 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"> 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 /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 6 Press Save to save the file.<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 14. Saving a DICOM image as an XML file<br /></font>'''</div> |
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[[Image:SelectDICOMTAGS.jpg]] | [[Image:SelectDICOMTAGS.jpg]] | ||
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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; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To save other images as XML files<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"> The Correct Image Spacing utility works only on XML files.<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 the image that has spacing problems if you have not already done so.<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 File > Save Image as in the MIPAV 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"> 3 Type the name for the file including the XML extension in 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 Medical, which includes XML files, in Files of Type.<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. The Save Range of Slices dialog box appears. Complete the dialog box and press OK. See | + | <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <br /></font></div><div style="font-style: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 14pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> To save other images as XML files<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"> The Correct Image Spacing utility works only on XML files.<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 the image that has spacing problems if you have not already done so.<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 File > Save Image as in the MIPAV 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"> 3 Type the name for the file including the XML extension in 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 Medical, which includes XML files, in Files of Type.<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. The Save Range of Slices dialog box appears. Complete the dialog box and press OK. See Figure 15.<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 The program saves the image as an XML file.<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"> |
{| 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 15. The Save Range of Slices dialog box options <br /></font>'''</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">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> | ||
| rowspan="2" colspan="1" | | | rowspan="2" colspan="1" | | ||
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[[Image:SaveRangeofSlicesa.jpg]] | [[Image:SaveRangeofSlicesa.jpg]] | ||
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<div class="CellBody">Displays online help for this dialog box.</div> | <div class="CellBody">Displays online help for this dialog box.</div> | ||
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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"> To correct image spacing<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 the image that contains spacing problems. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Tip:</font>'''</span><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"> To correct image spacing<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 the image that contains spacing problems. <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 7pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Tip:</font>'''</span><br clear="all" /> | ||
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[[Image:MIPAV_Utilities23.gif]] | [[Image:MIPAV_Utilities23.gif]] |
Revision as of 17:29, 15 February 2012
Correcting image spacing
Understanding contiguous planes' effect on image scanning
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.
Understanding how MIPAV solves the image spacing problem
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.
To use the Correct Image Spacing utility, DICOM images must first be saved in XML format. The following DICOM tags (Figure 13) are used:
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.
Case
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New slice thickness (N)
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Number of images in new set for each original image
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Number of blanks inserted for each original image
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Total images in set now
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New image set origin File:MIPAV Utilities24.gif
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2
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else
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don't handle, give message
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Legend: T = Original slice thickness S = Original space between slices
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 G = Gap = S - T M = Number of original images
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O = Original image set origin N = New slice thickness
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General Options
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Save image slices to separate files
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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. patientX001. Here patientX is the name of the original image and 001 is the number of the slice. Refer to [MIPAV_Utilities.html#1169544 "Understanding contiguous planes' effect on image scanning" on page 423].
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First File Starting Number File Name Number of Digits
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Set the start counter number and how many digits will appear in the counter number.
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Choose Range of Slices to Save
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First Slice
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Specify the number of the first slice.
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Last Slice
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Specify the number of the last slice.
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Choose Range of Time Periods to Save
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First Time period
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Specify the first time period.
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Last Time Period
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Specify the last time period.
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TIFF options
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Save with packed bit compression
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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.
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OK
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Applies the changes you made in this dialog box, saves the image as a range of slices, 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 save the image as a range of slices.
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Help
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Displays online help for this dialog box.
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To determine whether images contain spacing problems, remember to view them using the triplanar view or to view the header file.