Difference between revisions of "Correcting image spacing"
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==== Understanding contiguous planes' effect on image scanning ==== | ==== Understanding contiguous planes' effect on image scanning ==== | ||
| − | <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"> 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 /></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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Slice spacing is less than the slice thickness</font>'''</span>-In this case, although the images are, for example, | + | <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"> 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 /></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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Slice spacing is less than the slice thickness</font>'''</span>-In this case, although the images are, for example, 2 mm thick, they are spaced only 1Â 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 /></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"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Slice spacing is greater than the slice thickness</font>'''</span>-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 /></font></div> |
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. | 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. | ||
Revision as of 17:24, 15 February 2012
Correcting image spacing
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.
Understanding contiguous planes' effect on image scanning
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:
Slice spacing is less than the slice thickness-In this case, although the images are, for example, 2 mm thick, they are spaced only 1Â 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.
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.
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
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 [MIPAV_Utilities.html#1169929 Figure 233 on page 427] for triplanar views before and after correction). When the slice spacing is larger than the slice thickness (refer to [MIPAV_Utilities.html#1169929 Figure 233 on page 427] for triplanar views before and after correction), the utility inserts blank slices between the existing images.
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. [MIPAV_Utilities.html#1169607 Table 3] displays the most common combinations and the algorithms MIPAV uses for handling them.
T = Original slice thickness
S = Original space between slices
G = Gap = S - T
M = Number of original images
O = Original image set origin
N = New slice thickness
To use the Correct Image Spacing utility, DICOM images must first be saved in XML format. The following DICOM tags ([MIPAV_Utilities.html#1169929 Figure 233 on page 427]) are used:
(0018, 0050) Slice Thickness
(0018, 0088) Spacing Between Slices
You can also find this information listed in the Essential Image Information section of the image header ([MIPAV_Utilities.html#1169929 Figure 233 on page 427]) as Pixel resolution 2 (i.e., slice thickness) and Slice Spacing.
To view image attributes
1 Open an image.
2 Select Image > Attributes > View Header. The Header dialog box ([MIPAV_Utilities.html#1169929 Figure 233]) opens.
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.
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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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Â
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Â
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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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To save DICOM images as XML files
The Correct Image Spacing utility works only on XML files.
1 Open the DICOM image.
2 Select File > Save Image as in the MIPAV window. The Open dialog box appears.
3 Type the name for the file including the XML extension in File Name.
4 The Select DICOM tags to convert to XML dialog box opens.
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 [MIPAV_Utilities.html#1170915 Figure 234] for more information.
6 Press Save to save the file.
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To save other images as XML files
The Correct Image Spacing utility works only on XML files.
1 Open the image that has spacing problems if you have not already done so.
2 Select File > Save Image as in the MIPAV window. The Open dialog box appears.
3 Type the name for the file including the XML extension in File Name.
4 Select Medical, which includes XML files, in Files of Type.
5 Click OK. The Save Range of Slices dialog box appears. Complete the dialog box and press OK. See [MIPAV_Utilities.html#1194566 Figure 235].
6 The program saves the image as an XML file.
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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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Figure 235. The Save Range of Slices dialog box optionsÂ
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