Correcting image spacing

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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.

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 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.
  • 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 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.

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
S = Original space between slices<br / 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 (Figure 13) 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 (Figure 13) as Pixel resolution 2 (i.e., slice thickness) and Slice Spacing.

To view and edit image attributes

1 Open an image.
2 Select one of the tabs - Image Attributes > General, or Image Attributes >Orientation/Origin, or Image Attributes > Transformation matrix.
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.

Image Attributes dialog box


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 Figure 14 for more information.
6 Press Save to save the file.


Figure 14. Saving a DICOM image as an XML file

SelectDICOMTAGS.jpg

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 Figure 15.
6 The program saves the image as an XML file.


Figure 15. The Save Range of Slices dialog box options
General Options
Save image slices to separate files
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].

SaveRangeofSlicesa.jpg

First File Starting Number
File Name Number of Digits
Set the start counter number and how many digits will appear in the counter number.
Choose Range of Slices to Save
First Slice
Specify the number of the first slice.
Last Slice
Specify the number of the last slice.
Choose Range of Time Periods to Save
First Time period
Specify the first time period.
Last Time Period
Specify the last time period.
TIFF options
Save with packed bit compression
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.
OK
Applies the changes you made in this dialog box, saves the image as a range of slices, and closes the dialog box.
Cancel
Disregards any changes you made in this dialog box, closes the dialog box, and does not save the image as a range of slices.
Help
Displays online help for this dialog box.

To correct image spacing

1 Open the image that contains spacing problems.

To determine whether images contain spacing problems, remember to view them using the triplanar view or to view the header file.
2 Save the image as an XML file.
3 Select Utility > Correct Image Spacing.

  • If the image file does have spacing problems, then the program runs the utility.
  • If the image spacing is correct, the program displays a message indicating that the spacing is correct.
Cropping images