Slice tools

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Concatenating images

The Concatenate command on the Utilities menu provides you with a way to append, or add, two datasets together.

To concatenate image datasets
1 Open the two datasets that you want to join.
2 Select the dataset to which you want to append the other dataset.
3 Select Utilities > Concatenate. The Concatenate Images dialog box (Figure 56) opens.
4 Note that the dataset you selected appears in read-only form in the box labeled Image A.
5 Select Image B, which is the name of the dataset that you want to add to the end of Image A.
6 Select the dimensionality that you want for the resulting dataset by selecting either 3D or 4D.

Note: If both datasets contain the same number of slices, you can select either 3D or 4D. If the datasets contain a different number of slices, you can only select 3D.
7 Click OK. The program adds the Image B dataset to the end of the Image A dataset and displays the resulting dataset in a new image window.

Figure 56. Concatenate Images dialog box
Image A
Specifies the name of the dataset to which to append Image B. This dataset is the one you selected before using the Concatenate command.

ConcatenateImagesdialogBox.jpg

Image B
Specifies the name of the dataset that you want to append to the Image A dataset.
3D
Indicates that the dataset that results from appending Image B to Image A is three dimensional.
4D
Indicates that the dataset that results from appending Image B to Image A is four dimensional.
OK
Applies the changes you made in this dialog box and closes the dialog box.
Cancel
Disregards any changes you made in this dialog box, closes the dialog box, and does not append Image B to Image A.
Help
Displays online help for this dialog box.

To verify that the datasets are joined
1 Select the new dataset that resulted from concatenating the Image A and Image B datasets.
2 Notice the following on the MIPAV window:

  • If you selected 3D as the dimensionality of the resulting dataset in the Concatenate Images dialog box, the image slice slider (Figure 57 upper part) lists twice as many slices as either the Image A and Image B datasets.
  • If you selected 4D as the dimensionality of the resulting dataset, a time slice slider (Figure 57 lower part) appears beneath the image slice slider and the image slice slider lists the same number of slices as the Image A and Image B datasets.


Figure 57. The MIPAV window after concatenating datasets to generate 3D (upper) or 4D (lower) datasets

ZeroBasedConcatenateImages3D.jpg

ZeroBasedConcatenateImages4D.jpg

Extracting slices and volumes

The Extract Slices/Volume utility makes copies of the slices or volumes you select and displays them in separate image windows. Unlike the Remove Slices utility, the original image dataset is untouched.
There are several ways to select slices or volumes. You can select all slices; only specific slices; only the even-numbered slices; only the odd-numbered slices; or one or more ranges of slices.

To extract slices or volumes from image datasets
1 Select Utilities > Slice Tools>Extract Slices/Volumes. The Extract Slices/Volumes dialog box opens.
2 Use the image slider in the MIPAV window to locate slices that you want to extract.

3 Decide whether to remove:
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All of the slices-Click Select all. Check marks appear in all of the image slice check boxes.
One or more slices-Select the specific check boxes for the image slices. Check marks appear in only the check boxes you selected.
One or more ranges of slices-Select Specify range of slices, and then type the slice numbers or ranges of slice numbers in Enter slice numbers and/or slice ranges box.
All even-numbered slices-Click Check even. Check marks appear in only those check boxes for even-numbered slices, such as 2, 4, 6, and so on.
All odd-numbered slices-Click Check odd. Check marks appear in only those check boxes for odd-numbered slices, such as 1, 3, 5, and so on.
Tip: Use the image slider on the MIPAV window to look at specific slices to decide which slices to remove.

4 Click Extract. A status message appears. Then the MIPAV window refreshes and the slices you selected appear in new image windows.


Figure 58. Extract Slices/Volumes dialog box
Check the slices to extract
Indicates the slices that you want to extract from the dataset. You can scroll through the list to select one or more slices.

ZeroBased ExtractSlices.jpg

Select all
Selects all of the slices in the dataset to extract.
Clear
Clears all of the slices that are currently selected.
Check even
Selects all of the even-numbered slices to extract.
Check odd
Selects all of the odd-numbered slices to extract.
Specify range of slices
Indicates that you want to extract one or more specific slices or a range of slices from the dataset.
If you select this check box, you must specify the slices or ranges of slices you want to extract in the Slice number and/or range of slices box below.
Enter slice numbers and/or slice ranges
Indicates the slices and range of slices that you want to extract. This box only becomes available after you select Specify range of slices.
Extract
Makes copies of the slices/volumes you selected and displays them in separate image windows.
Cancel
Disregards any changes that you made in this dialog box and closes the dialog box.
Help
Displays online help for this dialog box.

Insert Missing Slices

The Insert Missing Slices utility insert slices into the image dataset. There are several ways insert a slice into the image dataset. You can select Average, or Blank, or Original.
If Average is selected, the inserted slice is set equal to the mean of the two surrounding slices, unless it is a new first of last slice. A new first or last slice preserves the usual slice spacing.
If Blank is selected, the slice with all pixel zero is inserted.

Image types

The algorithm works with 3D and 4D, grayscale, black and white, and color images. It preserves the image type when inserts slices, e.g. grayscale into grayscale images, color into color.

Applying insert missing slices

To insert a slice to an image dataset
1 Select Utilities > Slice tools>Insert Missing Slices. The Insert Missing Slices dialog box opens.
2 The dialog box appears displaying a note at the top of window that indicates how many slices are missing.
3 Now, you have to choose the method for slice insertion: Average, Blank, or Original.
4 Select the destination. Choose New image if you want the image with inserted slices appear in a new image frame; choose Replace image to replace the original image.
5 Click OK to proceed.

Figure 59. The Insert Missing Slice dialog box options
Insert before slice (1-n) or enter n 1 for new last slice
Specifies the position of the new slice.

InsertMissingSlicesDialogBox.jpg

Average
Inserts a slice that is the average the adjacent slices.
Copy previous adjacent
Insert a slice that is a copy of the preceding slice.
Copy next adjacent
Inserts a slice that is a copy of the following slice.
Blank
Inserts a blank slice.
Original
Inserts an image from the original dataset.
OK
Applies the parameters that you specified to insert the slice in the image dataset.
Cancel
Disregards any changes you made in this dialog box, closes the dialog box, and does not insert the slice into the image dataset.
Help
Displays online help for this dialog box.

See also: