Resampling Images with Multi-Planar Reconstruction

Multi-Planar Reconstruction (MPR)

You can interactively resample an existing image to have different numbers of slices, rows, and columns, different pixel sizes and fields of view, and different orientations of the slices using Jim's MPR tool images). Jim uses sophisticated resampling techniques to give the best possible quality in the re-sampled image.

To interactively resample an existing image, first load that image into Jim's display window, then select Multi-Planar Reconstruction from the Organise menu: organise_mpr of the main display frame.

This brings up:

mpr

The MPR tool shows the current loaded image, with the extent of the resample volume indicated by the extent of the yellow boxes. The image in the main display also shows the currently-defined resample volume as a cuboid superimposed on the loaded image. Solid lines are above the image slice, and dashed lines are below the image slice.

mpr_main_display

To help you orientate yourself, there are three coloured blobs (red, green and blue) on three edges of the cuboid that defines the resampling volume. These blobs can be seen both in the MPR tool, and in the main display.

mpr_blobs

mpr_blobs_main

Defining the Resample Volume

You can set the properties (size, number of samples and orientation) of the re-sampled image by:

Dragging the handles to resize, move and rotate the sample volume.
- A green handle at the centre of the sample volume will move the sample volume without changing its size or orientation .
- A green handle at the centre of one of the yellow sample volume sides will move that edge of the sample volume .
- A blue handle just outside the sample volume will rotate the sample volume .
Setting the pixel sizes in the re-sampled volume explicitly by typing in new values here:

Note: If you set very small pixel sizes, and very large numbers of samples, resampling of the image will be very slow, and Jim may run out of memory.
Setting the number of columns, rows and slices in the re-sampled volume explicitly by typing in new values here:

As you move and rotate the handles, you will see an indication of the position that the new sample volume will take. As you release the mouse button, or type in new values for the pixel sizes or number of pixels (and press return), the resampling volume is redefined, and the views of the image are updated.

When you are happy with the redefined sample volume, you can resample the original image with these settings to create a new image. Click the resample_button button to create the new dataset. The new image will be of the same type as the input image. The new image can either be saved to disk, or loaded into Jim depending on your selection:

load_save

If you selected "Save to disk", Jim will prompt you for a new image file name for the re-sampled image.

Type of Interpolation

If the pixel size is different from than the original in any dimension, or if the re-sampled image planes are not parallel to original planes, then the image must be interpolated to obtain the new intensity values.

mpr_interpolation_types

You can select from the three types of interpolation:

Nearest neighbour. The intensity of a pixel in the re-sampled image will be the same as the intensity of the nearest pixel in the original image. This is quick, but usually degrades the appearance of the interpolated image.
Linear. Linear interpolation is used to calculate the pixel intensity in the re-sampled image. This is the default, and gives a good compromise between speed and quality of the interpolated image.
Sinc. Sinc interpolation is used to calculate the pixel intensity in the re-sampled image. This gives the best results for MR images, but is relatively slow. When you use sinc interpolation with a large number of re-sampled pixels, you may find that interactivity is sluggish, and the final resampling to create a new dataset takes a long time.

Saving and Loading the MPR Geometry

You may want to save the geometry of the MPR volume and apply the same resampling volume to another image. To save the geometry of the MPR volume, select "Save Geometry..." from the File menu:

Save the MPR volume geometry to disk

This will bring up a File Chooser for you to select an XML file into which the geometry is to be saved.

After loading another image into Jim's display, to load this MPR geometry, select "Load Geometry..." from the File menu:

Load the MPR volume geometry from an XML
file

This will set the resampling volume and resampled pixel sizes exactly the same as when you saved the geometry.

Note: if the newly-loaded image does not have the same field-of-view and slice orientations/positions as the original image on which the geometry was saved, the MPR volume will not contain the same anatomy.

3-D Cut-Away View

The bottom right corner of the MPR toolkit shows a 3-D view of the orthogonal planes passing through the centre of the current resample volume.

mpr_ortho

You can rotate this view of the resample volume by clicking and dragging the mouse in this panel.

Click and drag to the left and right to rotate the volume around the polar axis.
Click and drag up and down to rotate the volume around an axis that lies in the equatorial plane.

Resizing the Panes

The four panes of the MPR tool can be resized to give a more detailed view of one aspect of the resampling. Simply drag the vertical and horizontal dividers between the panes.

mpr_pane_resized

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