Difference between revisions of "Transform"

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'''Pad image to include entire original image''' - if selected, this option pads the image. While using this option the user can also specify the intensity value for padding pixels (this works for 2D images only).  
 
'''Pad image to include entire original image''' - if selected, this option pads the image. While using this option the user can also specify the intensity value for padding pixels (this works for 2D images only).  
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'''Out of bounds data''' - TBD.
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'''Out of bounds intensity value''' - TBD.
  
 
'''Clip output values to input image''' - if checked, the option preserves the original image type. That means that, the transformed image minimum value cannot decrease below the original image minimum value, and the transformed image maximum value cannot increase above the original image maximum value. This check box is disabled if Nearest-Neighbor, Bilinear, or Trilinear interpolation is selected, because when using these interpolations, minimum values can not decrease and maximum values can not increase.  
 
'''Clip output values to input image''' - if checked, the option preserves the original image type. That means that, the transformed image minimum value cannot decrease below the original image minimum value, and the transformed image maximum value cannot increase above the original image maximum value. This check box is disabled if Nearest-Neighbor, Bilinear, or Trilinear interpolation is selected, because when using these interpolations, minimum values can not decrease and maximum values can not increase.  
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'''Invert matrix''' - if checked, this option inverts the transformation matrix, first, and then applies the transformation with the inverted matrix. This option can only be activated if the Use image's associated matrix or Read matrix from file option is selected.  
 
'''Invert matrix''' - if checked, this option inverts the transformation matrix, first, and then applies the transformation with the inverted matrix. This option can only be activated if the Use image's associated matrix or Read matrix from file option is selected.  
 
 
  
 
==== Examples ====
 
==== Examples ====

Revision as of 18:06, 7 November 2012

This page is a stub.

For the MIPAV HTML help, please use this link http://mipav.cit.nih.gov/documentation/HTML Algorithms/Transform.html

Background

The Transformation algorithm, transforms images (volumes) by resampling the image using transformation matrix and the choice of Nearest-Neighbor, Gaussian, Bilinear, Trilinear, 3rd order B-spline, 4th order B-spline, Cubic Lagrangian, Quintic Lagrangian, Heptic Lagrangian, or Windowed sinc.

The Transform/Resample dialog box provides the user interface for transforming and (or) resampling images. It offers multiple options that help the user to define the transformation matrix and execute the transformation and (or) resampling algorithm. The user is asked to provide the output volume's desired resolutions and dimensions.

The Transform dialog box

To learn more about interpolation techniques used in the method, refer to Interpolation methods used in MIPAV:

Transform dialog box

The dialog box has two tabs - Transform and Resample. The Transform tab allows the user to set up the transformation matrix and choose the interpolation method. The Resample tab is designed to set up the resampling interpolation.

Transformation matrix

The Transform tab of the dialog box allows the user to transform an image using the transformation matrix that can be either

  • A matrix associated with the image,
  • A matrix stored in a separate file,
  • The user defined matrix, defined in this dialog box.

Transform dialog box: Transform tab

Transform tab - transformation options
  • No transformation - if selected, this option disables all transformation options, but the interpolation options are still available. Therefore, the user can not perform the transformation, but is still able to run the interpolation for a chosen image.


Transformation options

  • Use image associated matrix - if checked, this option allows using a transformation matrix associated with the image.
  • Read matrix from file - if checked, reads the transformation matrix from a file. The user should select the file where the transformation matrix is stored.

User defined transformation matrix

User defined transformation matrix

The options available for defining a transformation matrix are as follows:

  • Tx, Ty, Tz in mm - translations in the X, Y, and Z directions;
  • Rx, Ry, Rz in degrees - rotations along the X, Y, and Z axis;
  • Sx, Sy, Sz - scales in the X, Y, and Z directions;
  • SKx, SKy, and SKz - skews in the X, Y, and Z directions.


MIPAV coordinate system and the image origin

ImageOriginCoordinates.png

In MIPAV, we use the right hand coordinate system.

The image origin is located in the upper left had corner on the first image slice.

Pay attention to a little diagram next to the user defined transformation matrix options.

Options

Interpolation list box is designed to help the user to select the interpolation technique. The list of available interpolation methods includes: Bilinear, Trilinear, 3rd order B-spline, 4th order B-spline, Cubic Lagrangian, Quintic Lagrangian, Heptic Lagrangian, Nearest-Neighbor, and Windowed sinc.

The default interpolation is Bilinear for 2D images and also for 3D or 4D images with each slice processed independently.

The default interpolation is Trilinear for 3D or 4D images when not using slice processing. To learn more about interpolation techniques used in the method, refer to Interpolation methods used in MIPAV.

Constant FOV - TBD.

Unrepeated Begin and End Matching - TBD.

Rotate about radio buttons should be used to specify the image rotation. If Origin is selected, the image will be rotated about the MIPAV origin which is the upper left hand corner of the image. If Center is selected, the image will be rotated about its center. If Use Scanner Center is selected, the image will be rotated about the scanner's center, this choice is available only for DICOM images.

Retain original image size - if selected, this option preserves the image size. The image will be either padded by pixels with zero intensity (black pixels) to preserve its size, or cropped.

Pad image to include entire original image - if selected, this option pads the image. While using this option the user can also specify the intensity value for padding pixels (this works for 2D images only).

Out of bounds data - TBD.

Out of bounds intensity value - TBD.

Clip output values to input image - if checked, the option preserves the original image type. That means that, the transformed image minimum value cannot decrease below the original image minimum value, and the transformed image maximum value cannot increase above the original image maximum value. This check box is disabled if Nearest-Neighbor, Bilinear, or Trilinear interpolation is selected, because when using these interpolations, minimum values can not decrease and maximum values can not increase.

Process each slice independently (2.5D) - if checked, this option allows transforming each image slice separately. This works for 3D and 4D images.

Update origin - if checked, this option updates the image origin according to the new image size and resolution. By default, this option is activated.

Transform VOIs - if checked, the transformation is applied to both the image and to all the VOI(s). Regardless of what interpolation is applied to the image, Nearest-Neighbor interpolation is always applied to the VOI(s).

Invert matrix - if checked, this option inverts the transformation matrix, first, and then applies the transformation with the inverted matrix. This option can only be activated if the Use image's associated matrix or Read matrix from file option is selected.

Examples

TBD.

Transform dialog box: Resample tab

Resampling images

TBD.


Hough transform

The Hough transform is a technique which is used to determine and isolate features of a particular shape within an image. The classical Hough transform requires that the desired shapes be specified in some parametric form. It is most commonly used for the detection of simple curves such as lines, circles, and ellipses within a given image. Read more: Hough Transform

Transform to power of 2

By default, this algorithm will use Bilinear interpolation for 2D images and Trilinear Interpolation for 3D images to resample the original image to dimensions that are powers of 2. Optionally, the user can select another type of interpolation that will be used in the algorithm. Read more: Transform to power of 2

Transform: Conformal Mapping Algorithms

A conformal mapping, is a transformation w=f(z) that preserves local angles. An analytic function is conformal at any point where it has a nonzero first derivative. A complex function is analytic on a region R if it is complex differentiable at every point in R. In a conformal mapping, in any small neighborhood the relative angle and shape are preserved. Read more: Transform: Conformal Mapping Algorithms

Transform nonlinear

Please, refer to the MIPAV HTML help [1]

See also: