Eigentool Restoration
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Restoration Dialog

Use this dialog to perform restoration on images to increase the Signal to Noise Ratio.

Note

Most of the settings for the Restoration Dialog can be set through a resource file that is loaded at the start of the program.

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Example performing restoration on an image set (reference)

  1. Load all  sequences from a single location from a patient study that are in alignment.  If the images are not aligned, run Registration.

  2. Select Automatic in the Region of Interest/Volume of Interest Dialog.

    1. Press the left button over the white matter area contralateral to the abnormal anatomy.

  3. Select Current Image from Region or Volume Operation and press Stats.

    Note

    The statistics should be for an individual image, do not use the All button.

  4. Calculate 2 x Sigma Avg. which will appear in the Information Window, and enter this value for sigma in the Restoration Window.

  5. Press Clear in the Region of Interest/Volume of Interest Dialog.

  6. Press Restore to perform restoration on the images.

  7. Check the resulting images for blurring. If images are blurry, reduce sigma and repeat Step 7. This can be repeated until the resulting images are satisfactory.

  8. Once the restoration is successful, press Repeat in the Restoration Dialog. Select a range of locations, if desired, ensuring this range contains usable images, and Press OK in the Repeat Dialog.

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Dialog Items

Note

The following items may or may not appear, depending on your selection of Restoration Method.

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# Images

Select n, the # Images, to use from the images loaded into the selected browser.  Only the last n images will be used to perform the restoration.

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# Out

Select n from # Out, the number of images to output.  Interpolation is used to create the extra images in between.

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Extra Output

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Select None to create only the restored images.

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Select Cor Coef to create a correlation coefficient image along with the restored images.

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Select # Avg to create an image of the number of pixels averaged to create each pixel, along with the restored images.

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Restore

Press Restore to perform the restoration, on each pixel vector, of the images in the selected browser.

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Restoration Method

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Select MLE to perform restoration using a maximum likelihood estimate to perform the restoration.

Warning

Do not use this method when using restoring less than 3 images.

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Select Kalman to perform restoration using a Kalman filter.

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Enter the P value in P(0).

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Enter the R value in R(i) for each image.

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Press Sel R to calculate the R value on each image using the current region of interest.

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Press Set Alpha to set the alpha values for the pixels in the current region of interest.

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Enter a value for Alpha.

Note

This restoration method has not yet been implemented.

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Select Average to perform restoration using the neighborhood average.

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Select Median to perform restoration using the neighborhood median.

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Select Average, Median to use the best fit between Average or Median on a per pixel basis.

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Select Average, MLE to use the Average method on all the images, followed by the MLE method on the first four.

Note

This restoration method has not yet been implemented.

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Select Butterworth to perform restoration using a butterworth filter with cosine extrapolation.

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Enter a value of the Butterworth filter in Order.

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Enter the cutoff frequency for the Butterworth filter in Cutoff.

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Select Exponential to perform restoration using the best fit to an exponential curve.

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Select 2-Gaussian to perform restoration using the best fit to 2 gaussian curves.

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Select Gaussian-Exponential to perform restoration using the best fit to a gaussian and exponential curve.

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Select LMRQ to perform restoration using the Levenberg-Marquardt method.

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Gamma

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Gaussian

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Select Spline to perform restoration using a spline fit.

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Select F(t) to perform equation analysis on the selected images. Images will be created that fit the original curve to a model of the passage of the bolus through the brain.

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Select -ln (S(t)/So) to calculate the -ln (S(t)/So) on the images in the selected browser.

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Skip

Select n, from Skip to ignore pixels within n pixels of the center pixel.  The center pixel is never ignored.

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X Function

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Select Linear to use linear value for X in the restoration.  1, 2, 3, .., n where n is the number of images will be used for the X values.

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Select Non-Linear to use non-linear values for X in the restoration.  The user supplies the values for X in X(i).

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Select Diffusion to use the gradient (squared) for the X values in the restoration.  The user supplies values for S in S(i) to be converted to gradient values.

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Select T2  to use TE values for X in the restoration.  A constant TR is assumed.  The user supplies the values for TE in TE(i) and TR in TR, if the values cannot be determined from the image header information.  The output will be the T2 slope.

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Select T1-Original to use TR values for X in the restoration using the original method.  A constant TE is assumed.  The user supplies the values for TR in TR(i) and TE in TE, if the values cannot be determined from the image header information.  The output will be the T1 slope.

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Select T1-Eigen to use TR values for X in the restoration using the eigen method.  A constant TE is assumed.  The user supplies the values for TR in TR(i) and TE in TE, if the values cannot be determined from the image header information.  The output will be the T1 slope.

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Y Function

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Select Linear to use the pixel values for the Y values.

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Select Log to use the log of the pixels values for the Y values.

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TR, TE, X, S, B

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Enter recovery time in TR(i) or TR.  TR(i) is used to specify a recovery time for each image.  TR is used to specify a constant recovery time.

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Enter echo time in TE(i) or TE.  TE(i) is used to specify an echo time for each image.  TE is to specify a constant echo time.

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Enter a value in X(i) for each image.

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Enter the S value in S(i) for each image.

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Enter the B value in B(i) for each image.

Note

These will only be displayed if needed and cannot be determined by the image header information.  See X Function for details on which values may be needed.

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Neighborhood

The neighborhood is defined as the pixels around a central pixel that satisfy the following constraints.  If a pixel is in the neighborhood, it is used to calculate the average pixel vector for calculating the restoration.  Also, that pixel's restoration results can be averaged with the center pixel's restoration results.  See Estimation Method for how the results are averaged over the neighborhood.

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Neighborhood size

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Select the size, in pixels, of the neighborhood in the X direction, centered on a pixel.

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Select the size, in pixels, of the neighborhood in the Y direction, centered on a pixel.

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Select the size, in pixels, of the neighborhood in the Z direction, centered on a pixel.

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Radius

Select Radius to use an elliptical/spherical shape for the neighborhood, instead of a rectangular/cubic shape.

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sigma

Enter the value for the euclidian distance between the center and non-center pixel in sigma.  If the euclidian-distance for a non-center pixel is less than sigma, that pixel is part of the neighborhood.

Note

The default is no limit.

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Estimation Method

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Select First Estimate to use the restoration results from the first pixel, within the neighborhood.

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Select Center Estimate to use the restoration results from the center pixel.

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Select Mean of All Estimates to average the restoration results from all pixels, within the neighborhood.

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Weight

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Select None to use no weighting in the fit of a pixel vector.

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Select Std Dev to use the standard deviation of the current region of interest, on each image, as the weights in the fit of the pixel vector.

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Select Pixel to use the pixel intensity of each image as the weights in the fit of the pixel vector.

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Repeat

Press Repeat to perform restoration on other browsers or files.

Note

Previous results of repeat processing need to be deleted manually for images saved in Dicom format.

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Cancel

Press Cancel to remove the Restoration dialog.

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Help

Press Help to display help for the Restoration dialog.

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Last modified: 01/17/05