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Eigentool User Resources
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User-Controlled Resources

 

Create a file in your home directory called .eigentool.  There are sample resources that you can copy into your .eigentool file.  You can also create and update this file using File->Save Settings from the Main window.

The resource file has the following lines:

# PERMANENT RESOURCES

Eigentool*permanent_resource_name1: permanent_resource_value1

Eigentool*permanent_resource_name2: permanent_resource_value2

. . .

Eigentool*permanent_resource_namen: permanent_resource_valuen

 

# REPLACEABLE RESOURCES

Eigentool*resource_name1: resource_value1

Eigentool*resource_name2: resource_value2

. . .

Eigentool*resource_namen: resource_valuen

 

Click one of the links below for instructions on setting the specific resources.

Font Resources

Link Resources

File Operation Resources

Image Load Resources

File Load Resources

Image Save Resources

File Save Resources

Region of Interest/Volume of Interest Resources

Display Resources

Browser Resources

Analysis Resources

Registration Resources

Restoration Resources

Segmentation Resources

Substance Resources

Iso-Data Resources

General Resources

Font Resources

Add the following lines to control the fonts used by eigentool, changing the font setting if desired.

Note

These should be in the permanent resources section of the file and cannot be saved using File->Save Settings.

 

Eigentool*Font: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*FontList: -dt-interface system-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*FontSet: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*XmText*FontList: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*XmTextField*FontList: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*buttonFontList: -dt-interface system-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*labelFontList: -dt-interface system-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*systemFont: -dt-interface system-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*textFontList: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

Eigentool*userFont: -dt-interface user-medium-r-normal-s*-*-*-*-*-*-*-*-*

 

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Link Resources

Add the following line to control the link settings used by eigentool.  (See Sample Resources for Links for sample entries)

Eigentool*sendLinkAs: 0

0: Send Region of Interest functions as the function, performing the function on the other browser.

1: Send Region of Interest functions as the region, copying the region to the other browser.

(See and Send Link As for details)

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Sample Resources for Links

Eigentool*sendLinkAs: 0

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Image Load Resources

Add the following lines to control the Image Load settings used in eigentool, changing the Image Load setting if desired. (See Sample Resources for Image Load for sample entries)


Eigentool*updateOtherPaths: true

true: copy the path entered in the Load dialogs to the Save dialogs.

false: do not copy the path entered in the Load dialogs to any other dialogs.

Eigentool*loadPath: /images

Enter any valid partition or path on your system to load images and files from.

(See Partition for details)

Eigentool*image_load*format: 3

0: List General Electric Signa format images.

1: List General Electric Genesis format images.

2: List Henry Ford Hospital format images.

3: List Dicom format images.

4: List Vicom format images.

5: List Genesis spectroscopy format images.

6: List images with unknown formats.

(See Format for details)

Eigentool*image_load*listImage: true

true: List images in the image list.

false: List the number of images in the image list.

(See List Images for details)

Eigentool*image_load*sort: true

true: Sort the images in the image list.

false: Do not sort the images in the image list.

(See Sort for details)

Eigentool*image_load*swapImageData: false

true: Swap bytes in the image data when images are loaded.

false: List the number of images in the image list.

(See Swap Image Data for details)

Eigentool*image_load*compressed: false

true: List the compressed images in the image list.

false: List the uncompressed images in the image list.

(See Compressed for details)

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Sample Resources for Image Load

Eigentool*updateOtherPaths: true
Eigentool*loadPath: /images
Eigentool*image_load*format: 3
Eigentool*image_load*listImage: true
Eigentool*image_load*sort: true
Eigentool*image_load*swapImageData: false
Eigentool*image_load*compressed: false
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File Load Resources

Add the following lines to control the File Load settings used in eigentool, changing the File Load setting if desired. (See Sample Resources for File Load for sample entries)

 

See loadPath in Image Load Resources for the default path used when loading files.

(See Partition for details)

Eigentool*file_load*format: 2

2: List Henry Ford Hospital format files.

3: List Dicom format files.

(See Format for details)

Eigentool*file_load*type: 0

0: List region of interest files.

1: List signature files.

(See File Type for details)

Eigentool*file_load*matchLocations: false

true: Load regions of interest on images with matching locations.

false: Load regions of interest on any image.

(See Match Locations for details)

Eigentool*file_load*compressed: false

true: List the compressed files in the file list.

false: List the uncompressed files in the file list.

(See Compressed for details)

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Sample Resources for File Load

Eigentool*file_load*format: 2

Eigentool*file_load*type: 0
Eigentool*file_load*matchLocations: false
Eigentool*file_load*compressed: false
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Image Save Resources

Add the following lines to control the Image Save settings used in eigentool, changing the Image Save setting if desired. (See Sample Resources for Image Save for sample entries)


Eigentool*savePath: /images

Enter any valid partition or path on your system to save images and files to.

(See Partition for details)

Eigentool*saveDirDate: None
Scan: Use the Study Date in HFH format directories.
Current: Use the Series Date in HFH format directories, this is the processing date.
None: Do not use any date in the HFH format directories.
Eigentool*saveDirStudy: true

true: Use the study number in HFH format directories.

false: Do not use the study number in HFH format directories.

Eigentool*image_save*format: 3

2: Save images in Henry Ford Hospital format.

3: Save images in Dicom format.

(See Format for details)

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Sample Resources for Image Save

Eigentool*savePath: /images
Eigentool*saveDirDate: None
Eigentool*saveDirStudy: true
Eigentool*image_save*format: 3

File Save Resources

Add the following lines to control the File Save settings used in eigentool, changing the File Save setting if desired. (See Sample Resources for File Save for sample entries)

 

See saveDirDate and saveDirStudy in Image Save Resources for resources on HFH directory naming.


See savePath in Image Save Resources for the default path used when saving files.

(See Partition for details)

Eigentool*file_save*format: 2

2: Save files in Henry Ford Hospital format.

3: Save files in Dicom format.

(See Format for details)

Eigentool*file_save*type: 0

0: Save region of interest files.

3: Save signature files.

(See File Type for details)

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Sample Resources for File Save

Eigentool*file_save*format: 2
Eigentool*file_save*type: 0
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Region of Interest/Volume of Interest Resources

Add the following lines to control the Region of Interest/Volume of Interest settings used in eigentool, changing the Region of Interest/Volume of Interest setting if desired. (See Sample Resources for Region of Interest/Volume of Interest for sample entries)

 

Eigentool*roi_voi*drawFunction: 0

0: Freehand region of interest drawing

1: Generate a region of interest from a single, or multiple, user-selected points.

2: Draw, erase, and move rectangular regions.

3: Draw, erase, and move elliptical regions.

4: Draw and move vector regions.

5: Draw and move arrow regions (vector with pointer at one end).

6: Generate a region based on the current window/level of the image.

7: Generate a region based on a threshold applied to an image.

8: Generate a region based on a slice applied to an image.

9: Move, rotate, and fill the currently display region.

10: Erase connected regions of interest.

11: Draw an area freehand and erase all points contained within the area.

12: Generate a contour of a region based on a slice applied to an image.

13: Interactively display and print pixel information, without modifying the region of interest.

(See Drawing Regions for details)

Eigentool*roi_voi*automaticOperation: 0

0: Perform on local area.

1: Perform on the whole image.

2: Perform on the interior of the skull.

3: Perform on local area with option to fill.

4: Perform on local area at each individual point.

(See Automatic for details)

Eigentool*roi_voi*mode: 0

0: Draw rectangles or ellipses.

1: Erase rectangles or ellipses.

(See Rectangle or Ellipse for details)

Eigentool*roi_voi*area: 1

0: Perform operation on region of interest only.

1: Perform operation on entire image.

2: Perform operation on pixels connected to the region of interest only.

(See Window, Threshold, or Slice for details)

Eigentool*roi_voi*operation: 0

0: Perform region of interest functions on single slices only.

1: Perform region of interest functions on all images as single slices.

2: Perform volum of interest functions on all images as a volume.

(See Region or Volume Operation for details)

Eigentool*roi_voi*voiStatisticsOutput: 0

0: Calculate mean, standard deviation, volume, and weight

1: Calculate mean and standard deviation

2: Calculate all statistics

(See Statistics for details)

Eigentool*roi_voi*voiAreaDirection: 0

0: Put coordinates in Top to Bottom, then Left to Right order

1: Put coordinates in Left to Rigth, then Top to Bottom order

(See Surface Area for details)

Eigentool*roi_voi*rotateCenter: true

true: Rotate regions of interest around the center of the region of interest.

false: Rotate regions of interest around the center of the image.

(See Rotate for details)

Eigentool*roi_voi*flipDirection: 0

0: Flip regions of interest horizontally.

1: Flip regions of interest vertically.

(See Flip for details)

Eigentool*roi_voi*viewMorphological: false

Eigentool*roi_voi*viewRoiVoiProcessing: false

Eigentool*roi_voi*viewImageProcessing: false

Eigentool*roi_voi*viewMacro: false

true: Display the Morphological, Roi/Voi Processing, Image Processing, or Macro operations.

false: Do not display the Morphological, Roi/Voi Processing, Image Processing, or Macro operations

(See Region of Interest/Volume of Interest Dialog Options for details)

Eigentool*roi_voi*eraseFillDirection: 0

0: Erase or fill objects less than a specified size

1: Erase or fill objects larger than a specified size

(See Erase/Fill Operations for details)

Eigentool*roi_voi*eraseFillSize: 1

n: Cutoff size of objects to erase or fill.

(See Erase/Fill Size for details)

Eigentool*roi_voi*cleanConnectSize: 4

n: Minimum # of neighbors an object must have to be kept.

(See Clean Connect Size for details)

Eigentool*roi_voi*cleanObjectSize: 0

n: Minimum size of an object to be kept.

(See Clean Object Size for details)

Eigentool*roi_voi*iterations: 1

n: # times to perform a morphological operation.

(See iterations for details)

Eigentool*roi_voi*boundaryValue: 0

0: Outside of image is treated as non region of interest.

1: Outside of image is treated as entirely a region of interest.

(See Boundary for details)

Eigentool*roi_voi*connectSpursCorners: true

true: Remove spur and corner pixels prior to connecting an incomplete contour.

false: Do not remove any pixels prior to connecting an incomplete contour.

(See Connect for details)

Eigentool*roi_voi*smoothNGauss: 1

n: # times to apply a gaussian smooth to a region of interest contour.

(See # Gauss for details)

Eigentool*roi_voi*voiKeepTopPercentagePercent: 25

%: The percentage of pixels to keep or remove.

(See Keep or Remove for details)

Eigentool*roi_voi*voiNeighborNonZeroPercent: 50

%: The percentage of edge pixels that must be adjacent to a non-zero pixel

(See Neighbor for details)

Eigentool*roi_voi*fillVoiSliceAdd: false

true: Add the results of the FilG operation to the current volume of interest.

false:  Replace the current volume of interest with the results of the FilG operation.

(see FilG for details)

Eigentool*roi_voi*voiFillVoiSliceLow: 0.0

n.m: The lower slice value.

(See Lo Hi Values for details)

Eigentool*roi_voi*voiFillVoiSliceHigh: 0.0

n.m: The upper slice value.

(See Lo Hi Values for details)

Eigentool*roi_voi*voiImageNumber: 1

n: The slice to apply the Lo and High values to.

(See # for details)

Eigentool*roi_voi*voiBoundDeleteCrossovers: true

true: Delete objects that crossover the boundary of the region of interest.

false: Do not delete objects that crossover the boundary of the region of interest.

(See Delete Crossovers for details)

Eigentool*roi_voi*roiGridSplitSizeY: 3

n: The grid size in the Y direction.

(See Grid, Y for details)

Eigentool*roi_voi*roiGridSplitSizeX: 3

n: The grid size in the X direction.

(See Grid, X or details)

Eigentool*roi_voi*sampleSize: 1

n: Sample 1 of every n pixels.

(See Sample for details)

Eigentool*roi_voi*voiThresholdAboveNoiseNumberStandardDeviations: 3

n: he nubmer of standard deviations.

(See # Std Dev for details)

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramMaximum: 127

n: The maximum value on the histogram.

(See Max for details)

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberBins: 128

n: The number of bins to use when calculating the histogram.

(See # bins for details)

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberGauss: 1

n: The number of gaussian smooths to use on the histogram.

(See # Gauss for details)

Eigentool*roi_voi*voiThresholdAboveNoiseOutput: 0

0: The largest peak from the histogram.

1: All peaks from the histogram that are higher than 1/2 the maximum of the histogram.

2: The largest peak closest to 1 on the histogram.

3: The largest peak closest to 0 on the histogram.

(See Operation for details)

Eigentool*roi_voi*voiThresholdAboveNoiseWholeImage: true

true: Use the whole image when using the slice values determined from the histogram.

false: Only slice under the regions of interest.

(See Whole Image for details)

Eigentool*roi_voi*voiPrincipalAxisXPixelSize: 0.0

n: X axis pixel size.

(See Principal Axis X for details)

Eigentool*roi_voi*voiPrincipalAxisYPixelSize: 0.0

n: Y axis pixel size.

(See Principal Axis Y for details)

Eigentool*roi_voi*voiPrincipalAxisZPixelSize: 0.0

n: Z axis pixel size.

(See Principal Axis Z for details)

Eigentool*roi_voi*voiPrincipalAxisGap: 0.0

n: The size of the gap between pixels.

(See Principal Axis Gap for details)

Eigentool*roi_voi*voiMakeSignatureNumberProcesses: 0

0: Single process is to be calculated from the region of interest.

1: Multiple processes are to be calculate from the region of interest, split into sections.

(See Processes for details)

Eigentool*roi_voi*voiMakeSignatureSplitSize: 1

n: Split the region of interest into n x n sections.

(See N x N for details)

Eigentool*roi_voi*macroMode: 1

0: Perform macro on current slice only.

1: Perform macro on each slice.

2: Perform macro on each slice and save each resulting region of interest.

(See Run Macro for details)

Eigentool*roi_voi*printMacro: false

true: Print each step of the macro as it is being performed.

false: Do not display any information while the macro is being performed.

(See Macro for details)

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Sample Resources for Region of Interest/Volume of Interest

Eigentool*roi_voi*drawFunction: 0

Eigentool*roi_voi*automaticOperation: 0

Eigentool*roi_voi*mode: 0

Eigentool*roi_voi*area: 1

Eigentool*roi_voi*operation: 0

Eigentool*roi_voi*voiStatisticsOutput: 0

Eigentool*roi_voi*voiAreaDirection: 0

Eigentool*roi_voi*rotateCenter: true

Eigentool*roi_voi*flipDirection: 0

Eigentool*roi_voi*viewMorphological: false

Eigentool*roi_voi*viewRoiVoiProcessing: false

Eigentool*roi_voi*viewImageProcessing: false

Eigentool*roi_voi*viewMacro: false

Eigentool*roi_voi*eraseFillDirection: 0

Eigentool*roi_voi*eraseFillSize: 1

Eigentool*roi_voi*cleanConnectSize: 4

Eigentool*roi_voi*cleanObjectSize: 0

Eigentool*roi_voi*iterations: 1

Eigentool*roi_voi*boundaryValue: 0

Eigentool*roi_voi*connectSpursCorners: true

Eigentool*roi_voi*smoothNGauss: 1

Eigentool*roi_voi*voiKeepTopPercentagePercent: 25

Eigentool*roi_voi*voiNeighborNonZeroPercent: 50

Eigentool*roi_voi*fillVoiSliceAdd: false

Eigentool*roi_voi*voiFillVoiSliceLow: 0.0

Eigentool*roi_voi*voiFillVoiSliceHigh: 0.0

Eigentool*roi_voi*voiImageNumber: 1

Eigentool*roi_voi*voiBoundDeleteCrossovers: true

Eigentool*roi_voi*roiGridSplitSizeY: 3

Eigentool*roi_voi*roiGridSplitSizeX: 3

Eigentool*roi_voi*sampleSize: 1

Eigentool*roi_voi*voiThresholdAboveNoiseNumberStandardDeviations: 3

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramMaximum: 127

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberBins: 128

Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberGauss: 1

Eigentool*roi_voi*voiThresholdAboveNoiseOutput: 0

Eigentool*roi_voi*voiThresholdAboveNoiseWholeImage: true

Eigentool*roi_voi*voiPrincipalAxisXPixelSize: 0.0

Eigentool*roi_voi*voiPrincipalAxisYPixelSize: 0.0

Eigentool*roi_voi*voiPrincipalAxisZPixelSize: 0.0

Eigentool*roi_voi*voiPrincipalAxisGap: 0.0

Eigentool*roi_voi*voiMakeSignatureNumberProcesses: 0

Eigentool*roi_voi*voiMakeSignatureSplitSize: 1

Eigentool*roi_voi*macroMode: 1

Eigentool*roi_voi*printMacro: false

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Display Resources

Add the following lines to control the Display Window View Options used in eigentool, changing the display setting if desired. These lines would only affect the first display. Replace display_image1 with display_image2 for the second display, up to four displays. You can leave the number out to have the same setting apply to all four displays. (See Sample Resources for Display for sample entries)


Eigentool*display_image1*imageScale:more:  0

0:  Scale the images to minimum and maximum of all the images loaded/created together.

1:  Scale each image individually.

2:  Do not scale the images.

(See Display->View->Scale for details)

Eigentool*display_image1*displaySize:  256

n: Enter n for the size of the image display.

(See Display->View->Zoom for details)

Eigentool*display_image1*displayMethod:  0

0: Sample or Replicate pixels to fit the size of the image display.

1: Average or Interpolate pixels to fit the size of the image display.

2: Average or use Bicubic spline so pixels to fit the size of the image display.

(See Display->View->Display Method for Details)

Eigentool*display_image1*splitDisplay:  0

0: Single Display

1: Split display into 2x2.

2: Split display into 4x4.

3: Split display into 8x8.

4: Split display into 16x16.

5: Split display into 32x32.

(See Display->View->Split Display for details)

Eigentool*display_image1*negative:  0

0: Do not display negative values.

1: Display negative values as their absolute value.

Eigentool*display_image1*smooth:  0

0: Do not smooth images before displaying.

1: Smooth images before displaying.

Eigentool*display_image1*colorMap:  0

0: Gray colormap

1: Thermal colormap

2: RGB Pseudocolor colormap

3: Fluorescent colormap

4: Rainbow colormap

5: Blue colormap

6: Red colormap

7: Green colormap

(See Display->Options->Colormap for details)

Eigentool*display_image1*windowFunction:  0

0: Mouse buttons set high and low values for the Window/Level Bar and High/Low or Window/Level Entries.

1: Mouse buttons set the center and width for the Window/Level Bar and High/Low or Window/Level Entries.

(See Display->Options->Window Function for details)



Eigentool*display_image1*windowForm:  0

0: Use a ramp for the window form.

1: Use a sawtooth for the window form.

2: Use a square for the window form.

3: Use a reverse for the window form.

4: Use a shark fin for the window form.

(See Display->Options->Window Form for details)

Eigentool*display_image1*roiColor:  0

0: White

1: Black

2: Red

3: Green

4: Blue

5: Yellow

6: Negative

7: Positive

(See Display->Options->Roi->Draw Color for details)

Eigentool*display_image1*roiEraseColor:  0

0: White

1: Black

2: Red

3: Green

4: Blue

5: Yellow

(See Display->Options->Roi->Erase Color for details)

Eigentool*display_image1*annotate:  0

0: White

1: Black

2: None

3: White-Blind

4: Black-Blind

(See Display->Options->Annotate for details)

Eigentool*display_image1*graticule:  2

0: White

1: Black

2: None

(See Display->Options->Graticule for details)

Eigentool*display_image1*cursorColor:  0

0: White

1: Black

2: Red

3: Green

4: Blue

5: Yellow

6: Cyan

7: Magenta

(See Display->Options->Cursor details)

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Sample Resources for Display

Eigentool*display_image*imageScale: 0

Eigentool*display_image*displaySize: 512

Eigentool*display_image*displayMethod: 0

Eigentool*display_image*splitDisplay: 0

Eigentool*display_image*negative: 0

Eigentool*display_image*smooth: 0

Eigentool*display_image*colorMap: 0

Eigentool*display_image*windowFunction: 0

Eigentool*display_image*windowForm: 0

Eigentool*display_image*roiColor: 0

Eigentool*display_image*roiEraseColor: 0

Eigentool*display_image*annotate: 0

Eigentool*display_image*graticule: 0

Eigentool*display_image*cursorColor: 0

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Browser Resources

Add the following lines to control the browser settings used in eigentool, changing the browser setting if desired. These lines would only affect the first browser. Replace browser1 with browser2 for the second display, up to four displays. You can leave the number out to have the same setting apply to all four browsers. (See Sample Resources for Browser for sample entries)



Eigentool*browser1*listAs:  0

0: Show images in browser as images.

1: Show images in browser as filenames.

2: Show images in browser as numbers.

(See Browser->View->Show Images as for details)

Eigentool*browser1*windowLevel:  1

0: Do not perform window and level on the browser images.

1: Do perform window and level on the browser images.

(See Browser->Options->Window/Level for details)

Eigentool*browser1*roiVoi:  1

0: Do not display the region (or volume) of interest on the browser images.

1: Display the region (or volume) of interest on the browser images.

(See Browser->Options->Window/Level for details)

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Sample Resources for Browser

Eigentool*browser*listAs: 0

Eigentool*browser*windowLevel: 1

Eigentool*browser*roiVoi 1

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Registration Resources

Add the following lines to control the Registration settings used in eigentool, changing the Registration setting if desired. (See Sample Resources for Registration for sample entries)

Eigentool*register*matchType: 0
0:  Use the Head in Hat method for registration.
1:  Use the AIR registration package for registration.
2:  Use the Mutual Information method for registration.
(See Match in the Registration dialog for details)
Eigentool*register*rotateOption: true
true:  Use rotation and translation when aligning images.
false:  Use translation only when aligning images.
(See Rotate option for details)

 

Sample Resources for Registration

Eigentool*register*matchType: 0
Eigentool*register*rotateOption: true

Restoration Resources

Add the following lines to control the Restoration settings used in eigentool, changing the Restoration setting if desired. (See Sample Resources for Restoration for sample entries)

Eigentool*fit*restorationMethod: 2
0:  Use Maximum Likelihood Estimate as the restoration filter.
1:  Use a Kalman filter as the restoration filter.
2:  Use an Average filter as the restoration filter.
3:  Use Average and Median filters for the restoration filters.
4:  Use Average and MLE filters for the restoration filters.
5:  Use a Butterworth filter as the restoration filter.
6:  Use a Exponential filter as the restoration filter.
7:  Use 2 Gaussian filters for the restoration filters.
8:  Use Gaussian and Exponential filters for the restoration filters.
9:  Use the Levenberg-Marquardt filter as the restoration filter.
10:  Use a Spline fit as the restoration filter.
11:  Use the F(t) filter as the restoration filter.
12:  Use -ln (S(t)/So) filter as the restoration filter.
(See Restoration Method for details)
Eigentool*fit*neighborhoodOutput: 2
0:  Use the first estimate in the neighborhood as the result for the center pixel.
1:  Use the center estimate in the neighborhood as the result for the center pixel.
2:  Use the mean of all estimates in the neighborhood as the result for the center pixel.
(See Estimation Method for details)
Eigentool*fit*neighborhoodXSize: 9
The size of the neighborhood in the X direction.
(See Neighborhood size for details)
Eigentool*fit*neighborhoodYSize: 9
The size of the neighborhood in the Y direction.
(See Neighborhood size for details)

Sample Resources for Restoration

Eigentool*fit*restorationMethod: 2
Eigentool*fit*neighborhoodOutput: 2
Eigentool*fit*neighborhoodXSize: 9
Eigentool*fit*neighborhoodYSize: 9

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Segmentation Resources

Add the following lines to control the Segmentation settings used in eigentool, changing the Segmentation setting if desired. (See Sample Resources for Segmentation for sample entries)

Eigentool*filter*filterImageMethod: 0

0:  Use a gram-schmidt filter.

1:  Use eigen analysis to calculate the filter. (reference)

2:  Use a gram-schmidt filter with rotation.

3:  Use a gram-schmidt filter with a constant.

4:  Use a matched filter without variance.

5:  Use a matched filter with variance.

6:  Use a correlation filter.

7:  Use an averaging filter (1 / # images).

8:  Use an energy difference filter.

9:  Use a difference of energy filter.

10:  Use a cross-product filter.

11:  Use a difference filter. (reference)

12:  Use a gram-schmidt filter with first process being redefined as process #1 - process #2.  Process # 3 now becomes the second process.

13:  Use a gram-schmidt filter with first process being redefined as process #1 - process #3.  Process # 2 remains the second process.

14:  Use a maximum-minimum contrast to noise ratio filter. (reference)

15:  Use a feature suppression filter.

16:  Use a filter equal to the inverse of the covariance matrix of the second process multiplied by the first process.

17:  Use a previously saved filter.  Either a signature (.sig) or report (.rep) file can be selected.

(See Filter Type for details)

Eigentool*filter*filterImageOutput: 1
0:  Calculate the filter image for the 1st selected process.
1:  Calculate the filter image for all processes.
2:  Calculate the filter images for all processes and calculate an orthogonal image.
3:  Calculate the filter images for all processes and calculate the correlation of the orthogonal vectors.
4:  Calculate the filter images for all processes and calculate images for the orthogonal vectors.
(See Output for details)
Eigentool*filter*filterNormalize: true
true:  Normalize the filter vector to create filter images with the desired process equal to 1.
false:  Do not normalize the filter vector.
(See Normalize for details)

Sample Resources for Segmentation

Eigentool*filter*filterImageMethod: 0
Eigentool*filter*filterImageOutput: 1
Eigentool*filter*filterNormalize: true

Substance Resources

Add the following lines to control the Substance settings used in eigentool, changing the Substance setting if desired. (See Sample Resources for Substance for sample entries)

Eigentool*substance*substanceOutput: 0
0:  Each substance is represented by a unique single value.
1:  Each substance is represented by a unique range of values.
(See Output for details)
Eigentool*substance*substancerangeInput: 1
0:  Use thresholds only for defining each anatomical region.
1:  Use regions on interest only to define each anatomical region.
2:  Use thresholds under a region of interest for defining each anatomical region.
(See Method for details)
Eigentool*substance*substanceCalculateLength: false
true:  Calculate the length of each substance in all 3 dimensions.
false:  Do not calculate the length of each substance.

(See Calculate Length for details)

Sample Resources for Substance

Eigentool*substance*substanceOutput: 0
Eigentool*substance*substancerangeInput: 1
Eigentool*substance*substanceCalculateLength: false

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Iso-Data Resources

Add the following lines to control the Iso-Data settings used in eigentool, changing the Iso-Data setting if desired. (See Sample Resources for Iso-Data for sample entries)

Eigentool*iso_data*isoDataOutput: 1
0:  Each cluster result in a single image, using 1 for the pixel assignment.
1:  All results in a single image, using the cluster # for the pixel assignment.
(See Iso-Data Results for details)
Eigentool*iso_data*isoDataMethod: 0
0:  Use a distance calculation to determine cluster classification.
1:  Use an alternate distance calculation to determine cluster classification.
2:  Use the projection of one cluster center onto another to determine cluster classification.
3:  Use a gramm-schmidt filter to determine cluster classification.
(See Iso-Data Method for details)
Eigentool*iso_data*isoDataNumClustersStart: 20
The # of clusters to start the iterations.
(See # Start Clusters for details)
Eigentool*iso_data*isoDataNumClustersEnd: 3
The expected # of clusters to have at the end of the iterations.
(See # Final Clusters for details)
Eigentool*iso_data*isoDataMinConnectSize: 0
The minimum # of pixels grouped together to be considered for inclusion in a cluster.
(See Minimum # of Connected Pixels for details)
Eigentool*iso_data*isoDataMinPixelsPerCluster: 500
The minimum # of pixels that can be in a cluster.
(See Minimum Pixels per Cluster for details)
Eigentool*iso_data*isoDataMaxPairsLump: 1
The # of pairs of clusters to lump together at a time.
(See Maximum Pairs to Lump for details)
Eigentool*iso_data*isoDataMaxIterations: 60
The maximum # of iterations allowed before a solution is reached.
(See Maximum # Iterations for details)
Eigentool*iso_data*isoDataNumPixelsConnected: 0
The minimum # of pixels connected within the window size, for the center pixel to be assigned to a cluster.
(See Minimum # Connected Pixels for details)
Eigentool*iso_data*isoDataWindowSize: 3
The size of the window to use to test for spatial connectivity for a cluster assignment.
(See Window Size for details)

Sample Resources for Iso-Data

Eigentool*iso_data*isoDataOutput: 1
Eigentool*iso_data*isoDataMethod: 0
Eigentool*iso_data*isoDataNumClustersStart: 20
Eigentool*iso_data*isoDataNumClustersEnd: 3
Eigentool*iso_data*isoDataMinConnectSize: 0
Eigentool*iso_data*isoDataMinPixelsPerCluster: 500
Eigentool*iso_data*isoDataMaxPairsLump: 1
Eigentool*iso_data*isoDataMaxIterations: 60
Eigentool*iso_data*isoDataNumPixelsConnected: 0
Eigentool*iso_data*isoDataWindowSize: 3
 

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General Resources

Choose from the following to control placement of scrollbars.  (See General Sample Resources for sample entries)

Note

These entries should be placed in the .Xdefaults file in your home directory, not .eigentool.

*scrollLeftSide:  true

true: Scrollbars on left side.

false: Scrollbars on right side.

*scrollBarPlacement:  XmTOP_LEFT

XmTOP_LEFT: Scrollbars on top and left sides.

XmBOTTOM_LEFT: Scrollbars on bottom and left sides.

XmTOP_RIGHT: Scrollbars on top and right sides.

XmBOTTOM_RIGHT: Scrollbars on bottom and right sides.

*enableToggleVisual:  false

true: Do not use checks in the check boxes and use diamond choice boxes.

false: Use checks in the check boxes and round choice boxes.

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General Sample Resources

*scrollLeftSide: true

*scrollBarPlacement: XmTOP_LEFT

*enableToggleVisual: true

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Last modified: 01/17/05