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User-Controlled Resources
Click one of the links below for instructions on setting the specific resources. Link Resources File Operation Resources Region of Interest/Volume of Interest Resources Font ResourcesAdd 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*-*-*-*-*-*-*-*-*
Link ResourcesAdd the following line to control the link settings used by eigentool. (See Sample Resources for Links for sample entries)Eigentool*sendLinkAs: 0
Image Load ResourcesAdd 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)
(See Partition for details) Eigentool*image_load*format: 3
(See Format for details) Eigentool*image_load*listImage: true
(See List Images for details) Eigentool*image_load*sort: true
(See Sort for details) Eigentool*image_load*swapImageData: false
(See Swap Image Data for details) Eigentool*image_load*compressed: false
(See Compressed for details)
File Load ResourcesAdd 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
(See Format for details) Eigentool*file_load*type: 0
(See File Type for details) Eigentool*file_load*matchLocations: false
(See Match Locations for details) Eigentool*file_load*compressed: false
(See Compressed for details)
Image Save ResourcesAdd 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)
(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
Eigentool*image_save*format: 3
(See Format for details)
File Save ResourcesAdd 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
(See Format for details) Eigentool*file_save*type: 0
(See File Type for details)
Region of Interest/Volume of Interest ResourcesAdd 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
(See Drawing Regions for details) Eigentool*roi_voi*automaticOperation: 0
(See Automatic for details) Eigentool*roi_voi*mode: 0
(See Rectangle or Ellipse for details) Eigentool*roi_voi*area: 1
(See Window, Threshold, or Slice for details) Eigentool*roi_voi*operation: 0
(See Region or Volume Operation for details) Eigentool*roi_voi*voiStatisticsOutput: 0
(See Statistics for details) Eigentool*roi_voi*voiAreaDirection: 0
(See Surface Area for details) Eigentool*roi_voi*rotateCenter: true
(See Rotate for details) Eigentool*roi_voi*flipDirection: 0
(See Flip for details) Eigentool*roi_voi*viewMorphological: false Eigentool*roi_voi*viewRoiVoiProcessing: false Eigentool*roi_voi*viewImageProcessing: false Eigentool*roi_voi*viewMacro: false
(See Region of Interest/Volume of Interest Dialog Options for details) Eigentool*roi_voi*eraseFillDirection: 0
(See Erase/Fill Operations for details) Eigentool*roi_voi*eraseFillSize: 1
(See Erase/Fill Size for details) Eigentool*roi_voi*cleanConnectSize: 4
(See Clean Connect Size for details) Eigentool*roi_voi*cleanObjectSize: 0
(See Clean Object Size for details) Eigentool*roi_voi*iterations: 1
(See iterations for details) Eigentool*roi_voi*boundaryValue: 0
(See Boundary for details) Eigentool*roi_voi*connectSpursCorners: true
(See Connect for details) Eigentool*roi_voi*smoothNGauss: 1
(See # Gauss for details) Eigentool*roi_voi*voiKeepTopPercentagePercent: 25
(See Keep or Remove for details) Eigentool*roi_voi*voiNeighborNonZeroPercent: 50
(See Neighbor for details) Eigentool*roi_voi*fillVoiSliceAdd: false
(see FilG for details) Eigentool*roi_voi*voiFillVoiSliceLow: 0.0
(See Lo Hi Values for details) Eigentool*roi_voi*voiFillVoiSliceHigh: 0.0
(See Lo Hi Values for details) Eigentool*roi_voi*voiImageNumber: 1
(See # for details) Eigentool*roi_voi*voiBoundDeleteCrossovers: true
(See Delete Crossovers for details) Eigentool*roi_voi*roiGridSplitSizeY: 3
(See Grid, Y for details) Eigentool*roi_voi*roiGridSplitSizeX: 3
(See Grid, X or details) Eigentool*roi_voi*sampleSize: 1
(See Sample for details) Eigentool*roi_voi*voiThresholdAboveNoiseNumberStandardDeviations: 3
(See # Std Dev for details) Eigentool*roi_voi*voiThresholdAboveNoiseHistogramMaximum: 127
(See Max for details) Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberBins: 128
(See # bins for details) Eigentool*roi_voi*voiThresholdAboveNoiseHistogramNumberGauss: 1
(See # Gauss for details) Eigentool*roi_voi*voiThresholdAboveNoiseOutput: 0
(See Operation for details) Eigentool*roi_voi*voiThresholdAboveNoiseWholeImage: true
(See Whole Image for details) Eigentool*roi_voi*voiPrincipalAxisXPixelSize: 0.0
(See Principal Axis X for details) Eigentool*roi_voi*voiPrincipalAxisYPixelSize: 0.0
(See Principal Axis Y for details) Eigentool*roi_voi*voiPrincipalAxisZPixelSize: 0.0
(See Principal Axis Z for details) Eigentool*roi_voi*voiPrincipalAxisGap: 0.0
(See Principal Axis Gap for details) Eigentool*roi_voi*voiMakeSignatureNumberProcesses: 0
(See Processes for details) Eigentool*roi_voi*voiMakeSignatureSplitSize: 1
(See N x N for details) Eigentool*roi_voi*macroMode: 1
(See Run Macro for details) Eigentool*roi_voi*printMacro: false
(See Macro for details)
Display ResourcesAdd 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
Eigentool*display_image1*displaySize: 256
Eigentool*display_image1*displayMethod: 0
Eigentool*display_image1*splitDisplay: 0
Eigentool*display_image1*negative: 0
Eigentool*display_image1*smooth: 0
Eigentool*display_image1*colorMap: 0
Eigentool*display_image1*windowFunction: 0
Eigentool*display_image1*windowForm: 0
(See Display->Options->Window Form for details) Eigentool*display_image1*roiColor: 0
(See Display->Options->Roi->Draw Color for details) Eigentool*display_image1*roiEraseColor: 0
(See Display->Options->Roi->Erase Color for details) Eigentool*display_image1*annotate: 0
(See Display->Options->Annotate for details) Eigentool*display_image1*graticule: 2
(See Display->Options->Graticule for details) Eigentool*display_image1*cursorColor: 0
(See Display->Options->Cursor details)
Browser ResourcesAdd 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
(See Browser->View->Show Images as for details) Eigentool*browser1*windowLevel: 1
(See Browser->Options->Window/Level for details) Eigentool*browser1*roiVoi: 1
(See Browser->Options->Window/Level for details)
Registration ResourcesAdd 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. Eigentool*register*rotateOption: true true: Use rotation and translation when aligning images.false: Use translation only when aligning images.
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)
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
(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)
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. 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)
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) Eigentool*iso_data*isoDataOutput: 1Eigentool*iso_data*isoDataMethod: 0Eigentool*iso_data*isoDataNumClustersStart: 20Eigentool*iso_data*isoDataNumClustersEnd: 3Eigentool*iso_data*isoDataMinConnectSize: 0Eigentool*iso_data*isoDataMinPixelsPerCluster: 500Eigentool*iso_data*isoDataMaxPairsLump: 1Eigentool*iso_data*isoDataMaxIterations: 60Eigentool*iso_data*isoDataNumPixelsConnected: 0Eigentool*iso_data*isoDataWindowSize: 3 General ResourcesChoose 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
*scrollBarPlacement: XmTOP_LEFT
*enableToggleVisual: false
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