diff --git a/ARCHIVE/BRAINSTalairach/BRAINSTalairach.xml b/ARCHIVE/BRAINSTalairach/BRAINSTalairach.xml index cd7d2697c4..bce3d35e90 100644 --- a/ARCHIVE/BRAINSTalairach/BRAINSTalairach.xml +++ b/ARCHIVE/BRAINSTalairach/BRAINSTalairach.xml @@ -8,7 +8,7 @@ This program creates a VTK structured grid defining the Talairach coordinate system based on four points: AC, PC, IRP, and SLA. The resulting structred grid can be written as either a classic VTK file or the new VTK XML file format. Two representations of the resulting grid can be written. The first is a bounding box representation that also contains the location of the AC and PC points. The second representation is the full Talairach grid representation that includes the additional rows of boxes added to the inferior allowing full coverage of the cerebellum. - 5.3.2 + 5.4.0 http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairach https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt diff --git a/ARCHIVE/BRAINSTalairach/BRAINSTalairachMask.xml b/ARCHIVE/BRAINSTalairach/BRAINSTalairachMask.xml index b815ca2ef1..4c1b2f482e 100644 --- a/ARCHIVE/BRAINSTalairach/BRAINSTalairachMask.xml +++ b/ARCHIVE/BRAINSTalairach/BRAINSTalairachMask.xml @@ -8,7 +8,7 @@ This program creates a binary image representing the specified Talairach region. The input is an example image to define the physical space for the resulting image, the Talairach grid representation in VTK format, and the file containing the Talairach box definitions to be generated. These can be combined in BRAINS to create a label map using the procedure Brains::WorkupUtils::CreateLabelMapFromBinaryImages. - 5.3.2 + 5.4.0 http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairachMask https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt diff --git a/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml index 72c0e3775d..d7e1b773e8 100644 --- a/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml +++ b/BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml @@ -5,7 +5,7 @@ Given a list of probability maps for labels, create a discrete label map where only the highest probability region is used for the labeling. - 5.3.2 + 5.4.0 University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu diff --git a/BRAINSABC/brainseg/GeneratePurePlugMask.xml b/BRAINSABC/brainseg/GeneratePurePlugMask.xml index 293ba3b780..3e548a8dea 100644 --- a/BRAINSABC/brainseg/GeneratePurePlugMask.xml +++ b/BRAINSABC/brainseg/GeneratePurePlugMask.xml @@ -5,7 +5,7 @@ This program gets several modality image files and returns a binary mask that defines the pure plugs. - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSCommonLib/TestSuite/FindCenterOfBrain.xml b/BRAINSCommonLib/TestSuite/FindCenterOfBrain.xml index 3b9eb62d5c..6267745dca 100644 --- a/BRAINSCommonLib/TestSuite/FindCenterOfBrain.xml +++ b/BRAINSCommonLib/TestSuite/FindCenterOfBrain.xml @@ -7,7 +7,7 @@ https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu Hans Johnson(1,3,4); Kent Williams(1); (1=University of Iowa Department of Psychiatry, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering - 5.3.2 + 5.4.0 diff --git a/BRAINSConstellationDetector/TestSuite/LandmarksCompare.xml b/BRAINSConstellationDetector/TestSuite/LandmarksCompare.xml index cfb8da3fbc..c24ca5dea3 100755 --- a/BRAINSConstellationDetector/TestSuite/LandmarksCompare.xml +++ b/BRAINSConstellationDetector/TestSuite/LandmarksCompare.xml @@ -5,7 +5,7 @@ Compares two .fcsv or .wts text files and verifies that they are identicle. Used for testing landmarks files. - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml index e83ae5eb67..aa46debb7f 100644 --- a/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml +++ b/BRAINSConstellationDetector/gui/BRAINSConstellationDetectorGUI.xml @@ -6,7 +6,7 @@ This program provides the user with a GUI tool to view/manipulate landmarks for an input volume. - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ diff --git a/BRAINSConstellationDetector/landmarkStatistics/GenerateAverageLmkFile.xml b/BRAINSConstellationDetector/landmarkStatistics/GenerateAverageLmkFile.xml index 07d651b4ef..aea2447d6a 100755 --- a/BRAINSConstellationDetector/landmarkStatistics/GenerateAverageLmkFile.xml +++ b/BRAINSConstellationDetector/landmarkStatistics/GenerateAverageLmkFile.xml @@ -5,7 +5,7 @@ This program gets several fcsv file each one contains several landmarks with the same name but slightly different coordinates. For EACH landmark we compute the average coordination. - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSConstellationDetector/src/BRAINSClipInferior.xml b/BRAINSConstellationDetector/src/BRAINSClipInferior.xml index 431f04fd32..4ec522d1c5 100644 --- a/BRAINSConstellationDetector/src/BRAINSClipInferior.xml +++ b/BRAINSConstellationDetector/src/BRAINSClipInferior.xml @@ -5,7 +5,7 @@ This program will read the inputVolume as a short int image, write the BackgroundFillValue everywhere inferior to the lower bound, and write the resulting clipped short int image in the outputVolume. - 5.3.2 + 5.4.0 inputVolume diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml index 542a25a418..f97a1ae63e 100644 --- a/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml +++ b/BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml @@ -7,7 +7,7 @@ Hans J. Johnson (hans-johnson -at- uiowa.edu), Ali Ghayoor - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt diff --git a/BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml b/BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml index 3fdc8d65fd..8c0c10930a 100644 --- a/BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml +++ b/BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml @@ -5,7 +5,7 @@ This program converts the original landmark file to the target landmark file using the input transform. - 5.3.2 + 5.4.0 Ali Ghayoor and Hans J. Johnson diff --git a/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml b/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml index 3b48fda9ef..1ed65bd7ae 100644 --- a/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml +++ b/BRAINSConstellationDetector/src/BRAINSEyeDetector.xml @@ -5,7 +5,7 @@ - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ diff --git a/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml index eb02ba3ba1..687ad8682d 100644 --- a/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml +++ b/BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml @@ -7,7 +7,7 @@ - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ diff --git a/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml b/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml index f5bc6c9055..5e8299966f 100644 --- a/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml +++ b/BRAINSConstellationDetector/src/BRAINSLmkTransform.xml @@ -6,7 +6,7 @@ This utility program estimates the affine transform to align the fixed landmarks to the moving landmarks, and then generate the resampled moving image to the same physical space as that of the reference image. - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ diff --git a/BRAINSConstellationDetector/src/BRAINSTransformFromFiducials.xml b/BRAINSConstellationDetector/src/BRAINSTransformFromFiducials.xml index 065dee9a37..41f8425144 100644 --- a/BRAINSConstellationDetector/src/BRAINSTransformFromFiducials.xml +++ b/BRAINSConstellationDetector/src/BRAINSTransformFromFiducials.xml @@ -3,7 +3,7 @@ Registration.Specialized Fiducial Registration (BRAINS) Computes a rigid, similarity or affine transform from a matched list of fiducials - 5.3.2 + 5.4.0 http://www.slicer.org/slicerWiki/index.php/Modules:TransformFromFiducials-Documentation-3.6 Casey B Goodlett diff --git a/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml index 6c813541a6..2ce6eaa6d4 100644 --- a/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml +++ b/BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml @@ -3,7 +3,7 @@ Utilities.BRAINS Trim Foreground In Direction (BRAINS) This program will trim off the neck and also air-filling noise from the inputImage. - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/art/ diff --git a/BRAINSConstellationDetector/src/BinaryMaskEditorBasedOnLandmarks.xml b/BRAINSConstellationDetector/src/BinaryMaskEditorBasedOnLandmarks.xml index 0bb80a75fc..b8674de168 100644 --- a/BRAINSConstellationDetector/src/BinaryMaskEditorBasedOnLandmarks.xml +++ b/BRAINSConstellationDetector/src/BinaryMaskEditorBasedOnLandmarks.xml @@ -5,7 +5,7 @@ - 5.3.2 + 5.4.0 http://www.nitrc.org/projects/brainscdetector/ diff --git a/BRAINSConstellationDetector/src/ComputeReflectiveCorrelationMetric.xml b/BRAINSConstellationDetector/src/ComputeReflectiveCorrelationMetric.xml index 23488b58a8..cd70841047 100644 --- a/BRAINSConstellationDetector/src/ComputeReflectiveCorrelationMetric.xml +++ b/BRAINSConstellationDetector/src/ComputeReflectiveCorrelationMetric.xml @@ -4,7 +4,7 @@ Compute RC metric values in exhausive search - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSConstellationDetector/src/insertMidACPCpoint.xml b/BRAINSConstellationDetector/src/insertMidACPCpoint.xml index a56597a76c..3c466b6cfc 100644 --- a/BRAINSConstellationDetector/src/insertMidACPCpoint.xml +++ b/BRAINSConstellationDetector/src/insertMidACPCpoint.xml @@ -5,7 +5,7 @@ This program gets a landmark fcsv file and adds a new landmark as the midpoint between AC and PC points to the output landmark fcsv file - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSConstellationDetector/src/landmarksConstellationAligner.xml b/BRAINSConstellationDetector/src/landmarksConstellationAligner.xml index 7edf620d4a..4a29bbddcb 100644 --- a/BRAINSConstellationDetector/src/landmarksConstellationAligner.xml +++ b/BRAINSConstellationDetector/src/landmarksConstellationAligner.xml @@ -5,7 +5,7 @@ This program converts the original landmark files to the acpc-aligned landmark files - 5.3.2 + 5.4.0 Ali Ghayoor diff --git a/BRAINSDWICleanup/BRAINSDWICleanup.xml b/BRAINSDWICleanup/BRAINSDWICleanup.xml index 517448482d..8583f77961 100644 --- a/BRAINSDWICleanup/BRAINSDWICleanup.xml +++ b/BRAINSDWICleanup/BRAINSDWICleanup.xml @@ -5,7 +5,7 @@ Remove bad gradients/volumes from DWI NRRD file. - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt This tool was developed by Kent Williams. diff --git a/BRAINSDeface/BRAINSDeface.xml b/BRAINSDeface/BRAINSDeface.xml index a63de69e82..bd4901c76f 100755 --- a/BRAINSDeface/BRAINSDeface.xml +++ b/BRAINSDeface/BRAINSDeface.xml @@ -5,7 +5,7 @@ This program: 1) will deface images from a set of images. Inputs must be ACPC aligned, and AC, PC, LE, RE provided. - 5.3.3 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt diff --git a/BRAINSFit/BRAINSFit.xml b/BRAINSFit/BRAINSFit.xml index 44c8e6d22e..a5c01aaa78 100644 --- a/BRAINSFit/BRAINSFit.xml +++ b/BRAINSFit/BRAINSFit.xml @@ -7,7 +7,7 @@ https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Hans J. Johnson (hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu), Ali Ghayoor - 5.3.2 + 5.4.0 diff --git a/BRAINSFit/PerformMetricTest.xml b/BRAINSFit/PerformMetricTest.xml index 40e03eb0b3..27f1e1c27a 100644 --- a/BRAINSFit/PerformMetricTest.xml +++ b/BRAINSFit/PerformMetricTest.xml @@ -5,7 +5,7 @@ Compare Mattes/MSQ metric value for two input images and a possible input BSpline transform. - 5.3.2 + 5.4.0 A utility to compare metric value between two input images. https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Ali Ghayoor diff --git a/BRAINSInitializedControlPoints/BRAINSInitializedControlPoints.xml b/BRAINSInitializedControlPoints/BRAINSInitializedControlPoints.xml index 45e3d66b97..4df8e3a506 100755 --- a/BRAINSInitializedControlPoints/BRAINSInitializedControlPoints.xml +++ b/BRAINSInitializedControlPoints/BRAINSInitializedControlPoints.xml @@ -5,7 +5,7 @@ Outputs bspline control points as landmarks - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Mark Scully diff --git a/BRAINSIntensityNormalize/BRAINSIntensityNormalize.xml b/BRAINSIntensityNormalize/BRAINSIntensityNormalize.xml index 225c3ac59f..1eeae31e8d 100644 --- a/BRAINSIntensityNormalize/BRAINSIntensityNormalize.xml +++ b/BRAINSIntensityNormalize/BRAINSIntensityNormalize.xml @@ -5,7 +5,7 @@ Computes the percentile rescaling of an image - 1.0 + 5.4.0 Alexander B. Powers and Hans J. Johnson @@ -106,4 +106,4 @@ - \ No newline at end of file + diff --git a/BRAINSLabelStats/BRAINSLabelStats.xml b/BRAINSLabelStats/BRAINSLabelStats.xml index 71c7b48f2b..499e99e35b 100644 --- a/BRAINSLabelStats/BRAINSLabelStats.xml +++ b/BRAINSLabelStats/BRAINSLabelStats.xml @@ -3,7 +3,7 @@ Quantification Label Statistics (BRAINS) Compute image statistics within each label of a label map. - 5.3.2 + 5.4.0 http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Vincent A. Magnotta diff --git a/BRAINSLandmarkInitializer/BRAINSLandmarkInitializer.xml b/BRAINSLandmarkInitializer/BRAINSLandmarkInitializer.xml index fbb033ddeb..1f2eebcf74 100644 --- a/BRAINSLandmarkInitializer/BRAINSLandmarkInitializer.xml +++ b/BRAINSLandmarkInitializer/BRAINSLandmarkInitializer.xml @@ -3,7 +3,7 @@ Utilities.BRAINS BRAINSLandmarkInitializer Create transformation file (*.h5) from a pair of landmarks (*fcsv) files. - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Eunyoung Regina Kim, Ali Ghayoor, and Hans J. Johnson diff --git a/BRAINSMultiModeSegment/BRAINSMultiModeSegment.xml b/BRAINSMultiModeSegment/BRAINSMultiModeSegment.xml index 425e76d86f..6ff50c6b75 100644 --- a/BRAINSMultiModeSegment/BRAINSMultiModeSegment.xml +++ b/BRAINSMultiModeSegment/BRAINSMultiModeSegment.xml @@ -4,7 +4,7 @@ Segment based on rectangular region of joint histogram (BRAINS) This tool creates binary regions based on segmenting multiple image modalitities at once. - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu diff --git a/BRAINSMush/BRAINSMush.xml b/BRAINSMush/BRAINSMush.xml index cf0194e4b0..b6fedae960 100755 --- a/BRAINSMush/BRAINSMush.xml +++ b/BRAINSMush/BRAINSMush.xml @@ -5,7 +5,7 @@ This program: 1) generates a weighted mixture image optimizing the mean and variance and 2) produces a mask of the brain volume - 5.3.2 + 5.4.0 http:://mri.radiology.uiowa.edu https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt diff --git a/BRAINSPosteriorToContinuousClass/BRAINSPosteriorToContinuousClass.xml b/BRAINSPosteriorToContinuousClass/BRAINSPosteriorToContinuousClass.xml index bc49c87b6b..fb7ab15bed 100644 --- a/BRAINSPosteriorToContinuousClass/BRAINSPosteriorToContinuousClass.xml +++ b/BRAINSPosteriorToContinuousClass/BRAINSPosteriorToContinuousClass.xml @@ -3,7 +3,7 @@ BRAINS.Classify Tissue Classification This program will generate an 8-bit continuous tissue classified image based on BRAINSABC posterior images. - 5.3.2 + 5.4.0 http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Vincent A. Magnotta diff --git a/BRAINSROIAuto/BRAINSROIAuto.xml b/BRAINSROIAuto/BRAINSROIAuto.xml index 928d2c0aaa..598d6bd1cb 100644 --- a/BRAINSROIAuto/BRAINSROIAuto.xml +++ b/BRAINSROIAuto/BRAINSROIAuto.xml @@ -4,7 +4,7 @@ Foreground masking (BRAINS) This program is used to create a mask over the most prominant forground region in an image. This is accomplished via a combination of otsu thresholding and a closing operation. More documentation is available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/ForegroundMasking. - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu diff --git a/BRAINSResample/BRAINSResample.xml b/BRAINSResample/BRAINSResample.xml index 34d12e911b..658eb3b822 100644 --- a/BRAINSResample/BRAINSResample.xml +++ b/BRAINSResample/BRAINSResample.xml @@ -6,7 +6,7 @@ This program collects together three common image processing tasks that all involve resampling an image volume: Resampling to a new resolution and spacing, applying a transformation (using an ITK transform IO mechanisms) and Warping (using a vector image deformation field). Full documentation available here: http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample. - 5.3.2 + 5.4.0 http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson. diff --git a/BRAINSResample/BRAINSResize.xml b/BRAINSResample/BRAINSResize.xml index a2e03c8e25..344010ca94 100644 --- a/BRAINSResample/BRAINSResize.xml +++ b/BRAINSResample/BRAINSResize.xml @@ -6,7 +6,7 @@ This program is useful for downsampling an image by a constant scale factor. - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt This tool was developed by Hans Johnson. diff --git a/BRAINSSnapShotWriter/BRAINSSnapShotWriter.xml b/BRAINSSnapShotWriter/BRAINSSnapShotWriter.xml index 18205caaf5..86c31b2aea 100644 --- a/BRAINSSnapShotWriter/BRAINSSnapShotWriter.xml +++ b/BRAINSSnapShotWriter/BRAINSSnapShotWriter.xml @@ -3,7 +3,7 @@ Utilities.BRAINS BRAINSSnapShotWriter Create 2D snapshot of input images. Mask images are color-coded - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Eunyoung Regina Kim diff --git a/BRAINSStripRotation/BRAINSStripRotation.xml b/BRAINSStripRotation/BRAINSStripRotation.xml index 52cb4354f4..d701a3e2c7 100644 --- a/BRAINSStripRotation/BRAINSStripRotation.xml +++ b/BRAINSStripRotation/BRAINSStripRotation.xml @@ -3,7 +3,7 @@ Utilities BRAINS Strip Rotation Read an Image, write out same image with identity rotation matrix plus an ITK transform file - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Kent WIlliams diff --git a/BRAINSSuperResolution/GenerateEdgeMap/GenerateEdgeMapImage.xml b/BRAINSSuperResolution/GenerateEdgeMap/GenerateEdgeMapImage.xml index baf3175e17..1992e3db7c 100644 --- a/BRAINSSuperResolution/GenerateEdgeMap/GenerateEdgeMapImage.xml +++ b/BRAINSSuperResolution/GenerateEdgeMap/GenerateEdgeMapImage.xml @@ -3,7 +3,7 @@ SuperResolution GenerateEdgeMapImage Inverse of Maximum Gradient Image - 5.3.2 + 5.4.0 https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Ali Ghayoor diff --git a/BRAINSTransformConvert/BRAINSTransformConvert.xml b/BRAINSTransformConvert/BRAINSTransformConvert.xml index 744cbf16a2..b687ae9773 100644 --- a/BRAINSTransformConvert/BRAINSTransformConvert.xml +++ b/BRAINSTransformConvert/BRAINSTransformConvert.xml @@ -3,7 +3,7 @@ Utilities.BRAINS BRAINS Transform Convert Convert ITK transforms to higher order transforms - 5.3.2 + 5.4.0 A utility to convert between transform file formats. https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Hans J. Johnson,Kent Williams, Ali Ghayoor diff --git a/CMake/ProjectSourceVersionVars.cmake b/CMake/ProjectSourceVersionVars.cmake index 23bbc81088..d4df2ee60f 100644 --- a/CMake/ProjectSourceVersionVars.cmake +++ b/CMake/ProjectSourceVersionVars.cmake @@ -5,8 +5,8 @@ macro( _set_if_not_empty var value ) endmacro() set( _GIT_VERSION_MAJOR "5" ) -set( _GIT_VERSION_MINOR "3" ) -_set_if_not_empty( _GIT_VERSION_PATCH "2" ) +set( _GIT_VERSION_MINOR "4" ) +_set_if_not_empty( _GIT_VERSION_PATCH "0" ) _set_if_not_empty( _GIT_VERSION_TWEAK "" ) _set_if_not_empty( _GIT_VERSION_RC "" ) ## DO NOT SET THE CONSTANTLY CHANGING VERSION_POST for DISTRIBUTION RELEASES diff --git a/CMakeLists.txt b/CMakeLists.txt index dfea464c04..e5fdefa386 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -37,8 +37,11 @@ set(LOCAL_PROJECT_NAME BRAINSTools) # <-- the primary product endpoint (Often ma project(${LOCAL_PROJECT_NAME} LANGUAGES C CXX DESCRIPTION "BRAINSTools see github at https://github.com/BRAINSia/BRAINSTools" #<-- cmake version 3.9 or greater - VERSION 5.3.2 + VERSION 5.4.0 ) +# VERSION 5.4.0 The version used to create the final PREDICTHD_BIDS_DEFACE dataset. +# VERSION 5.3.2 Many tools placed in ARCHIVE + #-- The project() command stores the version number and its components in variables #-- PROJECT_VERSION, _VERSION #-- PROJECT_VERSION_MAJOR, _VERSION_MAJOR diff --git a/DWIConvert/DWIConvert.xml b/DWIConvert/DWIConvert.xml index 7eee0b3011..372343bd34 100755 --- a/DWIConvert/DWIConvert.xml +++ b/DWIConvert/DWIConvert.xml @@ -3,7 +3,7 @@ Diffusion.Import and Export Diffusion-weighted DICOM Import (DWIConvert) - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Modules/DWIConverter Apache License Version 2.0 Hans Johnson (UIowa), Vince Magnotta (UIowa) Joy Matsui (UIowa), Kent Williams (UIowa), Mark Scully (Uiowa), Xiaodong Tao (GE) diff --git a/DWIConvert/TestSuite/DWICompare.xml b/DWIConvert/TestSuite/DWICompare.xml index 5348218928..fec4b223ed 100755 --- a/DWIConvert/TestSuite/DWICompare.xml +++ b/DWIConvert/TestSuite/DWICompare.xml @@ -3,7 +3,7 @@ Converters Nrrd DWI comparison - 5.3.2 + 5.4.0 http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DWIConvert https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Mark Scully (UIowa) diff --git a/DWIConvert/TestSuite/DWISimpleCompare.xml b/DWIConvert/TestSuite/DWISimpleCompare.xml index e03b49a1d2..3fc96d7c69 100644 --- a/DWIConvert/TestSuite/DWISimpleCompare.xml +++ b/DWIConvert/TestSuite/DWISimpleCompare.xml @@ -3,7 +3,7 @@ Converters Nrrd DWI comparison - 5.3.2 + 5.4.0 http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DWIConvert https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt Mark Scully (UIowa) diff --git a/GTRACT/Cmdline/compareTractInclusion.xml b/GTRACT/Cmdline/compareTractInclusion.xml index dcbe708c2e..d2aeae9ad7 100644 --- a/GTRACT/Cmdline/compareTractInclusion.xml +++ b/GTRACT/Cmdline/compareTractInclusion.xml @@ -5,7 +5,7 @@ This program will halt with a status code indicating whether a test tract is nearly enough included in a standard tract in the sense that every fiber in the test tract has a low enough sum of squares distance to some fiber in the standard tract modulo spline resampling of every fiber to a fixed number of points. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/extractNrrdVectorIndex.xml b/GTRACT/Cmdline/extractNrrdVectorIndex.xml index de3ab1f2c4..eb8f7f47ac 100644 --- a/GTRACT/Cmdline/extractNrrdVectorIndex.xml +++ b/GTRACT/Cmdline/extractNrrdVectorIndex.xml @@ -5,7 +5,7 @@ This program will extract a 3D image (single vector) from a vector 3D image at a given vector index. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/future_work/gtractCoRegAnatomyRigid.xml b/GTRACT/Cmdline/future_work/gtractCoRegAnatomyRigid.xml index 20d5a12cca..f87377f056 100644 --- a/GTRACT/Cmdline/future_work/gtractCoRegAnatomyRigid.xml +++ b/GTRACT/Cmdline/future_work/gtractCoRegAnatomyRigid.xml @@ -5,7 +5,7 @@ This program will register a NRRD diffusion weighted 4D vector image to a fixed anatomical image to produce a rigid fit. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/future_work/gtractFreeTracking.xml b/GTRACT/Cmdline/future_work/gtractFreeTracking.xml index 0c13f838eb..486590d63d 100644 --- a/GTRACT/Cmdline/future_work/gtractFreeTracking.xml +++ b/GTRACT/Cmdline/future_work/gtractFreeTracking.xml @@ -5,7 +5,7 @@ This program will use streamlines fiber tracking to identify fiber tracts in a tensor image. A seed region is specify for initializing the algorithm. All fibers are kept and are terminated based on the stopping criteria including anisotropy, curvature and length. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/future_work/gtractGraphSearchTracking.xml b/GTRACT/Cmdline/future_work/gtractGraphSearchTracking.xml index 94efe9df3b..13f0c0b474 100644 --- a/GTRACT/Cmdline/future_work/gtractGraphSearchTracking.xml +++ b/GTRACT/Cmdline/future_work/gtractGraphSearchTracking.xml @@ -5,7 +5,7 @@ This program implements the Graph Serach Tracking method proposed by Cheng et al. in NeuroImage Volume 31, Issue 3, 1 July 2006, Pages 1075-1085 for finding the tracks in a tensor image. This method to generate fibers in a Tensor representation where crossing fibers occur. This is defined by low anisotropy and high curvature. Both of these values are controlled by the user. In these regions, three directions for tracking are considered. This includes the primary eigenvector, secondary eigenvector, and a vector with random pertubations added pointing towards the ending region. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/future_work/gtractGuidedTracking.xml b/GTRACT/Cmdline/future_work/gtractGuidedTracking.xml index a2130d522a..daa49560ab 100644 --- a/GTRACT/Cmdline/future_work/gtractGuidedTracking.xml +++ b/GTRACT/Cmdline/future_work/gtractGuidedTracking.xml @@ -5,7 +5,7 @@ This program will use the Guided Tracking method proposed by Cheng et al. in NeuroImage Volume 31, Issue 3, 1 July 2006, Pages 1075-1085 for finding the tracks in a tensor image. The method will use a guide fiber as apriori information for the fiber tract position and orientation. If the current eigenvector direction is significantly different from the guide fiber direction at that point, then the guide fiber is used instead of the eigenvector direction. The distance for which the guide fiber has an effect is defined by the user. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/future_work/gtractStreamlineTracking.xml b/GTRACT/Cmdline/future_work/gtractStreamlineTracking.xml index c27bbbbb01..7c6cca988f 100644 --- a/GTRACT/Cmdline/future_work/gtractStreamlineTracking.xml +++ b/GTRACT/Cmdline/future_work/gtractStreamlineTracking.xml @@ -5,7 +5,7 @@ This program create fiber tracts in a tensor image using a basic streamlines algorithm. The algorithm requires a starting and ending region to be be defined for the fiber tracts. Only those that reach the ending region without terminating are kept. Criteria for termination include length, anisotropy, and curvature. These can be controlled by user. In addition, the TEND method as proposed by Lazar et al Human Brain Mapping 18:306-321(2003) has been instrumented. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractAnisotropyMap.xml b/GTRACT/Cmdline/gtractAnisotropyMap.xml index 15be930cbb..1a73a7bcb3 100644 --- a/GTRACT/Cmdline/gtractAnisotropyMap.xml +++ b/GTRACT/Cmdline/gtractAnisotropyMap.xml @@ -5,7 +5,7 @@ This program will generate a scalar map of anisotropy, given a tensor representation. Anisotropy images are used for fiber tracking, but the anisotropy scalars are not defined along the path. Instead, the tensor representation is included as point data allowing all of these metrics to be computed using only the fiber tract point data. The images can be saved in any ITK supported format, but it is suggested that you use an image format that supports the definition of the image origin. This includes NRRD, NifTI, and Meta formats. These images can also be used for scalar analysis including regional anisotropy measures or VBM style analysis. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractAverageBvalues.xml b/GTRACT/Cmdline/gtractAverageBvalues.xml index 715bad14f8..48dc5c8686 100644 --- a/GTRACT/Cmdline/gtractAverageBvalues.xml +++ b/GTRACT/Cmdline/gtractAverageBvalues.xml @@ -5,7 +5,7 @@ This program will directly average together the baseline gradients (b value equals 0) within a DWI scan. This is usually used after gtractCoregBvalues. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractClipAnisotropy.xml b/GTRACT/Cmdline/gtractClipAnisotropy.xml index c50ddec794..75dbd2158a 100644 --- a/GTRACT/Cmdline/gtractClipAnisotropy.xml +++ b/GTRACT/Cmdline/gtractClipAnisotropy.xml @@ -5,7 +5,7 @@ This program will zero the first and/or last slice of an anisotropy image, creating a clipped anisotropy image. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractCoRegAnatomy.xml b/GTRACT/Cmdline/gtractCoRegAnatomy.xml index 06a7574ce4..e3c5feaaf5 100644 --- a/GTRACT/Cmdline/gtractCoRegAnatomy.xml +++ b/GTRACT/Cmdline/gtractCoRegAnatomy.xml @@ -5,7 +5,7 @@ This program will register a Nrrd diffusion weighted 4D vector image to a fixed anatomical image. Two registration methods are supported for alignment with anatomical images: Rigid and B-Spline. The rigid registration performs a rigid body registration with the anatomical images and should be done as well to initialize the B-Spline transform. The B-SPline transform is the deformable transform, where the user can control the amount of deformation based on the number of control points as well as the maximum distance that these points can move. The B-Spline registration places a low dimensional grid in the image, which is deformed. This allows for some susceptibility related distortions to be removed from the diffusion weighted images. In general the amount of motion in the slice selection and read-out directions direction should be kept low. The distortion is in the phase encoding direction in the images. It is recommended that skull stripped (i.e. image containing only brain with skull removed) images shoud be used for image co-registration with the B-Spline transform. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractCoRegAnatomyBspline.xml b/GTRACT/Cmdline/gtractCoRegAnatomyBspline.xml index e122727795..b9aaf8561b 100644 --- a/GTRACT/Cmdline/gtractCoRegAnatomyBspline.xml +++ b/GTRACT/Cmdline/gtractCoRegAnatomyBspline.xml @@ -5,7 +5,7 @@ This program will register a NRRD diffusion weighted 4D vector image to a fixed anatomical image to produce a Bspline fit. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractConcatDwi.xml b/GTRACT/Cmdline/gtractConcatDwi.xml index 907785922d..d0e792619e 100644 --- a/GTRACT/Cmdline/gtractConcatDwi.xml +++ b/GTRACT/Cmdline/gtractConcatDwi.xml @@ -5,7 +5,7 @@ This program will concatenate two DTI runs together. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractCopyImageOrientation.xml b/GTRACT/Cmdline/gtractCopyImageOrientation.xml index 1f56e36f18..abd0822a70 100644 --- a/GTRACT/Cmdline/gtractCopyImageOrientation.xml +++ b/GTRACT/Cmdline/gtractCopyImageOrientation.xml @@ -5,7 +5,7 @@ This program will copy the orientation from the reference image into the moving image. Currently, the registration process requires that the diffusion weighted images and the anatomical images have the same image orientation (i.e. Axial, Coronal, Sagittal). It is suggested that you copy the image orientation from the diffusion weighted images and apply this to the anatomical image. This image can be subsequently removed after the registration step is complete. We anticipate that this limitation will be removed in future versions of the registration programs. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractCoregBvalues.xml b/GTRACT/Cmdline/gtractCoregBvalues.xml index b1a903f120..a1d9128ea6 100644 --- a/GTRACT/Cmdline/gtractCoregBvalues.xml +++ b/GTRACT/Cmdline/gtractCoregBvalues.xml @@ -5,7 +5,7 @@ This step should be performed after converting DWI scans from DICOM to NRRD format. This program will register all gradients in a NRRD diffusion weighted 4D vector image (moving image) to a specified index in a fixed image. It also supports co-registration with a T2 weighted image or field map in the same plane as the DWI data. The fixed image for the registration should be a b0 image. A mutual information metric cost function is used for the registration because of the differences in signal intensity as a result of the diffusion gradients. The full affine allows the registration procedure to correct for eddy current distortions that may exist in the data. If the eddyCurrentCorrection is enabled, relaxationFactor (0.25) and maximumStepSize (0.1) should be adjusted. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractCostFastMarching.xml b/GTRACT/Cmdline/gtractCostFastMarching.xml index ee16ca628f..441048f386 100644 --- a/GTRACT/Cmdline/gtractCostFastMarching.xml +++ b/GTRACT/Cmdline/gtractCostFastMarching.xml @@ -5,7 +5,7 @@ This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the first portion of the algorithm. The user must first run gtractFastMarchingTracking to generate the actual fiber tracts. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino. diff --git a/GTRACT/Cmdline/gtractCreateGuideFiber.xml b/GTRACT/Cmdline/gtractCreateGuideFiber.xml index b299d4f618..befcb11811 100644 --- a/GTRACT/Cmdline/gtractCreateGuideFiber.xml +++ b/GTRACT/Cmdline/gtractCreateGuideFiber.xml @@ -5,7 +5,7 @@ This program will create a guide fiber by averaging fibers from a previously generated tract. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractFastMarchingTracking.xml b/GTRACT/Cmdline/gtractFastMarchingTracking.xml index 82256b8f74..9a2699bec9 100644 --- a/GTRACT/Cmdline/gtractFastMarchingTracking.xml +++ b/GTRACT/Cmdline/gtractFastMarchingTracking.xml @@ -5,7 +5,7 @@ This program will use a fast marching fiber tracking algorithm to identify fiber tracts from a tensor image. This program is the second portion of the algorithm. The user must first run gtractCostFastMarching to generate the vcl_cost image. The second step of the algorithm implemented here is a gradient descent soplution from the defined ending region back to the seed points specified in gtractCostFastMarching. This algorithm is roughly based on the work by G. Parker et al. from IEEE Transactions On Medical Imaging, 21(5): 505-512, 2002. An additional feature of including anisotropy into the vcl_cost function calculation is included. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. The original code here was developed by Daisy Espino. diff --git a/GTRACT/Cmdline/gtractFiberTracking.xml b/GTRACT/Cmdline/gtractFiberTracking.xml index 6a1ae0aea8..ccc67c76b5 100644 --- a/GTRACT/Cmdline/gtractFiberTracking.xml +++ b/GTRACT/Cmdline/gtractFiberTracking.xml @@ -5,7 +5,7 @@ This program implements four fiber tracking methods (Free, Streamline, GraphSearch, Guided). The output of the fiber tracking is vtkPolyData (i.e. Polylines) that can be loaded into Slicer3 for visualization. The poly data can be saved in either old VTK format files (.vtk) or in the new VTK XML format (.xml). The polylines contain point data that defines ther Tensor at each point along the fiber tract. This can then be used to rendered as glyphs in Slicer3 and can be used to define severeal scalar measures without referencing back to the anisotropy images. (1) Free tracking is a basic streamlines algorithm. This is a direct implementation of the method original proposed by Basser et al. The tracking follows the primarty eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either as a result of maximum fiber length, low ansiotropy, or large curvature. This is a great way to explore your data. (2) The streamlines algorithm is a direct implementation of the method originally proposed by Basser et al. The tracking follows the primary eigenvector. The tracking begins with seed points in the starting region. Only those voxels above the specified anisotropy threshold in the starting region are used as seed points. Tracking terminates either by reaching the ending region or reaching some stopping criteria. Stopping criteria are specified using the following parameters: tracking threshold, curvature threshold, and max length. Only paths terminating in the ending region are kept in this method. The TEND algorithm proposed by Lazar et al. (Human Brain Mapping 18:306-321, 2003) has been instrumented. This can be enabled using the --useTend option while performing Streamlines tracking. This utilizes the entire diffusion tensor to deflect the incoming vector instead of simply following the primary eigenvector. The TEND parameters are set using the --tendF and --tendG options. (3) Graph Search tracking is the first step in the full GTRACT algorithm developed by Cheng et al. (NeuroImage 31(3): 1075-1085, 2006) for finding the tracks in a tensor image. This method was developed to generate fibers in a Tensor representation where crossing fibers occur. The graph search algorithm follows the primary eigenvector in non-ambigous regions and utilizes branching and a graph search algorithm in ambigous regions. Ambiguous tracking regions are defined based on two criteria: Branching Al Threshold (anisotropy values below this value and above the traching threshold) and Curvature Major Eigen (angles of the primary eigenvector direction and the current tracking direction). In regions that meet this criteria, two or three tracking paths are considered. The first is the standard primary eigenvector direction. The second is the seconadary eigenvector direction. This is based on the assumption that these regions may be prolate regions. If the Random Walk option is selected then a third direction is also considered. This direction is defined by a cone pointing from the current position to the centroid of the ending region. The interior angle of the cone is specified by the user with the Branch/Guide Angle parameter. A vector contained inside of the cone is selected at random and used as the third direction. This method can also utilize the TEND option where the primary tracking direction is that specified by the TEND method instead of the primary eigenvector. The parameter '--maximumBranchPoints' allows the tracking to have this number of branches being considered at a time. If this number of branch points is exceeded at any time, then the algorithm will revert back to a streamline alogrithm until the number of branches is reduced. This allows the user to constrain the computational complexity of the algorithm. (4) The second phase of the GTRACT algorithm is Guided Tracking. This method incorporates anatomical information about the track orientation using an initial guess of the fiber track. In the originally proposed GTRACT method, this would be created from the fibers resulting from the Graph Search tracking. However, in practice this can be created using any method and could be defined manually. To create the guide fiber the program gtractCreateGuideFiber can be used. This program will load a fiber tract that has been generated and create a centerline representation of the fiber tract (i.e. a single fiber). In this method, the fiber tracking follows the primary eigenvector direction unless it deviates from the guide fiber track by a angle greater than that specified by the '--guidedCurvatureThreshold' parameter. The user must specify the guide fiber when running this program. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta, Greg Harris and Yongqiang Zhao. diff --git a/GTRACT/Cmdline/gtractImageConformity.xml b/GTRACT/Cmdline/gtractImageConformity.xml index 7498f5a6f9..03a8196b96 100644 --- a/GTRACT/Cmdline/gtractImageConformity.xml +++ b/GTRACT/Cmdline/gtractImageConformity.xml @@ -5,7 +5,7 @@ This program will straighten out the Direction and Origin to match the Reference Image. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractInvertBSplineTransform.xml b/GTRACT/Cmdline/gtractInvertBSplineTransform.xml index ca8b95762b..d0729e7408 100644 --- a/GTRACT/Cmdline/gtractInvertBSplineTransform.xml +++ b/GTRACT/Cmdline/gtractInvertBSplineTransform.xml @@ -5,7 +5,7 @@ This program will invert a B-Spline transform using a thin-plate spline approximation. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractInvertDisplacementField.xml b/GTRACT/Cmdline/gtractInvertDisplacementField.xml index c88287fa9a..c5bbd2bebb 100644 --- a/GTRACT/Cmdline/gtractInvertDisplacementField.xml +++ b/GTRACT/Cmdline/gtractInvertDisplacementField.xml @@ -5,7 +5,7 @@ This program will invert a deformatrion field. The size of the deformation field is defined by an example image provided by the user Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta. diff --git a/GTRACT/Cmdline/gtractInvertRigidTransform.xml b/GTRACT/Cmdline/gtractInvertRigidTransform.xml index f5f4d9ea0f..dd0b9010ea 100644 --- a/GTRACT/Cmdline/gtractInvertRigidTransform.xml +++ b/GTRACT/Cmdline/gtractInvertRigidTransform.xml @@ -5,7 +5,7 @@ This program will invert a Rigid transform. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractResampleAnisotropy.xml b/GTRACT/Cmdline/gtractResampleAnisotropy.xml index c3593790cd..6fae63d3f2 100644 --- a/GTRACT/Cmdline/gtractResampleAnisotropy.xml +++ b/GTRACT/Cmdline/gtractResampleAnisotropy.xml @@ -5,7 +5,7 @@ This program will resample a floating point image using either the Rigid or B-Spline transform. You may want to save the aligned B0 image after each of the anisotropy map co-registration steps with the anatomical image to check the registration quality with another tool. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractResampleB0.xml b/GTRACT/Cmdline/gtractResampleB0.xml index 2023bca72f..3a2a18ab3d 100644 --- a/GTRACT/Cmdline/gtractResampleB0.xml +++ b/GTRACT/Cmdline/gtractResampleB0.xml @@ -5,7 +5,7 @@ This program will resample a signed short image using either a Rigid or B-Spline transform. The user must specify a template image that will be used to define the origin, orientation, spacing, and size of the resampled image. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractResampleCodeImage.xml b/GTRACT/Cmdline/gtractResampleCodeImage.xml index 750c703adc..51bea48bd1 100644 --- a/GTRACT/Cmdline/gtractResampleCodeImage.xml +++ b/GTRACT/Cmdline/gtractResampleCodeImage.xml @@ -5,7 +5,7 @@ This program will resample a short integer code image using either the Rigid or Inverse-B-Spline transform. The reference image is the DTI tensor anisotropy image space, and the input code image is in anatomical space. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractResampleDWIInPlace.xml b/GTRACT/Cmdline/gtractResampleDWIInPlace.xml index b875893ced..e6e45ba2fc 100644 --- a/GTRACT/Cmdline/gtractResampleDWIInPlace.xml +++ b/GTRACT/Cmdline/gtractResampleDWIInPlace.xml @@ -5,7 +5,7 @@ Resamples DWI image to structural image. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta, Greg Harris, Hans Johnson, and Joy Matsui. diff --git a/GTRACT/Cmdline/gtractResampleFibers.xml b/GTRACT/Cmdline/gtractResampleFibers.xml index a5f15f9ce4..f50c3bb6a5 100644 --- a/GTRACT/Cmdline/gtractResampleFibers.xml +++ b/GTRACT/Cmdline/gtractResampleFibers.xml @@ -5,7 +5,7 @@ This program will resample a fiber tract with respect to a pair of deformation fields that represent the forward and reverse deformation fields. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractTensor.xml b/GTRACT/Cmdline/gtractTensor.xml index f27eff7216..d5fe7544c3 100644 --- a/GTRACT/Cmdline/gtractTensor.xml +++ b/GTRACT/Cmdline/gtractTensor.xml @@ -5,7 +5,7 @@ This step will convert a b-value averaged diffusion tensor image to a 3x3 tensor voxel image. This step takes the diffusion tensor image data and generates a tensor representation of the data based on the signal intensity decay, b values applied, and the diffusion difrections. The apparent diffusion coefficient for a given orientation is computed on a pixel-by-pixel basis by fitting the image data (voxel intensities) to the Stejskal-Tanner equation. If at least 6 diffusion directions are used, then the diffusion tensor can be computed. This program uses itk::DiffusionTensor3DReconstructionImageFilter. The user can adjust background threshold, median filter, and isotropic resampling. Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta and Greg Harris. diff --git a/GTRACT/Cmdline/gtractTransformToDisplacementField.xml b/GTRACT/Cmdline/gtractTransformToDisplacementField.xml index 320805bf11..6ea935cd6a 100644 --- a/GTRACT/Cmdline/gtractTransformToDisplacementField.xml +++ b/GTRACT/Cmdline/gtractTransformToDisplacementField.xml @@ -5,7 +5,7 @@ This program will compute forward deformation from the given Transform. The size of the DF is equal to MNI space Funding for this version of the GTRACT program was provided by NIH/NINDS R01NS050568-01A2S1 - 5.3.2 + 5.4.0 http://wiki.slicer.org/slicerWiki/index.php/Modules:GTRACT http://mri.radiology.uiowa.edu/copyright/GTRACT-Copyright.txt This tool was developed by Vincent Magnotta, Madhura Ingalhalikar, and Greg Harris diff --git a/Version.cmake b/Version.cmake index 1b51d346b6..bc9428afc6 100644 --- a/Version.cmake +++ b/Version.cmake @@ -10,7 +10,7 @@ include(ProjectSourceVersion) ## NOTE: NEED TO MANUALLY UPDATE ALL XML FILES -## - vim $(git grep -l "" -- *.xml) +## - vim $(git grep -l "" -- '*.xml') ## :%s/< *version *> *[^<]*5.3.2