ENH: Updating version tag to v5.4.0

This is the tagged version for the PREDICTHD_BIDS_DEFACE
public dataset distribution.

ARCHIVE/BRAINSTalairach/BRAINSTalairach.xml

@@ -8,7 +8,7 @@
   </title>
   <description>
   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. </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairach</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>

ARCHIVE/BRAINSTalairach/BRAINSTalairachMask.xml

@@ -8,7 +8,7 @@
   </title>
   <description>
   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. </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSTalairachMask</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>

BRAINSABC/brainseg/GenerateLabelMapFromProbabilityMap.xml

@@ -5,7 +5,7 @@
   <description>
     Given a list of probability maps for labels, create a discrete label map where only the highest probability region is used for the labeling.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license></license>
   <contributor>University of Iowa Department of Psychiatry, http:://www.psychiatry.uiowa.edu

BRAINSABC/brainseg/GeneratePurePlugMask.xml

@@ -5,7 +5,7 @@
   <description>
     This program gets several modality image files and returns a binary mask that defines the pure plugs.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

BRAINSCommonLib/TestSuite/FindCenterOfBrain.xml

@@ -7,7 +7,7 @@
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu</contributor>
   <acknowledgements>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</acknowledgements>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <parameters advanced="false">
     <label>Required Input Parameters</label>
     <image>

BRAINSConstellationDetector/TestSuite/LandmarksCompare.xml

@@ -5,7 +5,7 @@
   <description>
     Compares two .fcsv or .wts text files and verifies that they are identicle.  Used for testing landmarks files.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

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.
     </description>
 
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
     <parameters>
         <image>

BRAINSConstellationDetector/landmarkStatistics/GenerateAverageLmkFile.xml

@@ -5,7 +5,7 @@
   <description>
     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.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

BRAINSConstellationDetector/src/BRAINSClipInferior.xml

@@ -5,7 +5,7 @@
     <description>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.
     </description>
 
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <parameters>
         <image>
             <name>inputVolume</name>

BRAINSConstellationDetector/src/BRAINSConstellationDetector.xml

@@ -7,7 +7,7 @@
   </description>
   <contributor>Hans J. Johnson (hans-johnson -at- uiowa.edu), Ali Ghayoor</contributor>
   <acknowledgements><![CDATA[Hans Johnson(1,2,3); Ali Ghayoor(3); Wei Lu(3) 1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Biomedical Engineering, 3=University of Iowa Department of Electrical and Computer Engineering]]>  </acknowledgements>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
 

BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml

@@ -5,7 +5,7 @@
   <description>
   This program converts the original landmark file to the target landmark file using the input transform.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor and Hans J. Johnson</contributor>

BRAINSConstellationDetector/src/BRAINSEyeDetector.xml

@@ -5,7 +5,7 @@
   <description>
   </description>
 
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
   <parameters>
     <integer>

BRAINSConstellationDetector/src/BRAINSLinearModelerEPCA.xml

@@ -7,7 +7,7 @@
 
     </description>
 
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
     <parameters>
         <file fileExtensions=".lst">

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.
     </description>
 
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
     <parameters>
         <file fileExtensions=".fcsv">

BRAINSConstellationDetector/src/BRAINSTransformFromFiducials.xml

@@ -3,7 +3,7 @@
   <category>Registration.Specialized</category>
   <title>Fiducial Registration (BRAINS)</title>
   <description>Computes a rigid, similarity or affine transform from a matched list of fiducials</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.slicer.org/slicerWiki/index.php/Modules:TransformFromFiducials-Documentation-3.6</documentation-url>
   <license></license>
   <contributor>Casey B Goodlett</contributor>

BRAINSConstellationDetector/src/BRAINSTrimForegroundInDirection.xml

@@ -3,7 +3,7 @@
     <category>Utilities.BRAINS</category>
     <title>Trim Foreground In Direction (BRAINS)</title>
     <description>This program will trim off the neck and also air-filling noise from the inputImage.</description>
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <documentation-url>http://www.nitrc.org/projects/art/</documentation-url>
     <parameters>
         <image>

BRAINSConstellationDetector/src/BinaryMaskEditorBasedOnLandmarks.xml

@@ -5,7 +5,7 @@
   <description>
   </description>
 
-    <version>5.3.2</version>
+    <version>5.4.0</version>
     <documentation-url>http://www.nitrc.org/projects/brainscdetector/</documentation-url>
     <parameters>
         <image>

BRAINSConstellationDetector/src/ComputeReflectiveCorrelationMetric.xml

@@ -4,7 +4,7 @@
   <title>Compute RC metric values in exhausive search</title>
   <description>
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

BRAINSConstellationDetector/src/insertMidACPCpoint.xml

@@ -5,7 +5,7 @@
   <description>
   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
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

BRAINSConstellationDetector/src/landmarksConstellationAligner.xml

@@ -5,7 +5,7 @@
   <description>
   This program converts the original landmark files to the acpc-aligned landmark files
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url> </documentation-url>
   <license> </license>
   <contributor>Ali Ghayoor</contributor>

BRAINSDWICleanup/BRAINSDWICleanup.xml

@@ -5,7 +5,7 @@
 
   <description>Remove bad gradients/volumes from DWI NRRD file.</description>
   <acknowledgements></acknowledgements>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>This tool was developed by Kent Williams.</contributor>

BRAINSDeface/BRAINSDeface.xml

@@ -5,7 +5,7 @@
     <description>
         This program: 1) will deface images from a set of images.  Inputs must be ACPC aligned, and AC, PC, LE, RE provided.
     </description>
-    <version>5.3.3</version>
+    <version>5.4.0</version>
     <documentation-url></documentation-url>
     <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
     <contributor>

BRAINSFit/BRAINSFit.xml

@@ -7,7 +7,7 @@
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Hans J. Johnson (hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu), Ali Ghayoor</contributor>
   <acknowledgements><![CDATA[Hans Johnson(1,3,4); Kent Williams(1); Gregory Harris(1), Vincent Magnotta(1,2,3);  Andriy Fedorov(5); Ali Ghayoor(4) 1=University of Iowa Department of Psychiatry, 2=University of Iowa Department of Radiology, 3=University of Iowa Department of Biomedical Engineering, 4=University of Iowa Department of Electrical and Computer Engineering, 5=Surgical Planning Lab, Harvard]]>  </acknowledgements>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
 
   <parameters advanced="false">
     <label>Input Images</label>

BRAINSFit/PerformMetricTest.xml

@@ -5,7 +5,7 @@
   <description>
     Compare Mattes/MSQ metric value for two input images and a possible input BSpline transform.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>A utility to compare metric value between two input images.</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Ali Ghayoor</contributor>

BRAINSInitializedControlPoints/BRAINSInitializedControlPoints.xml

@@ -5,7 +5,7 @@
   <description>
   Outputs bspline control points as landmarks
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Mark Scully</contributor>

BRAINSIntensityNormalize/BRAINSIntensityNormalize.xml

@@ -5,7 +5,7 @@
     <description>
         Computes the percentile rescaling of an image
     </description>
-    <version>1.0</version>
+    <version>5.4.0</version>
     <documentation-url></documentation-url>
     <license></license>
     <contributor>Alexander B. Powers and Hans J. Johnson</contributor>
@@ -106,4 +106,4 @@
         </image>
     </parameters>
 
-</executable>
+</executable>

BRAINSLabelStats/BRAINSLabelStats.xml

@@ -3,7 +3,7 @@
   <category>Quantification</category>
   <title>Label Statistics (BRAINS)</title>
   <description>Compute image statistics within each label of a label map. </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Vincent A. Magnotta</contributor>

BRAINSLandmarkInitializer/BRAINSLandmarkInitializer.xml

@@ -3,7 +3,7 @@
   <category>Utilities.BRAINS</category>
   <title>BRAINSLandmarkInitializer</title>
   <description>Create transformation file (*.h5) from a pair of landmarks (*fcsv) files.</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Eunyoung Regina Kim, Ali Ghayoor, and Hans J. Johnson</contributor>

BRAINSMultiModeSegment/BRAINSMultiModeSegment.xml

@@ -4,7 +4,7 @@
   <title>Segment based on rectangular region of joint histogram (BRAINS)</title>
   <description>This tool creates binary regions based on segmenting multiple image modalitities at once.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu</contributor>

BRAINSMush/BRAINSMush.xml

@@ -5,7 +5,7 @@
   <description>
   This program: 1) generates a weighted mixture image optimizing the mean and variance and 2) produces a mask of the brain volume
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http:://mri.radiology.uiowa.edu</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>

BRAINSPosteriorToContinuousClass/BRAINSPosteriorToContinuousClass.xml

@@ -3,7 +3,7 @@
   <category>BRAINS.Classify</category>
   <title>Tissue Classification</title>
   <description>This program will generate an 8-bit continuous tissue classified image based on BRAINSABC posterior images. </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.nitrc.org/plugins/mwiki/index.php/brains:BRAINSClassify</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Vincent A. Magnotta</contributor>

BRAINSROIAuto/BRAINSROIAuto.xml

@@ -4,7 +4,7 @@
   <title>Foreground masking (BRAINS)</title>
   <description>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.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Hans J. Johnson, hans-johnson -at- uiowa.edu, http://www.psychiatry.uiowa.edu</contributor>

BRAINSResample/BRAINSResample.xml

@@ -6,7 +6,7 @@
   <description>
     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.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/BRAINSResample</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson.</contributor>

BRAINSResample/BRAINSResize.xml

@@ -6,7 +6,7 @@
   <description>
 This program is useful for downsampling an image by a constant scale factor.
   </description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>This tool was developed by Hans Johnson.</contributor>

BRAINSSnapShotWriter/BRAINSSnapShotWriter.xml

@@ -3,7 +3,7 @@
   <category>Utilities.BRAINS</category>
   <title>BRAINSSnapShotWriter</title>
   <description>Create 2D snapshot of input images. Mask images are color-coded</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Eunyoung Regina Kim</contributor>

BRAINSStripRotation/BRAINSStripRotation.xml

@@ -3,7 +3,7 @@
   <category>Utilities</category>
   <title>BRAINS Strip Rotation</title>
   <description>Read an Image, write out same image with identity rotation matrix plus an ITK transform file</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Kent WIlliams</contributor>

BRAINSSuperResolution/GenerateEdgeMap/GenerateEdgeMapImage.xml

@@ -3,7 +3,7 @@
   <category>SuperResolution</category>
   <title>GenerateEdgeMapImage</title>
   <description>Inverse of Maximum Gradient Image</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url></documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Ali Ghayoor</contributor>

BRAINSTransformConvert/BRAINSTransformConvert.xml

@@ -3,7 +3,7 @@
   <category>Utilities.BRAINS</category>
   <title>BRAINS Transform Convert</title>
   <description>Convert ITK transforms to higher order transforms</description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>A utility to convert between transform file formats.</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Hans J. Johnson,Kent Williams, Ali Ghayoor</contributor>

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

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, <PROJECT-NAME>_VERSION
 #-- PROJECT_VERSION_MAJOR, <PROJECT-NAME>_VERSION_MAJOR

DWIConvert/DWIConvert.xml

@@ -3,7 +3,7 @@
   <category>Diffusion.Import and Export</category>
   <title>Diffusion-weighted DICOM Import (DWIConvert)</title>
   <description><![CDATA[Converts diffusion weighted MR images in DICOM series into NRRD format for analysis in Slicer. This program has been tested on only a limited subset of DTI DICOM formats available from Siemens, GE, and Philips scanners. Work in progress to support DICOM multi-frame data. The program parses DICOM header to extract necessary information about measurement frame, diffusion weighting directions, b-values, etc, and write out a NRRD image. For non-diffusion weighted DICOM images, it loads in an entire DICOM series and writes out a single dicom volume in a .nhdr/.raw pair.]]></description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.5/Modules/DWIConverter</documentation-url>
   <license>Apache License Version 2.0</license>
   <contributor>Hans Johnson (UIowa), Vince Magnotta (UIowa) Joy Matsui (UIowa), Kent Williams (UIowa), Mark Scully (Uiowa), Xiaodong Tao (GE)</contributor>

DWIConvert/TestSuite/DWICompare.xml

@@ -3,7 +3,7 @@
   <category>Converters</category>
   <title>Nrrd DWI comparison</title>
   <description><![CDATA[Compares two nrrd format DWI images and verifies that gradient magnitudes, gradient directions, measurement frame, and max B0 value are identicle.  Used for testing DWIConvert.]]></description>
-  <version>5.3.2</version>
+  <version>5.4.0</version>
   <documentation-url>http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DWIConvert</documentation-url>
   <license>https://www.nitrc.org/svn/brains/BuildScripts/trunk/License.txt</license>
   <contributor>Mark Scully (UIowa)</contributor>