ENH: Update BRAINTools
Ali Ghayoor (50):
BUG: fix BRAINSFitTest_ROIBSpline test failure
BUG: increase the tolerance for BRAINSFitTest_ROIBSpline
BUG: Symmetric bounding box in training and detection phases of BCD
ENH: perform the local search of BCD in Freq domain
ENH: Add version number to input template and LLS model files
ENH: add the new template files to ReferenceAtlas/20140916_BCD directory
ENH: Update the current address of BCD model files to the new one
ENH: Remove irrelevent parameters from BRAINSFit
ENH: add the new template files to ReferenceAtlas/20141004_BCD directory
ENH: Remove wrong model files and update AutoWorkup scripts
ENH: Update the BCD model files for internal TestSuite
ENH: Integration of ANTs Multimodal Registration into BRAINSFitHelper
ENH: Add multi-modal capsbilities to BRAINSFit
ENH: Change the classifier in BRAINSABC
ENH: Update the ITK tag
ENH: Write different posteriors for EM and KNN
BUG: Fix BCD test failures
BUG: Initialized m_UseKNN member variable on constructor
ENH: Add itkCompensatedSummation for MSP estimation
BUG: Fix 23 BCD test failures on medusa
ENH: Avereged warped intra subjects
ENH: Write debug warped intra subject images to the disk
ENH: InitializeTransformsPerStage is set on BFit
BUG: save-state transform should be cloned from the result transform in BFit
BUG: Update ITK tag and a temporary tag for ANTs so BTools can be compiled
BUG: Update save-state in BFit based on the last changes to ANTs
BUG: Update temporary tags for ITK and ANTs based on bia versions
BUG: Fix a bug in BABC when intial atlasToSubjectTx is missing
BUG: Avoid writing the inverse of the state file
ENH: Convert savedState file to the restored forward and inverse composites
BUG: Fix BRAINSABC Failure for single modal images
BUG: Fixed some bugs in BRAINSTransformConvert and verified its outputs
ENH: BRAINSLandmarkInitializer works with multiple transformTypes
BUG: No limit on usage of CompositeTransform for intialization in BABC
BUG: MultiModal registration bug in BRAINSABC and BRAINSFit
ENH: Add a GenerateCLP command line for GenerateAverageLmkFile
BUG: Fixed BCD Test failures on Dashboard
BUG: Fix BRAINSFitTest_ROIBSpline test failure
BUG: Replace the baselines of BCD tests based on CDash build
BUG: Fix a bug in BRAINSFit SyN registration
BUG: Fixed a bug in GenericTransformImage
BUG: Fixed output origin in ResampleInPlaceImageFilter
ENH: Add a regression test to BRAINSResample for ResampleInPlace
BUG: ReadTransformFromDisk can process a list of transforms now
BUG: Fixed a bug in gtractResampleDWIInPlace
ENH: Add a test for gtractResampleDWIInPlace
BUG: Fixed a bug BRAINSHoughEyeDetector
ENH: add reading from landmark file to BRAINSTalairach
ENH: Add a python script to create inputLmkFile for BTalairach
BUG: Fix BFit crash when only one value is set for splineGridSize
Hans Johnson (86):
ENH: Update to include ITKv4 Mattes Performance fixes.
ENH: Per requests of the slicer community, defaults changed.
ENH: Added --dry-run feature
WIP: Needs more work on SEM tools. DO NOT SUBMIT THIS.
COMP: ITK Components needed for build.
WIP: Removed BRAINSSurface building.
ENH: Updated SEMTools to new command line usage.
BUG: Filenames needed to change from hdf5 to h5 extension in autoworkup.
BUG: Eliminate unnecessary handling of version
COMP: Remove compiler warning
ENH: Added UseKNN on the command line.
STYLE: Remove unnecessary CLUSTER tag from config file
ENH: Improve SyN registration in BABC
ENH: Trying to add sqrt of multiplied posteriors
ENH: Automatically calculate the number of sampels to use
ENH: Add initial masking to Averaged images
ENH: Update to include SEM generated interfaces.
ENH: Fix BRAINSABC for AutoWorkup.
ENH: Improved fine grained control of processing
ENH: Added fixes for ITK FixedParameters.
ENH: Cleaned up logic for isolating separate processing steps
ENH: Added new command line for ANTS
BUG: Fixed order of imports
ENH: Updated Workflow for ANTs state saving.
ENH: Add saveState and storeState to BFit and BABC
ENH: Added stub restoring ANTs registration
ENH: Improved linkage of SyN to BRAINSABC.
ENH: Testing new ANTs registration values.
ENH: Provide consistent registration for ANTs.
ENH: ANTs testing with separate stages.
ENH: Remove requirement for atlasToSubjectIntialTransform flag.
ENH: Added cluster flags and remove debugging.
ENH: Fixed segmentation phase of processing
BUG: Need to ensure range of threads are integer values.
ENH: Improved registration parameters for optimization.
STYLE: Remove aliasing that was confusing
ENH: Added debugging info.
BUG: Missing update on averaging filter
STYLE: ::Zero and ::One have been deprecated since 2012
ENH: Syncronize with NAMICExternalProjects.
ENH: Improve logic for choosing registration mode.
ENH: Improve T1 only segmentations
ENH: Optimize registration parameters for ANTs template building.
BUG: Command line to limit subjects to process was incorrect.
STYLE: Hide debugging information.
ENH: Fine tuning ANTs registration to take less time
ENH: Limit the number of iterations for full size SyN
BUG: matplotlib is not a requirement.
ENH: Conversion to composite files continued
ENH: Provide skipping logic for template building phase.
ENH: FIXING BUGS IN template use for phase 3.
ENH: Added GenerateAverageLmkFile interface.
ENH: Split required and optional items from datagrabber.
BUG: Incorrect syntax for custom pipeline arguments
ENH: Try to fix Brainstem segmentations.
BUG: Connections to Segmentation were incorrect
ENH: Make segmentation connection.
ENH: Add feature for using ROIAuto for registration masking
ENH: Add r/l hemisphere separation.
COMP: Improve Compilation for ITK modules
ENH: Adding MALF label fusion to autoworkup
COMP: Fix compilation linkage errors.
ENH: Initial code copied directly from BRAINS3/src/iplProg/GenusZero
STYLE: Clean code for easier maintenance.
ENH: Copy vtkITK from Slicer
ENH: Migrate to Slicer version of vtkITK, and update to VTK version 6
COMP: Remove compilation warning of returning without value.
COMP: Fixed compilation problems
ENH: Improve quality of MALF outputs
ENH: Update ITKv4 to include performance fixes.
COMP: Incorrect function signature.
ENH: Lastest alpha ITK 4.7 release.
COMP: Consolidated duplicate code, fix include directory
ENH: Merged fusion and other knowlege
ENH: Update external packages.
COMP: C++11 style nullptr usage
COMP: Use C++11 keyword override for code maintenance
COMP: Remove unused typedefs
ENH: Updated VTK.
COMP: Improve VTK compilation options.
BUG: Changes to Fix 'space directions' field in the NRRD Header
BUG: Prevent infiinte loop for bad cases in BABC
COMP: Missing ITK_OVERRIDE substitution.
COMP: Fix VTK QT relationship builds.
ENH: Syncronized with NAMICExternalProjects.
ENH: Deprecate ::Zero and ::One
Kent Williams (14):
COMP: remove ITKV3_COMPATIBILITY entireley
COMP: Removed deprecated V3 filters
COMP: Remove shadow declaration warnings
COMP: fix core dump due to premature object destruction
COMP: Replace Rigod{2,3}Transform with derived classes
COMP: Initialize m_AtlasToSubjectInitialTransform
COMP: Turn off ITKV3Compatibility and ITKDeprecated
BUG: Fix scaling of vectors by b-values
COMP: fix some gcc 4.9.2 warnings
COMP: gcc4.9.1 warnings for ANTs
COMP: Enable BRAINSSurfaceTools by default
COMP: Fix warningsCOMP: get BRAINSSurfaceTools to build.
COMP: Remove gcc 4.9 warnings
COMP: Remove more gcc 4.9 warnings
Regina Kim (9):
ENH: BRAINSABC multimodal functionality
WIP: BRAINSABC multimodal functionality
WIP: working version with the local option
WIP: SyN Registration parameter tunning
BUG: Fix the bug introduced by merging
BUG: Multimodal registration into BABC
BUG: kNN output were improperly propagated. Fixed
ENH: By pass denoising for BCD failures
BUG: BRAINSCut DG move and template building fix BRAINSCut probablity DataGrabber were placed into segmentation section instead of default section.
eunyoung regina kim (2):
Update README
Create MALFLabel_neuromorphometrics_colortable.txt
fbudin69500 (1):
ENH: Addition of an option in DWIConvert to read input BVector files that are transposed when converting FSL images to NRRD images.
git-svn-id: http://svn.slicer.org/Slicer4/trunk@23872 3bd1e089-480b-0410-8dfb-8563597acbee |
