ENH: Update BRAINSTools to include DWIConvert bug fixes
BRAINSTools DWIConvert module has been updated
to address a problem identified the BWH team regarding
images being loaded up-side-down.
In addition, some types of nifti/nrrd conversions could result
in improper orientation of the images. A comprehensive bug fix
was implemented to refactor the fragile old code into a consistent
paradigm for managing image directions.
$ git shortlog 73a6e2d..980803c --no-merges
Alexander Leinoff (2):
DOC: Changes README file extension to .md
DOC: Adds intructions for OS X users to install xcode command line tools.
Ali Ghayoor (40):
ENH: Add new gtractResampleDWIInPlace tests for image meta data
ENH: Fix a bug in nrrd file header changes by gtractResampleDWIInPlace
BUG: BRAINSResample should have a default value for warpTransform
ENH: Add new gtractResampleDWIInPlace tests for image meta data
ENH: Fix a bug in nrrd file header changes by gtractResampleDWIInPlace
ENH: Add DWIWorkflow python file to AutoWorkup directory
ENH: Separate Cache dir from result dir in DWI pipline
ENH: add CorrectedDWI to dataSink of DWI pipeline
ENH: Add a python script to compute IPD
ENH: Improve DWIWorkflow with better registrtion
ENH: Write output transforms of BFit and BABCD in float
ENH: AutoWorkup runs antsRegistration and BRINSFit in float mode
ENH: Add a set of workflows for DWI data processing
ENH: Add recordLength to UKF traits
BUG: Fixed a bug in DWI measurement workflow
BUG: Avoid dtiprocess to stop nipype processing
BUG: Fix dtiestim cmdline parameters
ENH: freeSurfer extended labels config file is update with new label
ENH: Add MultiProc plugin to DWI pipeline
ENH: Add overwrite to DataSink of DWI pipeline
ENH: Run UKFTractography in a separate workflow
ENH: Use cubic BSpline interpolation for RIS
ENH: Add RIS computations from non compressed sensing DWI image
ENH: giving proper names to the dataSink outputs
ENH: Used FloatAlmostEqual for image info comaprison
ENH: Use vnl_vector/matrix.isequal to compare images information
ENH: Add comparison of the voxel values to DWICompare
Revert "BUG: Refactoring introduced direction swap error."
BUG: Fixed DWIConverter based on last changes to itkDCMTKFileReader
BUG: A hack solution for FslToNrrd test failure
ENH: Use vtp extension for output of UKFTractograhy
ENH: Add correction option to dtiprocess in estimationWF
ENH: Add correction option to SEMTools for dtiprocess and dtiestim
BUG: Enhance the non-negative preserving resampling
ENH: Fixed, enhanced and tested DWIMetaDataDictionaryValidator
BUG: Fixed FSLToNrrd converter
BUG: Fixed DeleteGradientTable bug in DWIMetaDataValidator
ENH: Update gtractResampleDWIInPlace using MetaDataDictionaryValidator
ENH: Provided build consistency with c++03
BUG: changing codes that were only compatible with c++11
Dave Welch (6):
WIP: adding a cross validation workflow for ANTs JointFusion() TODO: Test workflow (how?) Run and validate workflow outputs
STYLE: Added Ubuntu build directions for 14.04
STYLE: Fixed README.md formatting
STYLE: Added missing 3rd step to Ubuntu build
ENH: Python variables pass correctly to external projects
ENH: Python variables pass correctly to external projects
David Ellis (7):
COMP: Fixes compilation warning
BUG: Updates vtkImageGenus0MarchingCubes to the new vtk pipeline format.
BUG: Fixes bug causing the filter to abort.
BUG: Fixes GenusZeroImageFilter failure to output vtk file.
BUG: Fixes issues with the GenusZeroImageFilter tests
BUG: Fixes the failing tests for BRAINSAssignSurfaceFeatures
BUG: Fixes the COMPARE_SurfaceLabelCleanup test
Hans J. Johnson (30):
BUG: The program and python paths should be part of input args
BUG: add T2 and labelMap paths to input args of DWI pipeline
ENH: Added UKF Tractography to end of pipeline.
ENH: First pass at adding version control
ENH: Update many packages to be in sync with NEP
ENH: Improve mask processing for PREDICT-HD to include better FSWM defintions.
ENH: Syncronized Artichoke with Slicer updates (name change).
BUG: Fixed bugs in the BRAINSABC test suite
DOC: Improve documentation for error condidtions.
ENH: Update to syncronize with recent Artichoke commit fixes.
ENH: Updated to latest SVN version of teem.
COMP: Match cmake policy options of slicer.
ENH: Update support packages in preparation for UKF updates
BUG: Fixed tag for ANTS
BUG: Testing of images needs to verify all data
BUG: Refactoring introduced direction swap error.
ENH: Fixed automatic versioning
ENH: Added consistent tagging for xml's
BUG: Consistently use git tag for version
BUG: Automatic versioning based on git
BUG: Update itkDCMTKFileReader code
BUG: Backwards compatible with older ITK versions
COMP: Temporarily remove BRAINSCut, Need OpenCV 3.0
ENH: Syncronize with Slicer and NAMICExternalProjects.
ENH: Add utility class for managing DWI MetaData
ENH: Added mailmap
ENH: Second mailmap improvement.
ENH: Syncronized with NEP.
BUG: Incorrect initialiation
COMP: Syncronize with NEP configurations.
Jon Pipitone (1):
Updated README with some markdown formatting fixes
Regina Kim (11):
ENH: Add FreeSurfer Lobar Pacellation Mapping
ENH: Lobar Label fix
ENH: Add BRAINSCut README file to support usage
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
ENH: name change from sample to training set
From: Hans Johnson <hans-johnson@uiowa.edu>
git-svn-id: http://svn.slicer.org/Slicer4/trunk@24249 3bd1e089-480b-0410-8dfb-8563597acbee |
