Files

AutoWorkup
- SEMTools
- TestSuite
- brains
- '
- BAWantsRegistrationBuildTemplate.py
- BRAINSABCext.py
- BRAINSCutCMD.py
- CMakeLists.txt
- PipeLineFunctionHelpers.py
- README
- RF12BRAINSCutWrapper.py
- RF8BRAINSCutWrapper.py
- SessionDB.py
- ShortWorkupT1T2.py
- Template.config
- WorkupT1T2.py
- WorkupT1T2ANTS.py
- WorkupT1T2AtlasNode.py
- WorkupT1T2BRAINSCut.py
- WorkupT1T2FreeSurfer_custom.py
- WorkupT1T2LandmarkInitialization.py
- WorkupT1T2PERSISTANCE_CHECK.py
- WorkupT1T2Single.py
- WorkupT1T2SingleSubjectPhaseII.py
- WorkupT1T2TissueClassify.py
- baw_exp.py
- edited_example_autoworkup.csv
- example_autoworkup.csv
- example_blacklist.csv
- example_dwi.csv
- fsscript.py
- fswrap.py
- install_python_tools.sh
- local_generate_classes.py
- runOneAW.py
- subject_db.csv
- updateAutoWorkupFile.py
- updateAutoWorkupFile_DWI.py
BRAINSABC
BRAINSCommonLib
BRAINSConstellationDetector
BRAINSContinuousClass
BRAINSCreateLabelMapFromProbabilityMaps
BRAINSCut
BRAINSDemonWarp
BRAINSFit
BRAINSInitializedControlPoints
BRAINSLandmarkInitializer
BRAINSMultiModeSegment
BRAINSMultiSTAPLE
BRAINSMush
BRAINSPosteriorToContinuousClass
BRAINSROIAuto
BRAINSResample
BRAINSSnapShotWriter
BRAINSSurfaceTools
BRAINSTransformConvert
CMake
CMakeFiles
ConvertBetweenFileFormats
DWIConvert
DebugImageViewer
GTRACT
ICCDEF
ImageCalculator
SuperBuild
TestData
Testing
Utilities
.gitignore
BRAINSTools.cmake
CMakeLists.txt
CTestConfig.cmake
Common.cmake
CopyMeshToMesh
README
SuperBuild.cmake

AutoWorkup

hjmjohnson

ENH: Added dwiestim and dtiprocess to SEMTools

Feb 16, 2013

1525353 · Feb 16, 2013

History

This branch is 18 commits behind BRAINSia/BRAINSStandAlone:master.

Name	Name	Last commit message	Last commit date
parent directory ..
SEMTools	SEMTools	ENH: Added dwiestim and dtiprocess to SEMTools	Feb 16, 2013
TestSuite	TestSuite	ENH: Fix to include consistent naming of FreeSurfer spelling.	Jan 16, 2013
brains	brains	ENH: Added methods for accumulated posterior files	Jan 29, 2013
'	'	ENH: Fix to include consistent naming of FreeSurfer spelling.	Jan 16, 2013
BAWantsRegistrationBuildTemplate.py	BAWantsRegistrationBuildTemplate.py	ENH: Set ANTS Registraiton parameters based on experimental results	Jan 9, 2013
BRAINSABCext.py	BRAINSABCext.py	STYLE: Do PEP8 compliance	Jan 6, 2013
BRAINSCutCMD.py	BRAINSCutCMD.py	BUG: Writing a work around for caudates in images where subjects have…	Jan 15, 2013
CMakeLists.txt	CMakeLists.txt	ENH: Slicer requires special treatment.	Nov 14, 2012
PipeLineFunctionHelpers.py	PipeLineFunctionHelpers.py	BUG: Fixed logic bugs in computing the candidateRegion for Caudate.	Jan 15, 2013
README	README	ENH: Added pipeline for BRAINSTools to BRAINSTools	Mar 30, 2012
RF12BRAINSCutWrapper.py	RF12BRAINSCutWrapper.py	BUG: Writing a work around for caudates in images where subjects have…	Jan 15, 2013
RF8BRAINSCutWrapper.py	RF8BRAINSCutWrapper.py	STYLE: Do PEP8 compliance	Jan 6, 2013
SessionDB.py	SessionDB.py	STYLE: Do PEP8 compliance	Jan 6, 2013
ShortWorkupT1T2.py	ShortWorkupT1T2.py	BUG: Need to propogate FS failures from sub-scripts.	Jan 24, 2013
Template.config	Template.config	ENH: Added pipeline for BRAINSTools to BRAINSTools	Mar 30, 2012
WorkupT1T2.py	WorkupT1T2.py	BUG: Freesurfer modules re-written.	Feb 5, 2013
WorkupT1T2ANTS.py	WorkupT1T2ANTS.py	STYLE: Do PEP8 compliance	Jan 6, 2013
WorkupT1T2AtlasNode.py	WorkupT1T2AtlasNode.py	STYLE: Do PEP8 compliance	Jan 6, 2013
WorkupT1T2BRAINSCut.py	WorkupT1T2BRAINSCut.py	ENH: Fix T1-only segmentation processing.	Feb 2, 2013
WorkupT1T2FreeSurfer_custom.py	WorkupT1T2FreeSurfer_custom.py	BUG: Freesurfer modules re-written.	Feb 5, 2013
WorkupT1T2LandmarkInitialization.py	WorkupT1T2LandmarkInitialization.py	STYLE: Do PEP8 compliance	Jan 6, 2013
WorkupT1T2PERSISTANCE_CHECK.py	WorkupT1T2PERSISTANCE_CHECK.py	STYLE: Do PEP8 compliance	Jan 6, 2013
WorkupT1T2Single.py	WorkupT1T2Single.py	STYLE: Do PEP8 compliance	Jan 6, 2013
WorkupT1T2SingleSubjectPhaseII.py	WorkupT1T2SingleSubjectPhaseII.py	ENH: Fix to include consistent naming of FreeSurfer spelling.	Jan 16, 2013
WorkupT1T2TissueClassify.py	WorkupT1T2TissueClassify.py	COMP: Fixed transform type to be a list as is required.	Jan 13, 2013
baw_exp.py	baw_exp.py	BUG: Logic for re-running data sinks was incorrect	Feb 5, 2013
edited_example_autoworkup.csv	edited_example_autoworkup.csv	ENH: Added a script and files that puts DWI filenames in the autoWork…	Nov 7, 2012
example_autoworkup.csv	example_autoworkup.csv	ENH: Added updateAutoWorkupFile.py which reads a blacklist csv file a…	Sep 11, 2012
example_blacklist.csv	example_blacklist.csv	ENH: Added updateAutoWorkupFile.py which reads a blacklist csv file a…	Sep 11, 2012
example_dwi.csv	example_dwi.csv	ENH: Added a script and files that puts DWI filenames in the autoWork…	Nov 7, 2012
fsscript.py	fsscript.py	BUG: Freesurfer modules re-written.	Feb 5, 2013
fswrap.py	fswrap.py	BUG: Freesurfer modules re-written.	Feb 5, 2013
install_python_tools.sh	install_python_tools.sh	ENH: Fixed data types for new format, and updated Freesurfer processing.	Apr 20, 2012
local_generate_classes.py	local_generate_classes.py	ENH: Added dwiestim and dtiprocess to SEMTools	Feb 16, 2013
runOneAW.py	runOneAW.py	ENH: Fix to include consistent naming of FreeSurfer spelling.	Jan 16, 2013
subject_db.csv	subject_db.csv	ENH: Added pipeline for BRAINSTools to BRAINSTools	Mar 30, 2012
updateAutoWorkupFile.py	updateAutoWorkupFile.py	STYLE: Do PEP8 compliance	Jan 6, 2013
updateAutoWorkupFile_DWI.py	updateAutoWorkupFile_DWI.py	STYLE: Do PEP8 compliance	Jan 6, 2013

README

Inital version of BRAINS AutoWorkup built on Nipype.
Currently very rough, use at your own risk!

To use the code, build BRAINSTools with ITKv4 on.

Then install the nipype version in the BRAINSia github account.

The file Template.config should be copied and modified to define the
experiment that should be run.

python baw_exp.py -processingLevel 2 -ExperimentConfig Template.config -pe IPL_ENVIRONMENT

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