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IDProjectCategoryView StatusDate SubmittedLast Update
0003939Slicer4Module EMSegmentpublic2015-01-09 07:052017-06-10 08:51
Reporterhjmjohnson Assigned Tojcfr  
PrioritynormalSeverityblockReproducibilityalways
Status closedResolutionfixed 
Product VersionSlicer 4.4.0 
Target VersionSlicer 4.5.0-1Fixed in VersionSlicer 4.5.0-1 
Summary0003939: EMSegment command line option removals needed for BRAINSFit
Description

JC,

The following patch will remove deprecated (and unused for a long time) command line options from the most recent version of BRAINSTools. These command line options have been NO-OP operations for a long time now. We removed them from BRAINSFit in the latest code review cleanups.

Can you please apply these to EMSegment?

Hans

Additional Information

09:37 $ svn diff
Index: Tasks/GenericTask.tcl

--- Tasks/GenericTask.tcl (revision 17092)
+++ Tasks/GenericTask.tcl (working copy)
@@ -1030,7 +1030,6 @@
set CMD "$CMD --maskProcessingMode NOMASK"
set CMD "$CMD --numberOfHistogramBins 40"
set CMD "$CMD --numberOfMatchPoints 10"

  • set CMD "$CMD --useCachingOfBSplineWeightsMode ON"
    set CMD "$CMD --costMetric MMI"

Index: Tasks/Registration_BRAINS.tcl

--- Tasks/Registration_BRAINS.tcl (revision 17092)
+++ Tasks/Registration_BRAINS.tcl (working copy)
@@ -173,7 +173,6 @@
set CMD "$CMD --useBSpline"
set CMD "$CMD --splineGridSize 6,6,6"
set CMD "$CMD --maxBSplineDisplacement 0"

  • set CMD "$CMD --useCachingOfBSplineWeightsMode ON"
    }
    set CMD "$CMD --initializeTransformMode useCenterOfHeadAlign"
    set CMD "$CMD --minimumStepLength 0.005"
    @@ -193,7 +192,6 @@
    set CMD "$CMD --failureExitCode -1"

    set CMD "$CMD --medianFilterSize 0,0,0"

    -# set CMD "$CMD --useExplicitPDFDerivativesMode AUTO"

    set CMD "$CMD --relaxationFactor 0.5"

    set CMD "$CMD --maximumStepLength 0.2"

    set CMD "$CMD --costFunctionConvergenceFactor 1e+9"

    Index: Testing/resample.sh

    --- Testing/resample.sh (revision 17092)
    +++ Testing/resample.sh (working copy)
    @@ -9,7 +9,7 @@

    #xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

-time ${Slicer3_HOME}/Slicer3 --launch ${Slicer3_HOME}/lib/Slicer3/Plugins/BRAINSFit --fixedVolume ${TARGET} --movingVolume ${Slicer3_HOME}/share/Slicer3/Modules/EMSegment/Tasks/MRI-Human-Brain/atlas_t1.nrrd --outputVolume /tmp/outputbrainsfit.nrrd --bsplineTransform /tmp/transform.mat --maxBSplineDisplacement 10.0 --outputVolumePixelType short --backgroundFillValue 0.0 --interpolationMode Linear --maskProcessingMode ROIAUTO --ROIAutoDilateSize 3.0 --maskInferiorCutOffFromCenter 65.0 --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --useBSpline --numberOfSamples 100000 --numberOfIterations 1500 --minimumStepLength 0.005 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --maximumStepLength 0.2 --failureExitCode -1 --debugNumberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 --costMetric MMI
+time ${Slicer3_HOME}/Slicer3 --launch ${Slicer3_HOME}/lib/Slicer3/Plugins/BRAINSFit --fixedVolume ${TARGET} --movingVolume ${Slicer3_HOME}/share/Slicer3/Modules/EMSegment/Tasks/MRI-Human-Brain/atlas_t1.nrrd --outputVolume /tmp/outputbrainsfit.nrrd --bsplineTransform /tmp/transform.mat --maxBSplineDisplacement 10.0 --outputVolumePixelType short --backgroundFillValue 0.0 --interpolationMode Linear --maskProcessingMode ROIAUTO --ROIAutoDilateSize 3.0 --maskInferiorCutOffFromCenter 65.0 --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --useBSpline --numberOfSamples 100000 --numberOfIterations 1500 --minimumStepLength 0.005 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --relaxationFactor 0.5 --maximumStepLength 0.2 --failureExitCode -1 --debugNumberOfThreads -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 --costMetric MMI

#xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

TagsNo tags attached.

Activities

jcfr

jcfr

2015-01-09 07:46

administrator   ~0012872

Fixed in r23874
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23874

Related Changesets

Import 2017-06-07 23:51:09: master e7325e85

2015-01-09 12:23:53

jcfr

Details Diff 		BUG: Update EMSegment to avoid using invalid BRAINSFit argument. Fixes 0003939

// ---------------------
BUG: Remove invalid BRAINSFit argument

This commit removes deprecated (and unused for a long time) command line options
from the most recent version of BRAINSTools. These command line options have
been NO-OP operations for a long time. They have been removed in the version
of BRAINSTools now used in Slicer r23872.

Thanks to "Hans Johnson <hans-johnson@uiowa.edu>" for providing the patch.
// ---------------------

git-svn-id: http://svn.slicer.org/Slicer4/trunk@23874 3bd1e089-480b-0410-8dfb-8563597acbee
mod - SuperBuild.cmake Diff File

Issue History

Date Modified Username Field Change
2015-01-09 07:05 hjmjohnson New Issue
2015-01-09 07:05 hjmjohnson Status new => assigned
2015-01-09 07:05 hjmjohnson Assigned To => jcfr
2015-01-09 07:46 jcfr Note Added: 0012872
2015-01-09 07:46 jcfr Status assigned => resolved
2015-01-09 07:46 jcfr Fixed in Version => Slicer 4.4.1
2015-01-09 07:46 jcfr Resolution open => fixed
2015-01-09 07:46 jcfr Status resolved => closed
2015-09-09 08:29 jcfr Fixed in Version Slicer 4.4.1 => Slicer 4.5.0-1
2015-09-09 08:29 jcfr Target Version Slicer 4.4.1 => Slicer 4.5.0-1
2017-06-10 08:51 jcfr Changeset attached => Slicer master e7325e85