pushing elastix files

.gitignore

@@ -10,8 +10,6 @@
 #dicoms
 **/dicoms
 
-**/elastix_params
-
 # test data files
 **/temp
 **/ex_patient

elastix_params/parameters-affine.txt

@@ -0,0 +1,69 @@
+// *********************
+// * affine
+// *********************
+
+// *********************
+// * ImageTypes
+// *********************
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// *********************
+// * Components
+// *********************
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Metric "AdvancedMattesMutualInformation")
+(BSplineInterpolationOrder 1)
+(Resampler "DefaultResampler")
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "AffineTransform")
+
+// *********************
+// * Mask settings
+// *********************
+(ErodeMask "false")
+(ErodeFixedMask "false")
+
+// *********************
+// * Optimizer settings
+// *********************
+(NumberOfResolutions 1)
+(MaximumNumberOfIterations 1000)
+(ASGDParameterEstimationMethod "Original")
+(AutomaticParameterEstimation "true")
+(AutomaticTransformInitialization "true")
+(AutomaticScalesEstimation "true")
+
+// *********************
+// * Transform settings
+// *********************
+(HowToCombineTransforms "Compose")
+
+// *********************
+// * Pyramid settings
+// *********************
+(NumberOfHistogramBins 32)
+
+
+// *********************
+// * Sampler parameters
+// *********************
+(NumberOfSpatialSamples 2000)
+(ImageSampler "RandomCoordinate")
+(CheckNumberOfSamples "true")
+(NewSamplesEveryIteration "true")
+(FinalBSplineInterpolationOrder 3)
+
+// *********************
+// * Output settings
+// *********************
+(DefaultPixelValue 0)
+(WriteTransformParametersEachIteration "false")
+(WriteResultImage  "true")
+(ResultImageFormat "nii.gz")
+(ResultImagePixelType "float")

elastix_params/parameters-bspline.txt

@@ -0,0 +1,71 @@
+// *********************
+// * bspline
+// *********************
+
+// *********************
+// * ImageTypes
+// *********************
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// *********************
+// * Components
+// *********************
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Metric "AdvancedMattesMutualInformation")
+(BSplineInterpolationOrder 1)
+(Resampler "DefaultResampler")
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "BSplineTransform")
+(FinalGridSpacingInPhysicalUnits 30 30 30)
+(MovingImageDerivativeScales 1 1 1)
+
+// *********************
+// * Mask settings
+// *********************
+(ErodeMask "false")
+(ErodeFixedMask "false")
+
+// *********************
+// * Optimizer settings
+// *********************
+(NumberOfResolutions 3)
+(MaximumNumberOfIterations 1000)
+(ASGDParameterEstimationMethod "Original")
+(AutomaticParameterEstimation "true")
+(AutomaticTransformInitialization "true")
+(AutomaticScalesEstimation "true")
+
+// *********************
+// * Transform settings
+// *********************
+(HowToCombineTransforms "Compose")
+
+// *********************
+// * Pyramid settings
+// *********************
+(NumberOfHistogramBins 32)
+
+
+// *********************
+// * Sampler parameters
+// *********************
+(NumberOfSpatialSamples 2000)
+(ImageSampler "RandomCoordinate")
+(CheckNumberOfSamples "true")
+(NewSamplesEveryIteration "true")
+(FinalBSplineInterpolationOrder 3)
+
+// *********************
+// * Output settings
+// *********************
+(DefaultPixelValue 0)
+(WriteTransformParametersEachIteration "false")
+(WriteResultImage  "true")
+(ResultImageFormat "nii.gz")
+(ResultImagePixelType "float")

elastix_params/parameters-rigid.txt

@@ -0,0 +1,69 @@
+// *********************
+// * rigid
+// *********************
+
+// *********************
+// * ImageTypes
+// *********************
+(FixedInternalImagePixelType "float")
+(MovingInternalImagePixelType "float")
+(UseDirectionCosines "true")
+
+// *********************
+// * Components
+// *********************
+(FixedImagePyramid "FixedSmoothingImagePyramid")
+(MovingImagePyramid "MovingSmoothingImagePyramid")
+(Registration "MultiResolutionRegistration")
+(Interpolator "BSplineInterpolator")
+(ResampleInterpolator "FinalBSplineInterpolator")
+(Metric "AdvancedMattesMutualInformation")
+(BSplineInterpolationOrder 1)
+(Resampler "DefaultResampler")
+(Optimizer "AdaptiveStochasticGradientDescent")
+(Transform "EulerTransform")
+
+// *********************
+// * Mask settings
+// *********************
+(ErodeMask "false")
+(ErodeFixedMask "false")
+
+// *********************
+// * Optimizer settings
+// *********************
+(NumberOfResolutions 3)
+(MaximumNumberOfIterations 1000)
+(ASGDParameterEstimationMethod "Original")
+(AutomaticParameterEstimation "true")
+(AutomaticTransformInitialization "true")
+(AutomaticScalesEstimation "true")
+
+// *********************
+// * Transform settings
+// *********************
+(HowToCombineTransforms "Compose")
+
+// *********************
+// * Pyramid settings
+// *********************
+(NumberOfHistogramBins 32)
+
+
+// *********************
+// * Sampler parameters
+// *********************
+(NumberOfSpatialSamples 2000)
+(ImageSampler "RandomCoordinate")
+(CheckNumberOfSamples "true")
+(NewSamplesEveryIteration "true")
+(FinalBSplineInterpolationOrder 3)
+
+// *********************
+// * Output settings
+// *********************
+(DefaultPixelValue 0)
+(WriteTransformParametersEachIteration "false")
+(WriteResultImage  "true")
+(ResultImageFormat "nii.gz")
+(ResultImagePixelType "float")

scripts/test-script

@@ -1,5 +1,5 @@
 #!/bin/bash
-WEIGHTS_DIRECTORY="/Users/arjundesai/Documents/stanford/research/msk_pipeline_raw/weights"
+WEIGHTS_DIRECTORY=""
 if [ -z "$WEIGHTS_DIRECTORY" ]; then
     echo "Please define WEIGHTS_DIRECTORY in script. Use the absolute path"
     exit 125
@@ -63,5 +63,5 @@ for i in $FILES; do
     fi
 
     # analyze femoral cartilage
-    python -m pipeline -l $SAVE_DIRNAME knee -fc -t2 -t1_rho
+    python -m pipeline -l $SAVE_DIRNAME knee -fc -t2 -t1_rho -t2_star
 done