make all files writeable and executable

MIRTK · Oct 23, 2020 · 33ed778 · 33ed778
1 parent c8ec716
commit 33ed778
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Showing 73 changed files with 2 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
diff --git a/AUTHORS.txt b/AUTHORS.txt
diff --git a/Atlases.cmake b/Atlases.cmake
diff --git a/BasisProject.cmake b/BasisProject.cmake
diff --git a/CMakeLists.txt b/CMakeLists.txt
diff --git a/LICENSE.txt b/LICENSE.txt
diff --git a/README.md b/README.md
diff --git a/ThirdParty/ANTs/External_ITK.cmake b/ThirdParty/ANTs/External_ITK.cmake
diff --git a/ThirdParty/ANTs/LICENSE.txt b/ThirdParty/ANTs/LICENSE.txt
diff --git a/ThirdParty/ANTs/N4BiasFieldCorrection.cxx b/ThirdParty/ANTs/N4BiasFieldCorrection.cxx
diff --git a/ThirdParty/ANTs/antsCommandLineOption.cxx b/ThirdParty/ANTs/antsCommandLineOption.cxx
diff --git a/ThirdParty/ANTs/antsCommandLineOption.h b/ThirdParty/ANTs/antsCommandLineOption.h
diff --git a/ThirdParty/ANTs/antsCommandLineParser.cxx b/ThirdParty/ANTs/antsCommandLineParser.cxx
diff --git a/ThirdParty/ANTs/antsCommandLineParser.h b/ThirdParty/ANTs/antsCommandLineParser.h
diff --git a/config/FindMIRTK.cmake b/config/FindMIRTK.cmake
diff --git a/include/mirtk/BSplineBiasField.h b/include/mirtk/BSplineBiasField.h
diff --git a/include/mirtk/BiasCorrection.h b/include/mirtk/BiasCorrection.h
diff --git a/include/mirtk/BiasField.h b/include/mirtk/BiasField.h
diff --git a/include/mirtk/DrawEM.h b/include/mirtk/DrawEM.h
diff --git a/include/mirtk/EMBase.h b/include/mirtk/EMBase.h
diff --git a/include/mirtk/Gaussian.h b/include/mirtk/Gaussian.h
diff --git a/include/mirtk/HashProbabilisticAtlas.h b/include/mirtk/HashProbabilisticAtlas.h
diff --git a/include/mirtk/ImageHistogram1D.h b/include/mirtk/ImageHistogram1D.h
diff --git a/include/mirtk/KMeans.h b/include/mirtk/KMeans.h
diff --git a/include/mirtk/MeanShift.h b/include/mirtk/MeanShift.h
diff --git a/include/mirtk/NormalizeNyul.h b/include/mirtk/NormalizeNyul.h
diff --git a/include/mirtk/PolynomialBiasField.h b/include/mirtk/PolynomialBiasField.h
diff --git a/include/mirtk/ProbabilisticAtlas.h b/include/mirtk/ProbabilisticAtlas.h
diff --git a/label_names/ALBERT/all_labels_LUT_ITKSNAP.txt b/label_names/ALBERT/all_labels_LUT_ITKSNAP.txt
diff --git a/label_names/ALBERT/labels_LUT_ITKSNAP.txt b/label_names/ALBERT/labels_LUT_ITKSNAP.txt
diff --git a/label_names/ALBERT/tissue_labels_LUT_ITKSNAP.txt b/label_names/ALBERT/tissue_labels_LUT_ITKSNAP.txt
diff --git a/label_names/MCRIB/all_labels_LUT_ITKSNAP.txt b/label_names/MCRIB/all_labels_LUT_ITKSNAP.txt
diff --git a/label_names/MCRIB/labels_LUT_ITKSNAP.txt b/label_names/MCRIB/labels_LUT_ITKSNAP.txt
diff --git a/label_names/MCRIB/tissue_labels_LUT_ITKSNAP.txt b/label_names/MCRIB/tissue_labels_LUT_ITKSNAP.txt
diff --git a/parameters/ALBERT/LUT.txt b/parameters/ALBERT/LUT.txt
diff --git a/parameters/ALBERT/config.sh b/parameters/ALBERT/config.sh
@@ -8,7 +8,7 @@ export ATLAS_T2_DIR=$DRAWEMDIR/atlases/ALBERTs/T2
 export ATLAS_TISSUES_DIR=$DRAWEMDIR/atlases/ALBERTs/tissues-v3
 export ATLAS_SEGMENTATIONS_DIR=$DRAWEMDIR/atlases/ALBERTs/segmentations-v3
 export ATLAS_GM_POSTERIORS_DIR=$DRAWEMDIR/atlases/ALBERTs/gm-posteriors-v3
-export ATLASES=`ls $ATLAS_T2_DIR`
+export ATLASES=`ls $ATLAS_T2_DIR | sed -e 's:.nii.gz::g'`
 export ATLAS_TISSUES="outlier csf gm wm hwm lwm"
 export ATLAS_TISSUES_GROUPING="1 1 1 3"
 export HIGH_WM_TISSUE=4

diff --git a/parameters/ALBERT/connectivities.mrf b/parameters/ALBERT/connectivities.mrf
diff --git a/parameters/MCRIB/LUT.txt b/parameters/MCRIB/LUT.txt
diff --git a/parameters/MCRIB/config.sh b/parameters/MCRIB/config.sh
@@ -8,7 +8,7 @@ export ATLAS_T2_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/T2
 export ATLAS_TISSUES_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/tissues
 export ATLAS_SEGMENTATIONS_DIR=$DRAWEMDIR/atlases/M-CRIB_2.0/segmentations
 export ATLAS_GM_POSTERIORS_DIR=""
-export ATLASES=`ls $ATLAS_T2_DIR`
+export ATLASES=`ls $ATLAS_T2_DIR | sed -e 's:.nii.gz::g'`
 export ATLAS_TISSUES="outlier csf gm wm"
 export ATLAS_TISSUES_GROUPING="1 1 1 1"
 export HIGH_WM_TISSUE=

diff --git a/parameters/MCRIB/connectivities.mrf b/parameters/MCRIB/connectivities.mrf
diff --git a/parameters/connectivities_tissues.mrf b/parameters/connectivities_tissues.mrf
diff --git a/parameters/ireg-multichannel-structural.cfg b/parameters/ireg-multichannel-structural.cfg
diff --git a/parameters/ireg-structural.cfg b/parameters/ireg-structural.cfg
diff --git a/parameters/ireg.cfg b/parameters/ireg.cfg
diff --git a/scripts/register-multi-atlas.sh b/scripts/register-multi-atlas.sh
diff --git a/segmentation.png b/segmentation.png
diff --git a/src/BSplineBiasField.cc b/src/BSplineBiasField.cc
diff --git a/src/BiasCorrection.cc b/src/BiasCorrection.cc
diff --git a/src/BiasField.cc b/src/BiasField.cc
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
diff --git a/src/DrawEM.cc b/src/DrawEM.cc
diff --git a/src/EMBase.cc b/src/EMBase.cc
diff --git a/src/Gaussian.cc b/src/Gaussian.cc
diff --git a/src/ImageHistogram1D.cc b/src/ImageHistogram1D.cc
diff --git a/src/KMeans.cc b/src/KMeans.cc
diff --git a/src/MeanShift.cc b/src/MeanShift.cc
diff --git a/src/NormalizeNyul.cc b/src/NormalizeNyul.cc
diff --git a/src/PolynomialBiasField.cc b/src/PolynomialBiasField.cc
diff --git a/src/ProbabilisticAtlas.cc b/src/ProbabilisticAtlas.cc
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
diff --git a/tools/calculate-filtering.cc b/tools/calculate-filtering.cc
diff --git a/tools/calculate-gradients.cc b/tools/calculate-gradients.cc
diff --git a/tools/change-label.cc b/tools/change-label.cc
diff --git a/tools/draw-em.cc b/tools/draw-em.cc
diff --git a/tools/em-hard-segmentation.cc b/tools/em-hard-segmentation.cc
diff --git a/tools/em.cc b/tools/em.cc
diff --git a/tools/fill-holes-nn-based.cc b/tools/fill-holes-nn-based.cc
diff --git a/tools/fill-holes.cc b/tools/fill-holes.cc
diff --git a/tools/kmeans.cc b/tools/kmeans.cc
diff --git a/tools/measure-volume.cc b/tools/measure-volume.cc
diff --git a/tools/normalize.cc b/tools/normalize.cc
diff --git a/tools/padding.cc b/tools/padding.cc
diff --git a/tools/split-labels.cc b/tools/split-labels.cc