├── .gitignore ├── .travis.yml ├── AUTHORS ├── BrainstemSS ├── AtlasDump.mgz ├── AtlasMesh.gz ├── Makefile.am ├── compressionLookupTable.txt ├── linux_x86_64 │ ├── Makefile.am │ ├── SegmentSubject.bin │ └── run_SegmentSubject.sh ├── mac_osx │ ├── Makefile.am │ ├── run_SegmentSubject.sh │ └── segmentSubject.app │ │ └── Contents │ │ ├── Info.plist │ │ ├── MacOS │ │ ├── applauncher │ │ ├── prelaunch │ │ └── segmentSubject │ │ └── Resources │ │ ├── English.lproj │ │ ├── About.nib │ │ ├── MWOpenAccessoryView.nib │ │ ├── MWSaveAccessoryView.nib │ │ └── MainMenu.nib │ │ └── membrane.icns ├── quantifyBrainstemStructures.sh └── segmentBS.sh ├── CMakeLists.txt ├── COPYING ├── ChangeLog ├── Doxyfile ├── GEMS ├── Makefile.am ├── Makefile.kvlN4ITK.am ├── data │ ├── CurrentMeshCollection30.gz │ ├── Makefile.am │ ├── compressionLookupTable.txt │ ├── compressionLookupTable_left.txt │ ├── imageDump.mgz │ ├── kvlQuantifyHippocampalSubfieldSegmentations.sh.help.xml │ ├── kvlSegmentHippocampalSubfields.sh.help.xml │ ├── nonPartialVolumeStatsLeftReferenceForBert.txt │ └── nonPartialVolumeStatsRightReferenceForBert.txt ├── gzstream.cxx ├── gzstream.h ├── itkAffine3DTransform.h ├── itkAffine3DTransform.txx ├── itkMGHImageIOFactory.cxx ├── itkMGHImageIOFactory.h ├── kvlAddBorder.cxx ├── kvlAddCSFToBucknerData.cxx ├── kvlAddMeshToMeshCollection.cxx ├── kvlAddProbabilityImages.cxx ├── kvlApplyTransform.cxx ├── kvlAtlasMesh.h ├── kvlAtlasMeshAlphaDrawer.h ├── kvlAtlasMeshBuilder.cxx ├── kvlAtlasMeshBuilder.h ├── kvlAtlasMeshCollection.cxx ├── kvlAtlasMeshCollection.h ├── kvlAtlasMeshCollectionFastReferencePositionCost.cxx ├── kvlAtlasMeshCollectionFastReferencePositionCost.h ├── kvlAtlasMeshCollectionModelLikelihoodCalculator.cxx ├── kvlAtlasMeshCollectionModelLikelihoodCalculator.h ├── kvlAtlasMeshCollectionPositionCostCalculator.cxx ├── kvlAtlasMeshCollectionPositionCostCalculator.h ├── kvlAtlasMeshCollectionPositionCostCalculator2.cxx ├── kvlAtlasMeshCollectionPositionCostCalculator2.h ├── kvlAtlasMeshCollectionReferencePositionCost.cxx ├── kvlAtlasMeshCollectionReferencePositionCost.h ├── kvlAtlasMeshCollectionTest.cxx ├── kvlAtlasMeshCollectionValidator.cxx ├── kvlAtlasMeshCollectionValidator.h ├── kvlAtlasMeshDeformationLevenbergMarquardt.cxx ├── kvlAtlasMeshDeformationLevenbergMarquardt.h ├── kvlAtlasMeshHamiltonianPositionSampler.cxx ├── kvlAtlasMeshHamiltonianPositionSampler.h ├── kvlAtlasMeshLabelStatisticsCollector.h ├── kvlAtlasMeshMinLogLikelihoodCalculator.h ├── kvlAtlasMeshMultiAlphaDrawer.h ├── kvlAtlasMeshPositionGradientCalculator.h ├── kvlAtlasMeshRasterizor.h ├── kvlAtlasMeshRasterizor.txx ├── kvlAtlasMeshRasterizorTest.cxx ├── kvlAtlasMeshSegmentationDriver.cxx ├── kvlAtlasMeshSegmentationDriver.h ├── kvlAtlasMeshSegmenter.cxx ├── kvlAtlasMeshSegmenter.h ├── kvlAtlasMeshSegmenterConsole.cxx ├── kvlAtlasMeshSegmenterConsole.h ├── kvlAtlasMeshSegmenterConsoleGUI.fl ├── kvlAtlasMeshSmoother.cxx ├── kvlAtlasMeshSmoother.h ├── kvlAtlasMeshSummaryDrawer.h ├── kvlAtlasMeshToIntensityImageGradientCalculator.h ├── kvlAtlasMeshToIntensityImagePartialVolumeGradientCalculator.cxx ├── kvlAtlasMeshToIntensityImagePartialVolumeGradientCalculator.h ├── kvlAtlasMeshToProbabilityImageGradientCalculator.h ├── kvlAtlasMeshVertexProcessor.cxx ├── kvlAtlasMeshVertexProcessor.h ├── kvlAtlasMeshVertexProcessor2.cxx ├── kvlAtlasMeshVertexProcessor2.h ├── kvlAtlasMeshVertexProcessorTest.cxx ├── kvlAtlasMeshViewingConsole.cxx ├── kvlAtlasMeshViewingConsole.h ├── kvlAtlasMeshViewingConsoleGUI.fl ├── kvlAtlasMeshVisitCounter.h ├── kvlAtlasParameterEstimationConsole.cxx ├── kvlAtlasParameterEstimationConsole.h ├── kvlAtlasParameterEstimationConsoleGUI.cxx ├── kvlAtlasParameterEstimationConsoleGUI.fl ├── kvlAtlasParameterEstimationConsoleGUI.h ├── kvlAtlasParameterEstimator.cxx ├── kvlAtlasParameterEstimator.h ├── kvlAugmentManualSegmentationWithAutomatedSegmentation.cxx ├── kvlAutoCrop.cxx ├── kvlBinaryThresholdImage.cxx ├── kvlBuildAtlasMeshWithoutGUI.cxx ├── kvlCalculateAtlasMeshCollectionTotalCost.cxx ├── kvlCalculatePositionCost.cxx ├── kvlChangeKOfMeshCollection.cxx ├── kvlChangePointParametersOfMeshCollection.cxx ├── kvlColorCodeProbabilityImages.cxx ├── kvlColorTest.cxx ├── kvlCombineManualSegmentationProtocols.cxx ├── kvlCompressImage.cxx ├── kvlCompressionLookupTable.cxx ├── kvlCompressionLookupTable.h ├── kvlConstructMultiResolutionMeshCollection.cxx ├── kvlConstructSparseMeshCollection.cxx ├── kvlConvert.cxx ├── kvlCorrectLeftSideLabelsToRightSideLabels.cxx ├── kvlCrop.cxx ├── kvlCropImage.cxx ├── kvlCroppedImageReader.cxx ├── kvlCroppedImageReader.h ├── kvlEMSegment.cxx ├── kvlEMSegmenter.cxx ├── kvlEMSegmenter.h ├── kvlEstimateAtlasParameters.cxx ├── kvlEstimateAtlasParametersWithoutGUI.cxx ├── kvlEvaluateQuantitatively.cxx ├── kvlEvaluateQuantitativelyWithHausdorffDistance.cxx ├── kvlEvaluateSegmentation.cxx ├── kvlGenerateToyExampleData.cxx ├── kvlGenerateWeightedColorChannels.cxx ├── kvlImageSmoother.cxx ├── kvlImageSmoother.h ├── kvlImageThresholdingConsole.cxx ├── kvlImageThresholdingConsole.h ├── kvlImageThresholdingConsoleGUI.fl ├── kvlImageThresholdingConsoleGUI.h ├── kvlImageViewer.cxx ├── kvlImageViewer.h ├── kvlImageViewingConsole.cxx ├── kvlImageViewingConsole.h ├── kvlImageViewingConsoleGUI.fl ├── kvlImageViewingConsoleGUI.h ├── kvlLabelImageToCompactMeshRepresentation.cxx ├── kvlMapDeformationField.cxx ├── kvlMapLabels.cxx ├── kvlMapLabelsOfAtlasMesh.cxx ├── kvlMaskImage.cxx ├── kvlMathematicalMorphology.cxx ├── kvlMergeMeshCollections.cxx ├── kvlMultiResolutionAtlasMesher.cxx ├── kvlMultiResolutionAtlasMesher.h ├── kvlN4ITK.cxx ├── kvlOptimizePositionsWithICM.cxx ├── kvlOverwriteEmptySlices.cxx ├── kvlParameterOrderPowellOptimizer.h ├── kvlPartialVolumeSegmentationTest.cxx ├── kvlProgressReporter.h ├── kvlQuantifyPosteriorProbabilityImages.cxx ├── kvlRasterizeAtlasMesh.cxx ├── kvlReduceNumberOfIntensityLevels.cxx ├── kvlRegister.cxx ├── kvlRegisterer.cxx ├── kvlRegisterer.h ├── kvlResample.cxx ├── kvlResampler.cxx ├── kvlResampler.h ├── kvlSamplePositionsFromMeshCollection.cxx ├── kvlScaleMeshCollection.cxx ├── kvlSegment.cxx ├── kvlSegmentWithoutGUI.cxx ├── kvlSegmentationEvaluationConsole.cxx ├── kvlSegmentationEvaluationConsole.h ├── kvlSegmentationEvaluationConsoleGUI.fl ├── kvlSetReferencePosition.cxx ├── kvlSmoothMesh.cxx ├── kvlTestImageSmoother.cxx ├── kvlTetrahedronAspectRatio.h ├── kvlThresholdImage.cxx ├── kvlUpsample.cxx ├── kvlUpsampleMesh.cxx ├── kvlValidateMeshCollection.cxx ├── kvlViewImage.cxx ├── kvlViewMeshCollectionWithGUI.cxx ├── kvlViewerTest.cxx ├── scripts │ ├── Makefile.am │ ├── kvlQuantifyHippocampalSubfieldSegmentations.sh │ ├── kvlQuantifyHippocampalSubfieldSegmentations.sh.help.txt │ ├── kvlSegmentHippocampalSubfields.sh │ ├── kvlSegmentHippocampalSubfields.sh.help.txt │ └── kvlTestHippocampalSubfields.sh ├── vnl_kvl_qr.h ├── vnl_kvl_qr.txx ├── vtkFlRenderWindowInteractor.cxx └── vtkFlRenderWindowInteractor.h ├── HippoSF ├── AtlasDump.mgz ├── AtlasMesh.gz ├── Makefile.am ├── compressionLookupTable.txt ├── linux_x86_64 │ ├── Makefile.am │ ├── run_segmentSubjectT1T2_autoEstimateAlveusML.sh │ ├── run_segmentSubjectT1_autoEstimateAlveusML.sh │ ├── run_segmentSubjectT2_autoEstimateAlveusML.sh │ ├── segmentSubjectT1T2_autoEstimateAlveusML │ ├── segmentSubjectT1_autoEstimateAlveusML │ └── segmentSubjectT2_autoEstimateAlveusML ├── mac_osx │ ├── Makefile.am │ ├── run_segmentSubjectT1T2_autoEstimateAlveusML.sh │ ├── run_segmentSubjectT1_autoEstimateAlveusML.sh │ ├── run_segmentSubjectT2_autoEstimateAlveusML.sh │ ├── segmentSubjectT1T2_autoEstimateAlveusML.app │ │ └── Contents │ │ │ ├── Info.plist │ │ │ ├── MacOS │ │ │ ├── applauncher │ │ │ ├── prelaunch │ │ │ └── segmentSubjectT1T2_autoEstimateAlveusML │ │ │ └── Resources │ │ │ ├── English.lproj │ │ │ ├── About.nib │ │ │ ├── MWOpenAccessoryView.nib │ │ │ ├── MWSaveAccessoryView.nib │ │ │ └── MainMenu.nib │ │ │ └── membrane.icns │ ├── segmentSubjectT1_autoEstimateAlveusML.app │ │ └── Contents │ │ │ ├── Info.plist │ │ │ ├── MacOS │ │ │ ├── applauncher │ │ │ ├── prelaunch │ │ │ └── segmentSubjectT1_autoEstimateAlveusML │ │ │ └── Resources │ │ │ ├── English.lproj │ │ │ ├── About.nib │ │ │ ├── MWOpenAccessoryView.nib │ │ │ ├── MWSaveAccessoryView.nib │ │ │ └── MainMenu.nib │ │ │ └── membrane.icns │ └── segmentSubjectT2_autoEstimateAlveusML.app │ │ └── Contents │ │ ├── Info.plist │ │ ├── MacOS │ │ ├── applauncher │ │ ├── prelaunch │ │ └── segmentSubjectT2_autoEstimateAlveusML │ │ └── Resources │ │ ├── English.lproj │ │ ├── About.nib │ │ ├── MWOpenAccessoryView.nib │ │ ├── MWSaveAccessoryView.nib │ │ └── MainMenu.nib │ │ └── membrane.icns ├── quantifyHippocampalSubfields.sh ├── segmentSF_T1.sh ├── segmentSF_T1T2.sh └── segmentSF_T2.sh ├── INSTALL ├── LICENSE ├── Makefile.am ├── Makefile.extra ├── NEWS ├── NOTICE ├── README ├── acinclude.m4 ├── check_siemens_dir ├── CMakeLists.txt ├── Makefile.am └── check_siemens_dir.c ├── config ├── install-sh └── mkinstalldirs ├── configure.in ├── connectgraph ├── Makefile.am ├── MyCmdLineParser.cpp ├── MyCmdLineParser.h └── connectgraph.cpp ├── cudatest ├── Makefile.am ├── conv1d_test.cpp ├── convgaussian_test.cpp ├── gcamCompare.cpp ├── gcam_addstatus_test.cpp ├── gcam_applygradient_test.cpp ├── gcam_clear_test.cpp ├── gcam_cmp_test.cpp ├── gcam_jacobenergy_test.cpp ├── gcam_jacobterm_test.cpp ├── gcam_labelenergy_test.cpp ├── gcam_labelterm_copydeltas_test.cpp ├── gcam_labelterm_final_test.cpp ├── gcam_labelterm_mainloop_test.cpp ├── gcam_labelterm_postantconsist_test.cpp ├── gcam_labelterm_removeoutliers_test.cpp ├── gcam_labelterm_test.cpp ├── gcam_lle_test.cpp ├── gcam_llterm_test.cpp ├── gcam_removesingularities_test.cpp ├── gcam_removestatus_test.cpp ├── gcam_smoothgradient_test.cpp ├── gcam_smoothnessenergy_test.cpp ├── gcam_smoothnessterm_test.cpp ├── gcam_undogradient_test.cpp ├── gcam_write_test.cpp ├── gcatest │ ├── Makefile.am │ └── gca_read_test.cpp ├── kahan.hpp ├── meanfilter_test.cpp ├── mri2nc.cpp ├── mrilabeltest │ ├── Makefile.am │ ├── mriMarkLabelBorderVoxelTest.cpp │ └── mriVoxInLabelPartialVolumeTest.cpp └── volumecopy │ ├── Makefile.am │ ├── volcopy.cu │ ├── volcopy.hpp │ └── volume_copy_test.cpp ├── debian ├── TODO ├── blends ├── changelog ├── compat ├── control ├── copyright ├── freesurfer-sloppy-FSMAJORVER.install.template ├── freesurfer-sloppy-FSMAJORVER.links.template ├── freesurfer-sloppy-FSMAJORVER.lintian-overrides.template ├── freesurfer-sloppy-common-FSMAJORVER.install.template ├── freesurfer-sloppy-fsfast-FSMAJORVER.install.template ├── freesurfer-sloppy-fsfast-FSMAJORVER.lintian-overrides.template ├── freesurfer.sh.template ├── freesurfer_gui_app_wrapper.template ├── gbp.conf ├── matlab-freesurfer-sloppy-FSMAJORVER.install.template ├── patches │ ├── datapkg_split │ ├── deb_no_tktools │ ├── disable_to_be_fixed_pieces │ ├── dont_build_3rdparty │ ├── dump_ancient_libtoolm4 │ ├── dynamicfltk │ ├── femelasticbotch │ ├── fix_flirtsch_location │ ├── fix_install_destdir │ ├── fixanndetection │ ├── fixgtsdetection │ ├── fixupupstreamfiles │ ├── gemsinstallautocrop │ ├── ignorelicense │ ├── install_path_mri_cvs_register │ ├── internal_shared_libs │ ├── missing_shared_libs │ ├── no_morph_utils_warning │ ├── petsc_link_fix │ ├── petscupdate │ ├── prevent_segfaults │ ├── qt_build_compat │ ├── relocate_license_file │ ├── remove_3rdparty_code │ ├── series │ └── use_f2c_not_g2c ├── repack.sh ├── rules ├── scuba.desktop.template ├── scuba2.desktop.template ├── source │ └── format └── upstream │ └── metadata ├── dicom ├── CMakeLists.txt ├── Makefile.am ├── condition.c ├── ctnthread.c ├── dcm.c ├── dcmcond.c ├── dcmdict.c ├── dcmsupport.c └── lst.c ├── distribution ├── ASegStatsLUT.txt ├── DefectLUT.txt ├── DefectLUTRand.txt ├── FreeSurferColorLUT.txt ├── FreeSurferEnv.csh ├── FreeSurferEnv.sh ├── Mac_32b │ ├── freeview_Mac32.bin │ ├── qdec_Mac32.bin │ ├── tkmedit_Mac32.bin │ ├── tkregister2_Mac32.bin │ └── tksurfer_Mac32.bin ├── Makefile.am ├── SegmentNoLUT.txt ├── SetUpFreeSurfer-SAMPLE.csh ├── SetUpFreeSurfer-SAMPLE.sh ├── Simple_surface_labels2002.txt ├── Simple_surface_labels2005.txt ├── Simple_surface_labels2009.txt ├── UpdateFromSnapshot.sh ├── WMParcStatsLUT.txt ├── average │ ├── Buckner_JNeurophysiol11_MNI152 │ │ ├── Buckner2011_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Buckner2011_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Buckner2011_17Networks_ColorLUT.txt │ │ ├── Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Buckner2011_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Buckner2011_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Buckner2011_7Networks_ColorLUT.txt │ │ ├── Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Buckner_JNeurophysiol11_MNI152_README │ │ ├── FSL_MNI152_FreeSurferConformed_1mm.nii.gz │ │ └── Makefile.am │ ├── Choi_JNeurophysiol12_MNI152 │ │ ├── Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Choi2012_17Networks_ColorLUT.txt │ │ ├── Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Choi2012_7Networks_ColorLUT.txt │ │ ├── Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz │ │ ├── Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz │ │ ├── Choi_JNeurophysiol12_MNI152_README │ │ ├── FSL_MNI152_FreeSurferConformed_1mm.nii.gz │ │ └── Makefile.am │ ├── EC_average.tar.gz │ ├── HPMarch022005_ras.mgz │ ├── Makefile.am │ ├── RB_all_2008-03-26.2mm.lta │ ├── RB_all_2008-03-26.gca │ ├── RB_all_2008-03-26.mni152.2mm.lta │ ├── RB_all_2014-08-21.gca │ ├── RB_all_2015-08-04.gca │ ├── RB_all_2016-02-11.gca │ ├── RB_all_withskull_2008-03-26.gca │ ├── RB_all_withskull_2014-08-21.gca │ ├── V1_average.tar.gz │ ├── Yeo_Brainmap_MNI152.tar.gz │ ├── Yeo_JNeurophysiol11_MNI152 │ │ ├── FSL_MNI152_FreeSurferConformed_1mm.nii.gz │ │ ├── Makefile.am │ │ ├── Yeo2011_17Networks_ColorLUT.txt │ │ ├── Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz │ │ ├── Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz │ │ ├── Yeo2011_7Networks_ColorLUT.txt │ │ ├── Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz │ │ ├── Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz │ │ └── Yeo_JNeurophysiol11_MNI152_README │ ├── aseg+spmhead+vermis+pons.ixi.gca │ ├── aseg+spmhead.ixi.gca │ ├── build_gcs_morph.csh │ ├── colortable_BA.txt │ ├── colortable_desikan_killiany.txt │ ├── cvs_avg35.tar.gz │ ├── cvs_avg35_inMNI152.tar.gz │ ├── face.gca │ ├── fsaverage-fs3.tar.gz │ ├── fsaverage.tar.gz │ ├── fsaverage3.tar.gz │ ├── fsaverage4.tar.gz │ ├── fsaverage5.tar.gz │ ├── fsaverage6.tar.gz │ ├── fsaverage7.tar.gz │ ├── fsaverage_sym.tar.gz │ ├── label_scales.dat │ ├── lh.DKTatlas100.gcs │ ├── lh.DKTatlas40.gcs │ ├── lh.atlas2002_simple.gcs │ ├── lh.atlas2005_simple.gcs │ ├── lh.average.CURVATURE.tif │ ├── lh.average.curvature.filled.buckner40.tif │ ├── lh.average.tif │ ├── lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs │ ├── lh.destrieux.simple.2009-07-29.gcs │ ├── lh_trans_toSulc.gcs │ ├── mni152.1mm.register.dat │ ├── mni152.mni305.cor.subfov1.dat │ ├── mni152.mni305.cor.subfov2.dat │ ├── mni152.register.dat │ ├── mni305.cor.mgz │ ├── mni305.cor.readme │ ├── mni305.cor.subfov1.mgz │ ├── mni305.cor.subfov1.reg │ ├── mni305.cor.subfov2.mgz │ ├── mni305.cor.subfov2.reg │ ├── mni305.mask.cor.mgz │ ├── mult-comp-cor.tar.gz │ ├── pons.mni152.2mm.mgz │ ├── rh.DKTatlas100.gcs │ ├── rh.DKTatlas40.gcs │ ├── rh.atlas2002_simple.gcs │ ├── rh.atlas2005_simple.gcs │ ├── rh.average.CURVATURE.tif │ ├── rh.average.curvature.filled.buckner40.tif │ ├── rh.average.tif │ ├── rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs │ ├── rh.destrieux.simple.2009-07-29.gcs │ ├── rh_trans_toSulc.gcs │ ├── rigidly_aligned_brain_template.tif │ ├── surf │ │ ├── Makefile.am │ │ ├── README │ │ ├── lh.sphere.ico0.reg │ │ ├── lh.sphere.ico1.reg │ │ ├── lh.sphere.ico2.reg │ │ ├── lh.sphere.ico3.reg │ │ ├── lh.sphere.ico4.reg │ │ ├── lh.sphere.ico5.reg │ │ ├── lh.sphere.ico6.reg │ │ ├── lh.sphere.ico7.reg │ │ ├── lh.sphere.reg │ │ ├── rh.sphere.ico0.reg │ │ ├── rh.sphere.ico1.reg │ │ ├── rh.sphere.ico2.reg │ │ ├── rh.sphere.ico3.reg │ │ ├── rh.sphere.ico4.reg │ │ ├── rh.sphere.ico5.reg │ │ ├── rh.sphere.ico6.reg │ │ ├── rh.sphere.ico7.reg │ │ └── rh.sphere.reg │ ├── talairach_mixed_with_skull.gca │ ├── tissue_parms.txt │ └── wmsa_new_eesmith.gca ├── build_dev.csh ├── build_release_type.csh ├── build_scripts_README.txt ├── build_stable-pub.csh ├── build_stable.csh ├── cp_fscvs.csh ├── create_targz.csh ├── data │ ├── gradientNonlinearityAllegra.mff │ └── gradientNonlinearitySonata.mff ├── desikan_killiany_split_table.txt ├── diffusion │ ├── Makefile.am │ └── mgh-dti-seqpack │ │ ├── Makefile.am │ │ ├── README │ │ ├── gradient_mgh_dti06.gdt │ │ ├── gradient_mgh_dti12.gdt │ │ ├── gradient_mgh_dti13.gdt │ │ ├── gradient_mgh_dti14.gdt │ │ ├── gradient_mgh_dti15.gdt │ │ ├── gradient_mgh_dti16.gdt │ │ ├── gradient_mgh_dti17.gdt │ │ ├── gradient_mgh_dti18.gdt │ │ ├── gradient_mgh_dti19.gdt │ │ ├── gradient_mgh_dti20.gdt │ │ ├── gradient_mgh_dti21.gdt │ │ ├── gradient_mgh_dti22.gdt │ │ ├── gradient_mgh_dti23.gdt │ │ ├── gradient_mgh_dti24.gdt │ │ ├── gradient_mgh_dti240.gdt │ │ ├── gradient_mgh_dti25.gdt │ │ ├── gradient_mgh_dti26.gdt │ │ ├── gradient_mgh_dti27.gdt │ │ ├── gradient_mgh_dti28.gdt │ │ ├── gradient_mgh_dti29.gdt │ │ ├── gradient_mgh_dti30.gdt │ │ ├── gradient_mgh_dti31.gdt │ │ ├── gradient_mgh_dti32.gdt │ │ ├── gradient_mgh_dti33.gdt │ │ ├── gradient_mgh_dti34.gdt │ │ ├── gradient_mgh_dti35.gdt │ │ ├── gradient_mgh_dti36.gdt │ │ ├── gradient_mgh_dti37.gdt │ │ ├── gradient_mgh_dti38.gdt │ │ ├── gradient_mgh_dti39.gdt │ │ ├── gradient_mgh_dti40.gdt │ │ ├── gradient_mgh_dti41.gdt │ │ ├── gradient_mgh_dti42.gdt │ │ ├── gradient_mgh_dti43.gdt │ │ ├── gradient_mgh_dti44.gdt │ │ ├── gradient_mgh_dti45.gdt │ │ ├── gradient_mgh_dti46.gdt │ │ ├── gradient_mgh_dti47.gdt │ │ ├── gradient_mgh_dti48.gdt │ │ ├── gradient_mgh_dti49.gdt │ │ ├── gradient_mgh_dti50.gdt │ │ ├── gradient_mgh_dti51.gdt │ │ ├── gradient_mgh_dti52.gdt │ │ ├── gradient_mgh_dti53.gdt │ │ ├── gradient_mgh_dti54.gdt │ │ ├── gradient_mgh_dti55.gdt │ │ ├── gradient_mgh_dti56.gdt │ │ ├── gradient_mgh_dti57.gdt │ │ ├── gradient_mgh_dti58.gdt │ │ ├── gradient_mgh_dti59.gdt │ │ ├── gradient_mgh_dti6.gdt │ │ ├── gradient_mgh_dti60.gdt │ │ ├── gradient_mgh_dti61.gdt │ │ ├── gradient_mgh_dti62.gdt │ │ ├── gradient_mgh_dti63.gdt │ │ ├── gradient_mgh_dti64.gdt │ │ ├── gradient_mgh_dti65.gdt │ │ ├── gradient_mgh_dti66.gdt │ │ ├── gradient_mgh_dti67.gdt │ │ ├── gradient_mgh_dti68.gdt │ │ ├── gradient_mgh_dti69.gdt │ │ ├── gradient_mgh_dti70.gdt │ │ ├── gradient_mgh_dti71.gdt │ │ ├── gradient_mgh_dti72.gdt │ │ ├── gradient_mgh_dti73.gdt │ │ ├── gradient_mgh_dti74.gdt │ │ ├── gradient_mgh_dti75.gdt │ │ ├── gradient_mgh_dti76.gdt │ │ ├── gradient_mgh_dti77.gdt │ │ ├── gradient_mgh_dti78.gdt │ │ ├── gradient_mgh_dti79.gdt │ │ ├── gradient_mgh_dti80.gdt │ │ ├── gradient_mgh_dti81.gdt │ │ ├── gradient_mgh_dti82.gdt │ │ ├── gradient_mgh_dti83.gdt │ │ ├── gradient_mgh_dti84.gdt │ │ ├── gradient_mgh_dti85.gdt │ │ ├── gradient_mgh_dti86.gdt │ │ ├── gradient_mgh_dti87.gdt │ │ ├── gradient_mgh_dti88.gdt │ │ ├── gradient_mgh_dti89.gdt │ │ ├── gradient_mgh_dti90.gdt │ │ ├── gradient_mgh_dti91.gdt │ │ ├── gradient_mgh_dti92.gdt │ │ ├── gradient_mgh_dti93.gdt │ │ ├── gradient_mgh_dti94.gdt │ │ ├── gradient_mgh_dti95.gdt │ │ ├── gradient_mgh_dti96.gdt │ │ ├── gradient_mgh_dti97.gdt │ │ ├── gradient_mgh_dti98.gdt │ │ └── gradient_mgh_dti99.gdt ├── docs │ ├── Makefile.am │ ├── license.blt.txt │ ├── license.boost.txt │ ├── license.cortechs.txt │ ├── license.cuda.txt │ ├── license.dcmtk.txt │ ├── license.freesurfer_SLA.txt │ ├── license.fsl.txt │ ├── license.gifti.txt │ ├── license.itk.txt │ ├── license.lapack.txt │ ├── license.minc.txt │ ├── license.nifti.txt │ ├── license.nrrdio.txt │ ├── license.petsc.txt │ ├── license.qt.html │ ├── license.swig.txt │ ├── license.tcltk.txt │ ├── license.thrust.txt │ ├── license.tix.txt │ ├── license.vtk.txt │ └── license.vxl.txt ├── exclude_from_targz ├── fsafd │ ├── Makefile.am │ ├── PonsCutDice.adf │ ├── RibbonPlacementDice.adf │ ├── SubcorticalLabelingPercentVol.adf │ ├── TalairachingCovariance.adf │ ├── TalairachingMean.adf │ ├── TalairachingProbas.adf │ ├── WMsegmentationDice.adf │ ├── lh.CorpusCallosumCutDice.adf │ ├── lh.CorticalLabelingPercentArea_txt.adf │ ├── lh.EV90.mgh │ ├── lh.SurfRegistrationResidualVar.adf │ ├── lh.ThicknessMatrix.mgh │ ├── rh.CorpusCallosumCutDice.adf │ └── rh.CorticalLabelingPercentArea_txt.adf ├── fsl-extra │ ├── Makefile.am │ └── flirt.newdefault.20080811.sch ├── lib │ ├── Makefile.am │ └── bem │ │ ├── Makefile.am │ │ ├── ic0.tri │ │ ├── ic1.tri │ │ ├── ic2.tri │ │ ├── ic3.tri │ │ ├── ic4.tri │ │ ├── ic5.tri │ │ ├── ic6.tri │ │ ├── ic7.tri │ │ ├── inner_skull.dat │ │ ├── outer_skin.dat │ │ └── outer_skull.dat ├── nmr-dev-env ├── nmr-std-env ├── numaris4-protocols.unpackcfg ├── package_maker.tar.gz ├── postprocess_targz.csh ├── sample_colors ├── scanseq.unpackcfg ├── scanseq.unpackinfo ├── sessions │ ├── Makefile.am │ └── README ├── sources.csh ├── sources.sh ├── subjects │ ├── Makefile.am │ ├── README │ ├── sample-001.mgz │ └── sample-002.mgz ├── surface_labels.txt ├── tar-exclude ├── tar-exclude-gca ├── tkmeditColorsCMA ├── tkmeditParcColorsCMA ├── trctrain │ ├── Makefile.am │ └── trctraindata.tar.gz └── trunk ├── dmri_poistats ├── CMakeLists.txt ├── Makefile.am ├── TestPoistats.cxx ├── TestPoistatsReplica.cxx ├── TestPoistatsReplicas.cxx ├── datamodel │ ├── PoistatsModel.cxx │ ├── PoistatsModel.h │ ├── data │ │ ├── PoistatsReplica.cxx │ │ ├── PoistatsReplica.h │ │ ├── PoistatsReplicas.cxx │ │ └── PoistatsReplicas.h │ ├── events │ │ ├── CommandUpdate.cxx │ │ ├── CommandUpdate.h │ │ └── PoistatsEvents.h │ └── utils │ │ ├── EigenVectorInitPathStrategy.cxx │ │ ├── EigenVectorInitPathStrategy.h │ │ ├── FieldLineInitPathStrategy.cxx │ │ ├── FieldLineInitPathStrategy.h │ │ ├── InitializePath.cxx │ │ ├── InitializePath.h │ │ ├── itkPoistatsFilter.h │ │ └── itkPoistatsFilter.txx ├── dmri_initialize_path.cxx ├── dmri_mask.cxx ├── dmri_poistats.cxx ├── io │ ├── AsymmetricTensorReaderStrategy.cxx │ ├── AsymmetricTensorReaderStrategy.h │ ├── AsymmetricTensorVectorReaderStrategy.cxx │ ├── AsymmetricTensorVectorReaderStrategy.h │ ├── SymmetricTensorReaderStrategy.cxx │ ├── SymmetricTensorReaderStrategy.h │ ├── TensorReaderStrategy.cxx │ └── TensorReaderStrategy.h └── test │ └── data │ ├── FinalSeeds.nii.gz │ ├── HelixTensors.nii.gz │ └── Path.nii.gz ├── dmri_tensoreig ├── CMakeLists.txt ├── Makefile.am ├── dmri_tensoreig.c └── do.sh ├── dngtester ├── CMakeLists.txt ├── Makefile.am └── dngtester.c ├── docs ├── Automatic_Failure_Detection.doc ├── Automatic_Failure_Detection.ppt ├── Automatic_Failure_Detection.txt ├── CVS-lzollei.ppt ├── FreeSurfer_Course_Sep_2015_Diffusion.pdf ├── FreeSurfer_Course_Sep_2015_MRI_Basics.pdf ├── HippocampalSubfields-Koen.ppt ├── QArecon.ppt ├── coursedocs ├── dmri,fs.ppt ├── event-related.ppt ├── fMRI_intro.ppt ├── fmri.analysis-theory.ppt ├── fmri.preproc.ppt ├── freesurfer.applications.2009b.ppt ├── freesurfer.applications.2011.ppt ├── freesurfer.applications.njs.ppt ├── freesurfer.applications.ppt ├── freesurfer.failure_modes.AS.ppt ├── freesurfer.failure_modes.ppt ├── freesurfer.feat.ppt ├── freesurfer.fsfast.ppt ├── freesurfer.future_directions.2007.ppt ├── freesurfer.groupanalysis.ppt ├── freesurfer.groupanalysis.short.ppt ├── freesurfer.inferring_architectonics.ppt ├── freesurfer.intro.2011.ppt ├── freesurfer.intro.mmclass.ppt ├── freesurfer.intro.njs.ppt ├── freesurfer.intro.ppt ├── freesurfer.longitudinal.ppt ├── freesurfer.multiplecomparisons.ppt ├── freesurfer.recon.2007.ppt ├── freesurfer.reliability.ppt ├── fs.dt_recon-intro.ppt ├── fs.multimodal-integration.Part1.ppt ├── fs.multimodal-integration.Part2.ppt ├── fs.multimodal-integration.dti.ppt ├── fs.multimodal-integration.fmri.ppt ├── fs.multimodal-integration.ppt ├── fs.registration.ppt ├── fs.registration.pptx ├── fs.retinotopy.ppt ├── fs.roi.old.ppt ├── fs.roi.ppt ├── fs.surface-based-analysis.ppt ├── fscoordinates.ppt ├── fsfast.april2011.ppt ├── fsfast.whyhow.ppt ├── fsjargon.pptx ├── fsrecon.ppt ├── matrix.intro.ppt ├── mri_acquisition.ppt ├── mri_basics.AVDK.ppt ├── qdec-demo-notes.doc ├── qdec.ppt ├── recon-all.block.ppt ├── runningyourdata.ppt ├── savoy.fmri.firstlevel.ppt ├── savoy.fmri.groupana.ppt ├── savoy.fmri.inference.ppt ├── savoy.fmri.preproc.ppt ├── tracula,fs.ppt └── unix_tutorial.ppt ├── doxy-file-header ├── dummy ├── CMakeLists.txt ├── Doxyfile ├── Makefile.am ├── dummy.c └── myown.c ├── dummy_qt ├── Info.plist ├── MainWindow.cpp ├── MainWindow.h ├── MainWindow.ui ├── Makefile.am ├── dummy_qt.pro ├── dummy_qt.qrc ├── images │ └── file_open_16.png └── main.cpp ├── expat ├── Makefile.am ├── README ├── ascii.h ├── asciitab.h ├── chardata.c ├── chardata.h ├── codepage.c ├── codepage.h ├── expat.h ├── expat_external.h ├── filemap.h ├── iasciitab.h ├── internal.h ├── latin1tab.h ├── license.expat.txt ├── minicheck.c ├── minicheck.h ├── nametab.h ├── runtests.c ├── runtestspp.cpp ├── unixfilemap.c ├── utf8tab.h ├── xmlfile.c ├── xmlfile.h ├── xmlparse.c ├── xmlrole.c ├── xmlrole.h ├── xmltchar.h ├── xmltok.c ├── xmltok.h ├── xmltok_impl.c ├── xmltok_impl.h ├── xmltok_ns.c └── xmlwf.c ├── fem_elastic ├── Makefile.am ├── ZlibStringCompressor.cpp ├── ZlibStringCompressor.h ├── coords.h ├── cstats.h ├── element.h ├── exportGcam.cpp ├── fapplyMorph.cpp ├── fcreateMorph.cpp ├── fem_3d.cpp ├── fem_3d.h ├── fsurf2vol.cpp ├── gmpError.h ├── material.h ├── mesh.h ├── mesh_bfs.h ├── misc.h ├── misc_maths.cpp ├── misc_maths.h ├── morph.cpp ├── morph.h ├── morph_utils.cpp ├── morph_utils.h ├── node.h ├── pbCluster_mesh_crop.cpp ├── pbCluster_mesh_crop.h ├── pbmesh_crop.h ├── simple_timer.h ├── small_matrix.cpp ├── small_matrix.h ├── solver.h ├── stl_utils.hpp ├── streamIoMisc.h ├── surf_energy.cpp ├── surf_energy.h ├── surf_powell.cpp ├── surf_powell.h ├── surf_types.h ├── surf_utils.cpp ├── surf_utils.h ├── tag_fio.h ├── toctree.hpp ├── transformUtils.cpp ├── transformUtils.h ├── untangler.cpp └── untangler.h ├── freesurfer.cmake ├── freeview ├── Annotation2D.cpp ├── Annotation2D.h ├── BrushProperty.cpp ├── BrushProperty.h ├── CommandEdit.cpp ├── CommandEdit.h ├── CommonDataStruct.h ├── Contour2D.cpp ├── Contour2D.h ├── Cursor2D.cpp ├── Cursor2D.h ├── Cursor3D.cpp ├── Cursor3D.h ├── CursorFactory.cpp ├── CursorFactory.h ├── DialogAbout.cpp ├── DialogAbout.h ├── DialogAbout.ui ├── DialogCropVolume.cpp ├── DialogCropVolume.h ├── DialogCropVolume.ui ├── DialogGradientFilter.cpp ├── DialogGradientFilter.h ├── DialogGradientFilter.ui ├── DialogLabelStats.cpp ├── DialogLabelStats.h ├── DialogLabelStats.ui ├── DialogLineProfile.cpp ├── DialogLineProfile.h ├── DialogLineProfile.ui ├── DialogLoadConnectome.cpp ├── DialogLoadConnectome.h ├── DialogLoadConnectome.ui ├── DialogLoadDTI.cpp ├── DialogLoadDTI.h ├── DialogLoadDTI.ui ├── DialogLoadFCD.cpp ├── DialogLoadFCD.h ├── DialogLoadFCD.ui ├── DialogLoadPointSet.cpp ├── DialogLoadPointSet.h ├── DialogLoadPointSet.ui ├── DialogLoadSurface.cpp ├── DialogLoadSurface.h ├── DialogLoadSurface.ui ├── DialogLoadSurfaceOverlay.cpp ├── DialogLoadSurfaceOverlay.h ├── DialogLoadSurfaceOverlay.ui ├── DialogLoadVolume.cpp ├── DialogLoadVolume.h ├── DialogLoadVolume.ui ├── DialogNewPointSet.cpp ├── DialogNewPointSet.h ├── DialogNewPointSet.ui ├── DialogNewROI.cpp ├── DialogNewROI.h ├── DialogNewROI.ui ├── DialogNewVolume.cpp ├── DialogNewVolume.h ├── DialogNewVolume.ui ├── DialogPreferences.cpp ├── DialogPreferences.h ├── DialogPreferences.ui ├── DialogReloadLayer.cpp ├── DialogReloadLayer.h ├── DialogReloadLayer.ui ├── DialogReplaceLabel.cpp ├── DialogReplaceLabel.h ├── DialogReplaceLabel.ui ├── DialogRepositionSurface.cpp ├── DialogRepositionSurface.h ├── DialogRepositionSurface.ui ├── DialogSavePointSet.cpp ├── DialogSavePointSet.h ├── DialogSavePointSet.ui ├── DialogSaveScreenshot.cpp ├── DialogSaveScreenshot.h ├── DialogSaveScreenshot.ui ├── DialogSaveVolume.cpp ├── DialogSaveVolume.h ├── DialogSaveVolume.ui ├── DialogSetCamera.cpp ├── DialogSetCamera.h ├── DialogSetCamera.ui ├── DialogSmoothSurface.cpp ├── DialogSmoothSurface.h ├── DialogSmoothSurface.ui ├── DialogThresholdFilter.cpp ├── DialogThresholdFilter.h ├── DialogThresholdFilter.ui ├── DialogThresholdVolume.cpp ├── DialogThresholdVolume.h ├── DialogThresholdVolume.ui ├── DialogTransformVolume.cpp ├── DialogTransformVolume.h ├── DialogTransformVolume.ui ├── DialogVolumeFilter.cpp ├── DialogVolumeFilter.h ├── DialogVolumeFilter.ui ├── DialogVolumeSegmentation.cpp ├── DialogVolumeSegmentation.h ├── DialogVolumeSegmentation.ui ├── DialogWriteMovieFrames.cpp ├── DialogWriteMovieFrames.h ├── DialogWriteMovieFrames.ui ├── FSGroupDescriptor.cpp ├── FSGroupDescriptor.h ├── FSLabel.cpp ├── FSLabel.h ├── FSPointSet.cpp ├── FSPointSet.h ├── FSSurface.cpp ├── FSSurface.h ├── FSTrack.cpp ├── FSTrack.h ├── FSVolume.cpp ├── FSVolume.h ├── FloatingStatusBar.cpp ├── FloatingStatusBar.h ├── FloatingStatusBar.ui ├── GenericRenderView.cpp ├── GenericRenderView.h ├── Info.plist ├── InfoTreeWidget.cpp ├── InfoTreeWidget.h ├── Interactor.cpp ├── Interactor.h ├── Interactor2D.cpp ├── Interactor2D.h ├── Interactor2DMeasure.cpp ├── Interactor2DMeasure.h ├── Interactor2DNavigate.cpp ├── Interactor2DNavigate.h ├── Interactor2DPointSetEdit.cpp ├── Interactor2DPointSetEdit.h ├── Interactor2DROIEdit.cpp ├── Interactor2DROIEdit.h ├── Interactor2DVolumeCrop.cpp ├── Interactor2DVolumeCrop.h ├── Interactor2DVolumeEdit.cpp ├── Interactor2DVolumeEdit.h ├── Interactor2DVoxelEdit.cpp ├── Interactor2DVoxelEdit.h ├── Interactor3D.cpp ├── Interactor3D.h ├── Interactor3DMeasure.cpp ├── Interactor3DMeasure.h ├── Interactor3DNavigate.cpp ├── Interactor3DNavigate.h ├── Interactor3DVolumeCrop.cpp ├── Interactor3DVolumeCrop.h ├── Json.cpp ├── Json.h ├── LUTDataHolder.cpp ├── LUTDataHolder.h ├── LabelTreeWidget.cpp ├── LabelTreeWidget.h ├── Layer.cpp ├── Layer.h ├── LayerCollection.cpp ├── LayerCollection.h ├── LayerConnectomeMatrix.cpp ├── LayerConnectomeMatrix.h ├── LayerDTI.cpp ├── LayerDTI.h ├── LayerEditable.cpp ├── LayerEditable.h ├── LayerFCD.cpp ├── LayerFCD.h ├── LayerFCDWorkerThread.cpp ├── LayerFCDWorkerThread.h ├── LayerLandmarks.cpp ├── LayerLandmarks.h ├── LayerLineProfile.cpp ├── LayerLineProfile.h ├── LayerMRI.cpp ├── LayerMRI.h ├── LayerMRIWorkerThread.cpp ├── LayerMRIWorkerThread.h ├── LayerPLabel.cpp ├── LayerPLabel.h ├── LayerPointSet.cpp ├── LayerPointSet.h ├── LayerProperty.cpp ├── LayerProperty.h ├── LayerPropertyConnectomeMatrix.cpp ├── LayerPropertyConnectomeMatrix.h ├── LayerPropertyDTI.cpp ├── LayerPropertyDTI.h ├── LayerPropertyFCD.cpp ├── LayerPropertyFCD.h ├── LayerPropertyLineProfile.cpp ├── LayerPropertyLineProfile.h ├── LayerPropertyMRI.cpp ├── LayerPropertyMRI.h ├── LayerPropertyPointSet.cpp ├── LayerPropertyPointSet.h ├── LayerPropertyROI.cpp ├── LayerPropertyROI.h ├── LayerPropertySurface.cpp ├── LayerPropertySurface.h ├── LayerPropertyTrack.cpp ├── LayerPropertyTrack.h ├── LayerROI.cpp ├── LayerROI.h ├── LayerSurface.cpp ├── LayerSurface.h ├── LayerTrack.cpp ├── LayerTrack.h ├── LayerTreeWidget.cpp ├── LayerTreeWidget.h ├── LayerVolumeBase.cpp ├── LayerVolumeBase.h ├── LayerVolumeTrack.cpp ├── LayerVolumeTrack.h ├── LivewireTool.cpp ├── LivewireTool.h ├── MainApplication.cpp ├── MainApplication.h ├── MainWindow.cpp ├── MainWindow.h ├── MainWindow.ui ├── Makefile.am ├── MyCmdLineParser.cpp ├── MyCmdLineParser.h ├── MyUtils.cpp ├── MyUtils.h ├── MyVTKUtils.cpp ├── MyVTKUtils.h ├── PanelAllLayers.cpp ├── PanelAllLayers.h ├── PanelAllLayers.ui ├── PanelConnectomeMatrix.cpp ├── PanelConnectomeMatrix.h ├── PanelConnectomeMatrix.ui ├── PanelFCD.cpp ├── PanelFCD.h ├── PanelFCD.ui ├── PanelLayer.cpp ├── PanelLayer.h ├── PanelPointSet.cpp ├── PanelPointSet.h ├── PanelPointSet.ui ├── PanelROI.cpp ├── PanelROI.h ├── PanelROI.ui ├── PanelSurface.cpp ├── PanelSurface.h ├── PanelSurface.ui ├── PanelTrack.cpp ├── PanelTrack.h ├── PanelTrack.ui ├── PanelVolume.cpp ├── PanelVolume.h ├── PanelVolume.ui ├── ProgressCallback.cpp ├── ProgressCallback.h ├── QVTKPaintEngine.cxx ├── QVTKPaintEngine.h ├── QVTKWidget.cxx ├── QVTKWidget.h ├── QVTKWin32Header.h ├── Region2D.cpp ├── Region2D.h ├── Region2DLine.cpp ├── Region2DLine.h ├── Region2DPolyline.cpp ├── Region2DPolyline.h ├── Region2DRectangle.cpp ├── Region2DRectangle.h ├── RenderView.cpp ├── RenderView.h ├── RenderView2D.cpp ├── RenderView2D.h ├── RenderView3D.cpp ├── RenderView3D.h ├── StockColorMap.h ├── SurfaceAnnotation.cpp ├── SurfaceAnnotation.h ├── SurfaceLabel.cpp ├── SurfaceLabel.h ├── SurfaceOverlay.cpp ├── SurfaceOverlay.h ├── SurfaceOverlayProperty.cpp ├── SurfaceOverlayProperty.h ├── SurfaceROI.cpp ├── SurfaceROI.h ├── SurfaceRegion.cpp ├── SurfaceRegion.h ├── SurfaceRegionGroups.cpp ├── SurfaceRegionGroups.h ├── SurfaceSpline.cpp ├── SurfaceSpline.h ├── TermWidget.cpp ├── TermWidget.h ├── TermWidget.ui ├── ThreadBuildContour.cpp ├── ThreadBuildContour.h ├── ThreadIOWorker.cpp ├── ThreadIOWorker.h ├── ToolWindowEdit.cpp ├── ToolWindowEdit.h ├── ToolWindowEdit.ui ├── ToolWindowMeasure.cpp ├── ToolWindowMeasure.h ├── ToolWindowMeasure.ui ├── ToolWindowROIEdit.cpp ├── ToolWindowROIEdit.h ├── ToolWindowROIEdit.ui ├── Track.cpp ├── Track.h ├── TrackData.cpp ├── TrackData.h ├── TrackGroup.cpp ├── TrackGroup.h ├── UIUpdateHelper.cpp ├── UIUpdateHelper.h ├── VolumeCropper.cpp ├── VolumeCropper.h ├── VolumeFilter.cpp ├── VolumeFilter.h ├── VolumeFilterClose.cpp ├── VolumeFilterClose.h ├── VolumeFilterConvolve.cpp ├── VolumeFilterConvolve.h ├── VolumeFilterDilate.cpp ├── VolumeFilterDilate.h ├── VolumeFilterErode.cpp ├── VolumeFilterErode.h ├── VolumeFilterGradient.cpp ├── VolumeFilterGradient.h ├── VolumeFilterMean.cpp ├── VolumeFilterMean.h ├── VolumeFilterMedian.cpp ├── VolumeFilterMedian.h ├── VolumeFilterOpen.cpp ├── VolumeFilterOpen.h ├── VolumeFilterSobel.cpp ├── VolumeFilterSobel.h ├── VolumeFilterThreshold.cpp ├── VolumeFilterThreshold.h ├── VolumeFilterWorkerThread.cpp ├── VolumeFilterWorkerThread.h ├── WidgetGroupPlot.cpp ├── WidgetGroupPlot.h ├── WidgetHistogram.cpp ├── WidgetHistogram.h ├── WidgetTimeCoursePlot.cpp ├── WidgetTimeCoursePlot.h ├── WindowConfigureOverlay.cpp ├── WindowConfigureOverlay.h ├── WindowConfigureOverlay.ui ├── WindowGroupPlot.cpp ├── WindowGroupPlot.h ├── WindowGroupPlot.ui ├── WindowQuickReference.cpp ├── WindowQuickReference.h ├── WindowQuickReference.ui ├── WindowTimeCourse.cpp ├── WindowTimeCourse.h ├── WindowTimeCourse.ui ├── freeview.pro ├── freeview.qrc ├── main.cpp ├── qtcolorpicker.cpp ├── qtcolorpicker.h ├── resource │ ├── FreeviewBackground.png │ ├── QuickRef.html │ ├── icons │ │ ├── app_128.png │ │ ├── app_16.png │ │ ├── app_24.png │ │ ├── app_32.png │ │ ├── app_64.png │ │ ├── app_about.png │ │ ├── cursor_add.png │ │ ├── cursor_colorpicker.png │ │ ├── cursor_contour.png │ │ ├── cursor_fill.png │ │ ├── cursor_grab.png │ │ ├── cursor_measure_line.png │ │ ├── cursor_measure_polyline.png │ │ ├── cursor_measure_rectangle.png │ │ ├── cursor_pan.png │ │ ├── cursor_pencil.png │ │ ├── cursor_polyline.png │ │ ├── cursor_remove.png │ │ ├── cursor_zoom.png │ │ ├── edit_copy.png │ │ ├── edit_copy_16.png │ │ ├── edit_paste.png │ │ ├── edit_paste_16.png │ │ ├── edit_redo.png │ │ ├── edit_redo_16.png │ │ ├── edit_undo.png │ │ ├── edit_undo_16.png │ │ ├── file_open.png │ │ ├── file_open_16.png │ │ ├── file_screenshot.png │ │ ├── file_screenshot_16.png │ │ ├── freeview.icns │ │ ├── layout_1n3.png │ │ ├── layout_1n3_h.png │ │ ├── layout_1x1.png │ │ ├── layout_2x2.png │ │ ├── measure.png │ │ ├── measure_label.png │ │ ├── measure_line.png │ │ ├── measure_polyline.png │ │ ├── measure_rectangle.png │ │ ├── measure_spline.png │ │ ├── measure_surface_region.png │ │ ├── move_down.png │ │ ├── move_up.png │ │ ├── navigate.png │ │ ├── recon_edit.png │ │ ├── reset_view.png │ │ ├── roi_delete.png │ │ ├── roi_draw_fill.png │ │ ├── roi_draw_freehand.png │ │ ├── roi_draw_polyline.png │ │ ├── roi_edit.png │ │ ├── roi_load.png │ │ ├── roi_new.png │ │ ├── roi_save.png │ │ ├── surface.png │ │ ├── surface_annot.png │ │ ├── surface_curvature.png │ │ ├── surface_delete.png │ │ ├── surface_inflated.png │ │ ├── surface_load.png │ │ ├── surface_load_16.png │ │ ├── surface_main.png │ │ ├── surface_original.png │ │ ├── surface_overlay.png │ │ ├── surface_pial.png │ │ ├── surface_white.png │ │ ├── tool_goto_point.png │ │ ├── tool_rotate_volume.png │ │ ├── tool_save_point.png │ │ ├── track_delete.png │ │ ├── track_load.png │ │ ├── view_3d.png │ │ ├── view_3d_old.png │ │ ├── view_axial.png │ │ ├── view_axial_old.png │ │ ├── view_command_console.png │ │ ├── view_control_panel.png │ │ ├── view_coordinate.png │ │ ├── view_coronal.png │ │ ├── view_coronal_old.png │ │ ├── view_histogram.png │ │ ├── view_sagittal.png │ │ ├── view_sagittal_old.png │ │ ├── view_scalar_bar.png │ │ ├── view_time_course.png │ │ ├── volume_copy_setting.png │ │ ├── volume_delete.png │ │ ├── volume_load.png │ │ ├── volume_load_16.png │ │ ├── volume_lock.png │ │ ├── volume_new.png │ │ ├── volume_paste_setting.png │ │ ├── volume_paste_setting_all.png │ │ ├── volume_save.png │ │ ├── voxel_draw_clone.png │ │ ├── voxel_draw_colorpicker.png │ │ ├── voxel_draw_contour.png │ │ ├── voxel_draw_fill.png │ │ ├── voxel_draw_freehand.png │ │ ├── voxel_draw_livewire.png │ │ ├── voxel_draw_polyline.png │ │ ├── voxel_draw_replace_color.png │ │ ├── voxel_edit.png │ │ ├── waypoints_delete.png │ │ ├── waypoints_edit.png │ │ ├── waypoints_load.png │ │ ├── waypoints_new.png │ │ └── waypoints_save.png │ ├── template.psd │ └── template16.psd ├── track_io │ ├── ByteSwap.h │ ├── ErrorCode.h │ ├── TrackIO.cpp │ └── TrackIO.h ├── vtkSimpleLabelEdgeFilter.cpp └── vtkSimpleLabelEdgeFilter.h ├── fsfast ├── CMakeLists.txt ├── Makefile.am ├── bin │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── acfseg-sess │ ├── acorfunc-sess │ ├── addmcparams │ ├── afni2bvol │ ├── aseg2funcmask-sess │ ├── autoreg-fsl │ ├── autoreg-sess │ ├── avgraw │ ├── bfile2afni │ ├── bfileconvert │ ├── bfvcheck │ ├── bgmask-sess │ ├── bvol2afni │ ├── cat-bvolume │ ├── check-sliceres-sess │ ├── checkmincdir │ ├── cluster-sess │ ├── clusterspec2mask │ ├── cmpanalyses-sess │ ├── cmpsesssnr-sess │ ├── cmpsnr-sess │ ├── compress-sess │ ├── concat-bvolumes │ ├── conmask-sess │ ├── cordiff │ ├── countncond │ ├── cp-bvolume │ ├── crossrun.ffx.fsf │ ├── df-sess │ ├── diag-fmri │ ├── diag-optseq │ ├── difffsfast │ ├── du-sess │ ├── editmask │ ├── evfunc │ ├── evfunc-jk-sess │ ├── evfunc-sess │ ├── evpve-sess │ ├── evspatfil │ ├── evspatfil-jk-sess │ ├── evspatfil-sess │ ├── extract-roi-tc-sess │ ├── fast-log-preamble.csh │ ├── fast_getext │ ├── fast_selxavg3b.glnxa64 │ ├── fcreg-sess │ ├── fcseed-config │ ├── fcseed-sess │ ├── fcseedcor │ ├── feat.fsfast-patch │ ├── feat.fsfast-patch.tcl │ ├── fftfunc-sess │ ├── fieldsign-sess │ ├── fixseqinfo-sess │ ├── flacproc-sess │ ├── fmreigen │ ├── fmreigen-jk │ ├── fsf-glmfit │ ├── fsf-kmnacf │ ├── fsf-kmracf │ ├── fsfast-gui-bug │ ├── fsfast-version │ ├── fsfeat │ ├── fsfeat-sess │ ├── fsfeatffx │ ├── fsl2par │ ├── fslregister-sess │ ├── func2acf │ ├── func2label │ ├── func2roi-sess │ ├── func2roi-sess-mrun │ ├── func2sph-sess │ ├── func2sph-sess-new │ ├── func2tal │ ├── func2tal-sess │ ├── funcroi-config │ ├── funcroi-sess │ ├── funcroi-table-sess │ ├── functcvm │ ├── functcvm-sess │ ├── functwf-sess │ ├── fwhmest │ ├── fwhmest-sess │ ├── getana │ ├── getbext │ ├── getbfvdim │ ├── getendian │ ├── getfirstrundir-sess │ ├── getfirstsliceno │ ├── getformat_from_stem │ ├── getfullpath │ ├── geticoorder │ ├── getlastsliceno │ ├── getmatlab │ ├── getncols │ ├── getnconds │ ├── getnframes │ ├── getnrows │ ├── getnslices │ ├── getpwdcmd │ ├── getrunlist │ ├── getsesspath │ ├── getsliceno │ ├── getslicestr │ ├── getspacetype │ ├── getstem │ ├── gettalres │ ├── ghostdet │ ├── ghostdet-sess │ ├── glmest │ ├── glmfourier │ ├── glmfourier-sess │ ├── glmstats │ ├── groupreg-sess │ ├── inorm │ ├── inorm-sess │ ├── inorm2 │ ├── inorm3 │ ├── intergroupavg-sess │ ├── ipfsl │ ├── isargflag │ ├── isroiavg │ ├── isxavg-fe │ ├── isxavg-fe-abb-sess │ ├── isxavg-fe-sess │ ├── isxavg-fe-sess-1.3 │ ├── isxavg-re │ ├── isxavg-re-abb-sess │ ├── isxavg-re-sess │ ├── isxconcat-sess │ ├── isxconcat0-sess │ ├── kmacf-sess │ ├── kmacfcond-sess │ ├── kmacfwht-sess │ ├── ksgrinder │ ├── ksgrinder-sess │ ├── latgrinder-sess │ ├── latgroup-sess │ ├── lrst-blk │ ├── lrst-blk-sess │ ├── mc-afni │ ├── mc-afni2 │ ├── mc-bbr │ ├── mc-sess │ ├── mcdat2mcextreg │ ├── mcparams2extreg │ ├── meanimg │ ├── mergeanalyses-sess │ ├── mergecontrasts-sess │ ├── mergecontrasts-xsess │ ├── mkanalysis-sess │ ├── mkanalysis-sess.old │ ├── mkblockpar │ ├── mkbrainmask │ ├── mkbrainmask-sess │ ├── mkbrainmask.fsl │ ├── mkcmanova-sess │ ├── mkcontrast │ ├── mkcontrast-sess │ ├── mkcontrast2 │ ├── mkcontrast2m.glnxa64 │ ├── mkdesignmtx │ ├── mkdesmtx-sess │ ├── mkfeat-sess │ ├── mkfieldsign │ ├── mkmosaic │ ├── mkprestimcon │ ├── mktalreg │ ├── mktalxfm-sess │ ├── mktemplate-sess │ ├── mkvoxshiftmap │ ├── mris_glm-sess │ ├── optseq │ ├── optseq.matlab │ ├── paint-fieldsign-sess │ ├── paint-sess │ ├── paint-sess-new │ ├── par2fsl │ ├── par2fsl3 │ ├── par2kspar │ ├── par2schedule │ ├── par2stf │ ├── parse-measasc │ ├── plot-pve │ ├── plot-twf-sess │ ├── ppcheck-sess │ ├── preproc-sess │ ├── prmerge-sess │ ├── qmedit │ ├── qsurfer │ ├── rawavg-sess │ ├── rawfunc2surf-sess │ ├── rawfunc2tal │ ├── rawfunc2tal-sess │ ├── reg2subj │ ├── register-sess │ ├── rocview │ ├── roiavg │ ├── roiavgraw │ ├── roisummary-sess │ ├── roitxt2tbl │ ├── roixrunsum-sess │ ├── segregister-sess │ ├── selfreqavg │ ├── selfreqavg-sess │ ├── selfreqcomb │ ├── selxavg-jk-sess │ ├── selxavg-sess │ ├── selxavg-sess-perrun │ ├── selxavg2 │ ├── selxavg3-sess │ ├── selxavg3-sess.v5.3 │ ├── seqefficiency │ ├── sfa-sess │ ├── sliceview-sess │ ├── spatev │ ├── spatev-sess │ ├── spatevfilter │ ├── spatevfilter-sess │ ├── spatfil │ ├── spatialsmooth-sess │ ├── sphsmooth-sess │ ├── spikedet │ ├── spikedet-sess │ ├── splitstr │ ├── spmimg2bvolume │ ├── spmregister-sess │ ├── stc-sess │ ├── stc.fsl │ ├── stem2fmt │ ├── stfreqgrinder │ ├── stripsessargs │ ├── stxgpredict │ ├── stxgrinder │ ├── stxgrinder-sess │ ├── stxgrinder-sess-perrun │ ├── stxgrinder0-sess │ ├── subject-sess │ ├── surf-sess │ ├── surf-sess-new │ ├── surfsmooth-sess │ ├── svdfunctcvm │ ├── svdfunctcvm-sess │ ├── swfflac-sess │ ├── sxacfg-get │ ├── synth-phenc │ ├── synth-sess │ ├── synth-tr-sess │ ├── synthfmri │ ├── synthrawroi │ ├── synthstudy │ ├── tar-sess │ ├── tdr-avgechoes │ ├── tdr-fidmat │ ├── tdr-ghostcomp │ ├── tdr-rcolmat │ ├── tdr-recon │ ├── tkmedit-sess │ ├── tkregister-sess │ ├── tksurfer-sess │ ├── txt2bfile │ ├── vertavg-group │ ├── vertavg-sess │ ├── vlrmerge │ ├── yakview │ └── zpadfmri ├── docs │ ├── CMakeLists.txt │ ├── INSTALL.pdf │ ├── INSTALL.tex │ ├── MGH-NMR-StdProc-Handbook.doc │ ├── Makefile.am │ ├── avgavg.info │ ├── bert-functional.howto.pdf │ ├── bert-functional.howto.tex │ ├── bfile.pdf │ ├── bfile.tex │ ├── condfit.pdf │ ├── condfit.tex │ ├── fmri-analysis-theory.pdf │ ├── fmri-analysis-theory.tex │ ├── func2roi-sess.pdf │ ├── func2roi-sess.tex │ ├── hvol.txt │ ├── inorm.pdf │ ├── inorm.tex │ ├── intergroup-sess.pdf │ ├── intergroup-sess.tex │ ├── isxavg-fe.pdf │ ├── isxavg-fe.tex │ ├── isxavg-re.pdf │ ├── isxavg-re.tex │ ├── mc-afni.pdf │ ├── mc-afni.tex │ ├── mkcontrast.pdf │ ├── mkcontrast.tex │ ├── mkmosaic.pdf │ ├── mkmosaic.tex │ ├── mkmosaic16.pdf │ ├── mkmosaic16.tex │ ├── mtp-repack.pdf │ ├── mtp-repack.tex │ ├── optseq.pdf │ ├── optseq.tex │ ├── overview.pdf │ ├── overview.tex │ ├── paint.pdf │ ├── paint.tex │ ├── paradigm.pdf │ ├── paradigm.tex │ ├── register.info │ ├── retinotopy-fsf │ ├── selfreq.pdf │ ├── selfreq.tex │ ├── selxavg.pdf │ ├── selxavg.tex │ ├── seq.info.example │ ├── seqefficiency.pdf │ ├── seqefficiency.tex │ ├── sliceview.tal.txt │ ├── stgrinder2.info │ ├── stxgrinder.pdf │ ├── stxgrinder.tex │ ├── univar-analysis.pdf │ ├── univar-analysis.tex │ ├── vertavg.txt │ ├── vol2roi.pdf │ ├── vol2roi.tex │ ├── yakview.pdf │ └── yakview.tex └── toolbox │ ├── ComputeFPR.m │ ├── ComputePDF.m │ ├── FTest.m │ ├── Makefile.am │ ├── ReadAFNIHead2.m │ ├── ReadBRIK2.m │ ├── afni2bvol.m │ ├── arCorrFun.m │ ├── avgrandeff.m │ ├── basename.m │ ├── binomialcdf.m │ ├── binomialconf.m │ ├── binomialpdf.m │ ├── bliweights.m │ ├── boldview.m │ ├── bvbinomialpdf.m │ ├── cor2bshort.m │ ├── corbfile2register.m │ ├── defmossize.m │ ├── direxists.m │ ├── dirname.m │ ├── drclip.m │ ├── drsqueeze.m │ ├── dumphdrest.m │ ├── editmask.m │ ├── erlang.m │ ├── fast_aareg.m │ ├── fast_aaz.m │ ├── fast_acf2ar.m │ ├── fast_acf_3dgsm.m │ ├── fast_acf_err.m │ ├── fast_acf_svdreg.m │ ├── fast_acfcond.m │ ├── fast_acfseg.m │ ├── fast_acorr.m │ ├── fast_anova_rm_oneway.m │ ├── fast_anovamtx.m │ ├── fast_ar12fwhm.m │ ├── fast_ar1_fiterr.m │ ├── fast_ar1err.m │ ├── fast_ar1mtx.m │ ├── fast_ar1w_acf.m │ ├── fast_ar1w_fit.m │ ├── fast_ar1w_fiterr.m │ ├── fast_ar1w_mse.m │ ├── fast_ar1w_opt.m │ ├── fast_ar2acf.m │ ├── fast_arnw_acf.m │ ├── fast_arnw_fiterr.m │ ├── fast_asorder.m │ ├── fast_baselinemtx.m │ ├── fast_beta2sxa.m │ ├── fast_bfileconvert.m │ ├── fast_bgmask.m │ ├── fast_binmean.m │ ├── fast_blockdiag.m │ ├── fast_blockdiag2.m │ ├── fast_blockident.m │ ├── fast_boxcarmat.m │ ├── fast_cbm.m │ ├── fast_cbm2.m │ ├── fast_clip.m │ ├── fast_cmpdesign_nsd.m │ ├── fast_compute_cvm.m │ ├── fast_condctrstmtx.m │ ├── fast_condfit.m │ ├── fast_contrastmtx.m │ ├── fast_conv_invirf.m │ ├── fast_corrcoef.m │ ├── fast_corsort.m │ ├── fast_crf.m │ ├── fast_crs_scnfilter.m │ ├── fast_cvm2acor.m │ ├── fast_cvm2corm.m │ ├── fast_cvm2whtn.m │ ├── fast_cvm_condrgl.m │ ├── fast_cvm_normalize.m │ ├── fast_cvm_normposdef.m │ ├── fast_cvm_normrgl.m │ ├── fast_cvm_pvergl.m │ ├── fast_cvm_regularize.m │ ├── fast_dftmtx.m │ ├── fast_dilate.m │ ├── fast_dirname.m │ ├── fast_dlh.m │ ├── fast_ecm2invlambda.m │ ├── fast_ecvm2wmtx.m │ ├── fast_erm2Xtask.m │ ├── fast_estdimsvd.m │ ├── fast_esttrans.m │ ├── fast_evfunc.m │ ├── fast_evspatfil.m │ ├── fast_exptrendmtx.m │ ├── fast_fbmacf.m │ ├── fast_fcreg.m │ ├── fast_fcseedcor.m │ ├── fast_fdrthresh.m │ ├── fast_fftaxis.m │ ├── fast_ffx.m │ ├── fast_ffx_osgm.m │ ├── fast_fgnoise.m │ ├── fast_fildecomp.m │ ├── fast_fileexists.m │ ├── fast_fla_desmat.m │ ├── fast_fla_irf.m │ ├── fast_flacfg_load.m │ ├── fast_flacfg_struct.m │ ├── fast_flacfg_write.m │ ├── fast_flacproc_sess.m │ ├── fast_flafit0.m │ ├── fast_flip2wvar.m │ ├── fast_fmri2tcvm.m │ ├── fast_fmrimovie.m │ ├── fast_fmriqa.m │ ├── fast_fnorm.m │ ├── fast_fourier_reg.m │ ├── fast_fratio.m │ ├── fast_fratiow.m │ ├── fast_fread3.m │ ├── fast_fslgamma.m │ ├── fast_func2acor.m │ ├── fast_func2roi.m │ ├── fast_functwf.m │ ├── fast_fwhm2std.m │ ├── fast_fwrite3.m │ ├── fast_fxcfg.m │ ├── fast_fxcfg_extreg.m │ ├── fast_fxcfg_fir.m │ ├── fast_fxcfg_fourier.m │ ├── fast_fxcfg_gamma.m │ ├── fast_fxcfg_poly.m │ ├── fast_fxcfg_spmhrf.m │ ├── fast_fxcfg_struct.m │ ├── fast_gamma.m │ ├── fast_gammaderiv.m │ ├── fast_gaussian.m │ ├── fast_getvolformat.m │ ├── fast_ghostdet.m │ ├── fast_ghostmask.m │ ├── fast_glm2anova_mtx.m │ ├── fast_glm_pcc.m │ ├── fast_glmfit.m │ ├── fast_glmfitw.m │ ├── fast_glmpower.m │ ├── fast_group_glm.m │ ├── fast_gui_bug.m │ ├── fast_hann.m │ ├── fast_histeq.m │ ├── fast_hlist.m │ ├── fast_hrf_halfcos.m │ ├── fast_hypospec2cmtx.m │ ├── fast_idealXtX.m │ ├── fast_igxavg.m │ ├── fast_igxavg2.m │ ├── fast_indfreq.m │ ├── fast_inorm.m │ ├── fast_intergroupavg.m │ ├── fast_invlambda.m │ ├── fast_isbvol.m │ ├── fast_isminc.m │ ├── fast_ismincvol.m │ ├── fast_isxavg_fe.m │ ├── fast_isxavg_re.m │ ├── fast_isxavg_re_abb_sess.m │ ├── fast_jkz.m │ ├── fast_kjw_mtx.m │ ├── fast_kmacf.m │ ├── fast_kmeans.m │ ├── fast_ldanacfg.m │ ├── fast_ldanaflac.m │ ├── fast_ldanalyze.m │ ├── fast_ldbfile.m │ ├── fast_ldbfiletp.m │ ├── fast_ldbhdr.m │ ├── fast_ldbslice.m │ ├── fast_ldbvoxel.m │ ├── fast_ldcorslice.m │ ├── fast_ldflac.m │ ├── fast_ldfslabel.m │ ├── fast_ldlabel.m │ ├── fast_ldmri.m │ ├── fast_ldpar4.m │ ├── fast_ldretpar.m │ ├── fast_ldroisum.m │ ├── fast_ldslice.m │ ├── fast_ldstf.m │ ├── fast_ldsurfglmmat.m │ ├── fast_ldsxabfile.m │ ├── fast_ldsxabvolume.m │ ├── fast_ldsxavol.m │ ├── fast_ldtable.m │ ├── fast_ldtpexcl.m │ ├── fast_ldwfile.m │ ├── fast_lmfit.m │ ├── fast_log10p.m │ ├── fast_lpfmtx.m │ ├── fast_lsc.m │ ├── fast_maskvol.m │ ├── fast_mat2vol.m │ ├── fast_mergesxa.m │ ├── fast_mkdesignmtx.m │ ├── fast_mkgausmtx.m │ ├── fast_mkoverlay.m │ ├── fast_monotonize.m │ ├── fast_mri_struct.m │ ├── fast_mrivolstruct.m │ ├── fast_mshift.m │ ├── fast_nirs2oxy.m │ ├── fast_norm_con.m │ ├── fast_normcovmtx.m │ ├── fast_npernull.m │ ├── fast_nswfflac_sess.m │ ├── fast_omnibusmtx.m │ ├── fast_orthog.m │ ├── fast_outliermtx.m │ ├── fast_overlay.m │ ├── fast_p2z.m │ ├── fast_par2Xfir.m │ ├── fast_par2Xtask.m │ ├── fast_par2nconds.m │ ├── fast_par2st.m │ ├── fast_parabfit.m │ ├── fast_pearsoncor.m │ ├── fast_pixrep.m │ ├── fast_polyorder.m │ ├── fast_polytrendmtx.m │ ├── fast_polyzacf_fit.m │ ├── fast_prayleigh.m │ ├── fast_psc2t2s.m │ ├── fast_psdwin.m │ ├── fast_pvs.m │ ├── fast_quadtrendmtx.m │ ├── fast_racf_exp.m │ ├── fast_randrundist.m │ ├── fast_randschedule.m │ ├── fast_raygaus.m │ ├── fast_raygauscost.m │ ├── fast_raygausinit.m │ ├── fast_raygausthresh.m │ ├── fast_read_curv.m │ ├── fast_read_wfile.m │ ├── fast_rescalefactor.m │ ├── fast_retroicor.m │ ├── fast_rfm2nrho1.m │ ├── fast_rmzerocols.m │ ├── fast_rphacf.m │ ├── fast_rphacfrmse.m │ ├── fast_rrf.m │ ├── fast_runlist.m │ ├── fast_runlistfile.m │ ├── fast_rvt.m │ ├── fast_sched2Xerm.m │ ├── fast_sched2Xfir.m │ ├── fast_sched2Xgamma.m │ ├── fast_sched2Xgammaderiv.m │ ├── fast_schedseq.m │ ├── fast_selfreqavg.m │ ├── fast_selxavg.m │ ├── fast_selxavg2.m │ ├── fast_selxavg3.m │ ├── fast_selxavg3b.m │ ├── fast_sesscfg_struct.m │ ├── fast_sigmoid.m │ ├── fast_sim_acfsvd.m │ ├── fast_sincmtx.m │ ├── fast_slicedelay.m │ ├── fast_smooth1d.m │ ├── fast_smooth2d.m │ ├── fast_smooth3d.m │ ├── fast_spatcornoise.m │ ├── fast_spatev.m │ ├── fast_spatevfilter.m │ ├── fast_spatialacf.m │ ├── fast_spmhrf.m │ ├── fast_spmhrf_sampled.m │ ├── fast_sratio.m │ ├── fast_st2fir.m │ ├── fast_stxgrinder2_sess.m │ ├── fast_stxgrinder3_sess.m │ ├── fast_svana.m │ ├── fast_svanalyze.m │ ├── fast_svbhdr.m │ ├── fast_svbslice.m │ ├── fast_svcor.m │ ├── fast_svcorslice.m │ ├── fast_svd.m │ ├── fast_svdfilter.m │ ├── fast_svdfunctcvm.m │ ├── fast_svdregpct.m │ ├── fast_svextreg.m │ ├── fast_svlabel.m │ ├── fast_svpar4.m │ ├── fast_svtable.m │ ├── fast_swfflac_nbhd_sess.m │ ├── fast_swfflac_sess.m │ ├── fast_synthnoise.m │ ├── fast_tcvm_rmrun.m │ ├── fast_tnorm.m │ ├── fast_trendmtx.m │ ├── fast_trf_sup_surf.m │ ├── fast_tspvsrank.m │ ├── fast_unmask.m │ ├── fast_uvffx.m │ ├── fast_viewvol.m │ ├── fast_vol2mat.m │ ├── fast_volstruct.m │ ├── fast_volview.m │ ├── fast_voxthresh.m │ ├── fast_vvglm.m │ ├── fast_weiskopf.m │ ├── fast_weiskopf_perm.m │ ├── fast_wopt.m │ ├── fast_wopt2x2.m │ ├── fast_wparnonlin.m │ ├── fast_write_curv.m │ ├── fast_write_wfile.m │ ├── fast_xcorr.m │ ├── fast_xmat2xtxt.m │ ├── fast_yacf_kjw.m │ ├── fast_z2p.m │ ├── fbirn_mktable.m │ ├── fbirn_sitelist.m │ ├── fbirn_sitename.m │ ├── fbirn_siteno.m │ ├── fidinterp.m │ ├── flac_conindex.m │ ├── flac_conmat.m │ ├── flac_customize.m │ ├── flac_desmat.m │ ├── flac_ev2irf.m │ ├── flac_ev_parse.m │ ├── flac_evconw.m │ ├── flac_evindex.m │ ├── flac_evregind.m │ ├── flac_evtaskind.m │ ├── flac_funcstem.m │ ├── flac_nuisregind.m │ ├── flac_resynth.m │ ├── flac_taskregind.m │ ├── flac_tfilter.m │ ├── flac_tfilter_parse.m │ ├── flacffx.m │ ├── flacrfx.m │ ├── flacview.m │ ├── fmri_abjackknife.m │ ├── fmri_accrandeff.m │ ├── fmri_acorr.m │ ├── fmri_acorr2covmtx.m │ ├── fmri_acorrfit.m │ ├── fmri_acorrsig.m │ ├── fmri_acorrsynth.m │ ├── fmri_avgmtx_is.m │ ├── fmri_avgrandeff.m │ ├── fmri_avgxavg.m │ ├── fmri_axaslice.m │ ├── fmri_bfiledim.m │ ├── fmri_boxcar.m │ ├── fmri_bvoldim.m │ ├── fmri_cvmstruct.m │ ├── fmri_detrend.m │ ├── fmri_dof.m │ ├── fmri_ecovar.m │ ├── fmri_estsignal.m │ ├── fmri_fstem.m │ ├── fmri_getstem.m │ ├── fmri_hankernel.m │ ├── fmri_havg_is.m │ ├── fmri_hcovar.m │ ├── fmri_hdrdatstruct.m │ ├── fmri_hemodyn.m │ ├── fmri_idealcbpm.m │ ├── fmri_idealxtx.m │ ├── fmri_imresize.m │ ├── fmri_indfreqfft.m │ ├── fmri_isavgstg.m │ ├── fmri_isavgstruct.m │ ├── fmri_isconsec.m │ ├── fmri_isroiavg.m │ ├── fmri_isxavg_fe.m │ ├── fmri_isxgrinder.m │ ├── fmri_isxgslice.m │ ├── fmri_jackknife.m │ ├── fmri_ldbfile.m │ ├── fmri_ldbheader.m │ ├── fmri_ldbvolume.m │ ├── fmri_ldcor.m │ ├── fmri_ldcvm.m │ ├── fmri_lddat.m │ ├── fmri_lddat2.m │ ├── fmri_lddat3.m │ ├── fmri_lddof.m │ ├── fmri_lddot.m │ ├── fmri_ldpar.m │ ├── fmri_ldsadof.m │ ├── fmri_ldsfa.m │ ├── fmri_ldslicedelay.m │ ├── fmri_ldsynch.m │ ├── fmri_ldtpexcl.m │ ├── fmri_lmsfit.m │ ├── fmri_mcorrrestriction.m │ ├── fmri_minseqcbe.m │ ├── fmri_minseqtr.m │ ├── fmri_minsig.m │ ├── fmri_mrestriction.m │ ├── fmri_mrestriction2.m │ ├── fmri_nmjackknife.m │ ├── fmri_norm.m │ ├── fmri_normcovar.m │ ├── fmri_optseq.m │ ├── fmri_optseqstruct.m │ ├── fmri_par2sam.m │ ├── fmri_par2scm.m │ ├── fmri_par2scm0.m │ ├── fmri_par2scm2.m │ ├── fmri_parsebfilename.m │ ├── fmri_pcacovmtx.m │ ├── fmri_pmax.m │ ├── fmri_pmin.m │ ├── fmri_pscavg.m │ ├── fmri_qrplusc.m │ ├── fmri_qsvd.m │ ├── fmri_qweiner.m │ ├── fmri_randc.m │ ├── fmri_randeff.m │ ├── fmri_readreg.m │ ├── fmri_rescale.m │ ├── fmri_residual.m │ ├── fmri_rhaslice.m │ ├── fmri_roiavg.m │ ├── fmri_sa2sxa.m │ ├── fmri_saxslice.m │ ├── fmri_scm2gcm.m │ ├── fmri_segment.m │ ├── fmri_selsum.m │ ├── fmri_seq2scm.m │ ├── fmri_seqbase.m │ ├── fmri_seqmutate.m │ ├── fmri_sfastruct.m │ ├── fmri_sfaunpack.m │ ├── fmri_shiftcol.m │ ├── fmri_sigmin.m │ ├── fmri_sobel.m │ ├── fmri_spatfilter.m │ ├── fmri_srchseq.m │ ├── fmri_stxgrinder.m │ ├── fmri_stxgslice.m │ ├── fmri_subsampmat.m │ ├── fmri_svbfile.m │ ├── fmri_svbvolume.m │ ├── fmri_svcvm.m │ ├── fmri_svdat2.m │ ├── fmri_svdat3.m │ ├── fmri_svpar.m │ ├── fmri_svsfa.m │ ├── fmri_sxa2sa.m │ ├── fmri_sxaslice.m │ ├── fmri_sxavol.m │ ├── fmri_synth_phenc_sig.m │ ├── fmri_synthpar.m │ ├── fmri_synthpar2.m │ ├── fmri_synthpar3.m │ ├── fmri_synthrun.m │ ├── fmri_synthrunstruct.m │ ├── fmri_tavgslice.m │ ├── fmri_touch.m │ ├── fmri_untangle.m │ ├── fmri_untangle2.m │ ├── fmri_voxvar.m │ ├── fmri_vrestriction.m │ ├── fmri_wisxavg_fe.m │ ├── fmri_xtx2cbp.m │ ├── fslmat2register.m │ ├── gammadist.m │ ├── gaussian.m │ ├── gensynthdata.m │ ├── gr1dmin_update.m │ ├── hdrview.m │ ├── hdrviewlite.m │ ├── hsa_convert.m │ ├── hview.m │ ├── imagesc1d.m │ ├── imgoverlay.m │ ├── imgoverlaytc.m │ ├── imgoverlaytc2.m │ ├── imgto1d.m │ ├── indbrain2ghost.m │ ├── invillcond.m │ ├── kimgfunc.m │ ├── krfunc_lsqr.m │ ├── kspacevector2.m │ ├── ldstruct.m │ ├── linfit.m │ ├── load_corinfo.m │ ├── mar.m │ ├── maxmd.m │ ├── mkanalysis_gui.fig │ ├── mkanalysis_gui.m │ ├── mkcontrast2m.m │ ├── mkcontrast_gui.m │ ├── mkdirp.m │ ├── mkmosaic.m │ ├── mkprestimcon.m │ ├── mos2vol.m │ ├── mosind2volind.m │ ├── mossub2volsub.m │ ├── mrsignalsample.m │ ├── mstk2mos.m │ ├── nmrcolormap.m │ ├── ovstruct.m │ ├── pairedtx.m │ ├── par2condidmap.m │ ├── par_recode.m │ ├── parboxcar.m │ ├── pdf_gamma.m │ ├── pdf_rayleigh.m │ ├── pedmatrix.m │ ├── permutation.m │ ├── pertrapezoid.m │ ├── pkpulse.m │ ├── plot_detrend5.m │ ├── plthankernels.m │ ├── pulsespectrum.m │ ├── pvecovmtx.m │ ├── qoe.m │ ├── rande.m │ ├── randnorm.m │ ├── randr.m │ ├── rawplot.fig │ ├── rawplot.m │ ├── readln.m │ ├── register2fslmat.m │ ├── remap_par.m │ ├── reshape1d.m │ ├── reshape2d.m │ ├── rft_zcluster_cdf.m │ ├── rimgfunc.m │ ├── roi2ind.m │ ├── samp2pdf.m │ ├── samplecdf.m │ ├── showfigxy.m │ ├── silverstein.m │ ├── splitstring.m │ ├── spm_to_bfloat.m │ ├── spm_to_bshort.m │ ├── spm_to_sagbshort.m │ ├── spmhrf.m │ ├── sscanfitem.m │ ├── stxgpredict.m │ ├── sub2indmask.m │ ├── subbrain2ghost.m │ ├── svdfunctcvm.m │ ├── svstruct.m │ ├── swapview.m │ ├── synthcornoise.m │ ├── tTest.m │ ├── tal_csr2xyz.m │ ├── tal_xyz2csr.m │ ├── tdr_b1map2d.m │ ├── tdr_deghost.m │ ├── tdr_dftmtx2d.m │ ├── tdr_epi_phtraj.m │ ├── tdr_epirecon.m │ ├── tdr_fftshift2d.m │ ├── tdr_fidb0.m │ ├── tdr_fidmat.m │ ├── tdr_fidmat2.m │ ├── tdr_fidt2star.m │ ├── tdr_ghostcomp.m │ ├── tdr_graddumpinterp.m │ ├── tdr_gradmtx.m │ ├── tdr_ifftslice.m │ ├── tdr_intpertrap.m │ ├── tdr_kshift.m │ ├── tdr_ldgraddump.m │ ├── tdr_lininterp.m │ ├── tdr_measasc.m │ ├── tdr_pedmatrix.m │ ├── tdr_peshift.m │ ├── tdr_phdist_est.m │ ├── tdr_rcolmat.m │ ├── tdr_recon.m │ ├── tdr_recon_cols.m │ ├── tdr_recon_rows.m │ ├── tdr_recon_sim.m │ ├── tdr_regrid.m │ ├── tdr_rledecode.m │ ├── tdr_rotate_ktraj.m │ ├── tdr_rtraj.m │ ├── tdr_sliceorder.m │ ├── tdr_smooth2d.m │ ├── tdr_trapspect2d.m │ ├── tdr_uniform_dft1d.m │ ├── tdr_uniform_idft2d.m │ ├── tdr_uniform_phtraj.m │ ├── tliweights.m │ ├── trapezoid.m │ ├── tukeytaper.m │ ├── uliweights.m │ ├── univarlab.fig │ ├── univarlab.m │ ├── vol2mos.m │ ├── volind2mosind.m │ ├── volsub2mossub.m │ ├── vqm.m │ ├── yak.m │ ├── yak2.m │ ├── yakview.m │ ├── yvplt_acffit.m │ └── yvpltraw.m ├── fsgdf ├── CMakeLists.txt ├── FsgdfPlot.cxx ├── Makefile.am ├── fsgdf.c ├── fsgdf.i ├── fsgdf_wrap.c ├── setup_test_data ├── test.c ├── test.tcl └── test_data.tar.gz ├── fslutils ├── CMakeLists.txt ├── Makefile.am └── fsl_label2voxel.cpp ├── glut ├── Makefile.am ├── VERSION ├── glut.h ├── glut_8x13.c ├── glut_9x15.c ├── glut_bitmap.c ├── glut_bwidth.c ├── glut_cindex.c ├── glut_cmap.c ├── glut_cursor.c ├── glut_dials.c ├── glut_dstr.c ├── glut_event.c ├── glut_ext.c ├── glut_fullscrn.c ├── glut_gamemode.c ├── glut_get.c ├── glut_glxext.c ├── glut_hel10.c ├── glut_hel12.c ├── glut_hel18.c ├── glut_init.c ├── glut_input.c ├── glut_joy.c ├── glut_key.c ├── glut_keyctrl.c ├── glut_keyup.c ├── glut_menu.c ├── glut_menu2.c ├── glut_mesa.c ├── glut_modifier.c ├── glut_mroman.c ├── glut_overlay.c ├── glut_roman.c ├── glut_shapes.c ├── glut_space.c ├── glut_stroke.c ├── glut_swap.c ├── glut_swidth.c ├── glut_tablet.c ├── glut_teapot.c ├── glut_tr10.c ├── glut_tr24.c ├── glut_util.c ├── glut_vidresize.c ├── glut_warp.c ├── glut_win.c ├── glut_winmisc.c ├── glutbitmap.h ├── glutint.h ├── glutstroke.h ├── layerutil.c ├── layerutil.h ├── license.glut.txt └── test_glut.c ├── gnuwin32.cmake ├── gpu_utils ├── Makefile.am └── cudadetect.cpp ├── graphics.cmake ├── hiam_make_surfaces ├── CMakeLists.txt ├── Makefile.am └── hiam_make_surfaces.c ├── hiam_make_template ├── CMakeLists.txt ├── Makefile.am └── hiam_make_template.c ├── hiam_register ├── CMakeLists.txt ├── Makefile.am └── hiam_register.c ├── hipsstubs ├── CMakeLists.txt ├── Makefile.am ├── hipsrepl.c └── hipsstubs.c ├── histo_compute_joint_density ├── CMakeLists.txt ├── Makefile.am └── histo_compute_joint_density.c ├── histo_fix_topology ├── Makefile.am └── histo_fix_topology.c ├── histo_register ├── Main.cc ├── Makefile.am ├── ParticleVideoLib │ ├── Makefile.am │ ├── build │ │ ├── ParticleVideoLib.vcproj │ │ └── makefile │ ├── changes.txt │ ├── doc │ │ └── pvl_doxygen.txt │ ├── include │ │ └── pvl │ │ │ ├── Occlusion.h │ │ │ ├── SimpleParticleBuild.h │ │ │ ├── SimpleParticleData.h │ │ │ ├── SimpleParticleOptimize.h │ │ │ ├── SparseSystem.h │ │ │ ├── VarMotion.h │ │ │ ├── VarMotionMultiRes.h │ │ │ └── VarMotionUtil.h │ ├── license.txt │ ├── sample │ │ ├── ParticleVideoSample.sln │ │ ├── ParticleVideoSample.vcproj │ │ ├── bak_makefile │ │ ├── main.cc │ │ ├── path.conf │ │ ├── readme.txt │ │ ├── simpleParticle.conf │ │ └── varMotion.conf │ ├── src │ │ ├── Occlusion.cc │ │ ├── SimpleParticleBuild.cc │ │ ├── SimpleParticleData.cc │ │ ├── SimpleParticleOptimize.cc │ │ ├── SparseSystem.cc │ │ ├── VarMotion.cc │ │ ├── VarMotionMultiRes.cc │ │ └── VarMotionUtil.cc │ └── version.txt ├── README.txt ├── SimpleBaseLib │ ├── Makefile.am │ ├── build │ │ ├── SimpleBaseLib_all.vcproj │ │ ├── SimpleBaseLib_min.vcproj │ │ ├── SimpleBaseLib_nocv.vcproj │ │ ├── SimpleBaseLib_nogui.vcproj │ │ └── bak_makefile │ ├── external │ │ ├── CDT │ │ │ ├── CDT-LICENSE.txt │ │ │ ├── CDT.cc │ │ │ └── CDT.h │ │ ├── win_dirent.h │ │ └── win_timegm.h │ ├── include │ │ └── sbl │ │ │ ├── core │ │ │ ├── Array.h │ │ │ ├── Command.h │ │ │ ├── Config.h │ │ │ ├── Dict.h │ │ │ ├── Display.h │ │ │ ├── File.h │ │ │ ├── Init.h │ │ │ ├── PathConfig.h │ │ │ ├── Pointer.h │ │ │ ├── String.h │ │ │ ├── StringUtil.h │ │ │ ├── Table.h │ │ │ └── UnitTest.h │ │ │ ├── gui │ │ │ ├── ConfigEditor.h │ │ │ ├── ConfigViewer.h │ │ │ ├── GraphicViewer.h │ │ │ ├── ImageSeqViewer.h │ │ │ ├── ImageViewer.h │ │ │ ├── MainWindow.h │ │ │ └── MiscWidgets.h │ │ │ ├── image │ │ │ ├── Filter.h │ │ │ ├── Image.h │ │ │ ├── ImageDraw.h │ │ │ ├── ImageRegister.h │ │ │ ├── ImageSeqUtil.h │ │ │ ├── ImageTransform.h │ │ │ ├── ImageUtil.h │ │ │ ├── MotionField.h │ │ │ ├── MotionFieldSeq.h │ │ │ ├── MotionFieldUtil.h │ │ │ ├── Track.h │ │ │ └── Video.h │ │ │ ├── math │ │ │ ├── ConfigOptimizer.h │ │ │ ├── Geometry.h │ │ │ ├── KMeans.h │ │ │ ├── MathUtil.h │ │ │ ├── Matrix.h │ │ │ ├── MatrixUtil.h │ │ │ ├── Optimizer.h │ │ │ ├── OptimizerUtil.h │ │ │ ├── Tensor.h │ │ │ ├── TensorUtil.h │ │ │ ├── TimeSeries.h │ │ │ ├── Triangulation.h │ │ │ ├── Vector.h │ │ │ └── VectorUtil.h │ │ │ ├── other │ │ │ ├── CodeCheck.h │ │ │ ├── DrawingLayer.h │ │ │ ├── ImageDrawingLayer.h │ │ │ ├── Plot.h │ │ │ ├── SVG.h │ │ │ ├── Scripting.h │ │ │ └── TaggedFile.h │ │ │ └── system │ │ │ ├── FileSystem.h │ │ │ ├── Microcontroller.h │ │ │ ├── SerialPort.h │ │ │ ├── Signal.h │ │ │ ├── Socket.h │ │ │ ├── TimeUtil.h │ │ │ └── Timer.h │ ├── license.txt │ ├── notes.txt │ ├── src │ │ ├── core │ │ │ ├── Command.cc │ │ │ ├── Config.cc │ │ │ ├── Display.cc │ │ │ ├── File.cc │ │ │ ├── Init.cc │ │ │ ├── PathConfig.cc │ │ │ ├── String.cc │ │ │ ├── StringUtil.cc │ │ │ ├── Table.cc │ │ │ └── UnitTest.cc │ │ ├── gui │ │ │ ├── ConfigEditor.cc │ │ │ ├── ConfigViewer.cc │ │ │ ├── GraphicViewer.cc │ │ │ ├── ImageSeqViewer.cc │ │ │ ├── ImageViewer.cc │ │ │ ├── MainWindow.cc │ │ │ └── MiscWidgets.cc │ │ ├── image │ │ │ ├── Filter.cc │ │ │ ├── Image.cc │ │ │ ├── ImageDraw.cc │ │ │ ├── ImageRegister.cc │ │ │ ├── ImageSeqUtil.cc │ │ │ ├── ImageTransform.cc │ │ │ ├── ImageUtil.cc │ │ │ ├── MotionField.cc │ │ │ ├── MotionFieldSeq.cc │ │ │ ├── MotionFieldUtil.cc │ │ │ ├── Track.cc │ │ │ └── Video.cc │ │ ├── math │ │ │ ├── ConfigOptimizer.cc │ │ │ ├── Geometry.cc │ │ │ ├── KMeans.cc │ │ │ ├── MathUtil.cc │ │ │ ├── MatrixUtil.cc │ │ │ ├── Optimizer.cc │ │ │ ├── OptimizerUtil.cc │ │ │ ├── TensorUtil.cc │ │ │ ├── TimeSeries.cc │ │ │ ├── Triangulation.cc │ │ │ └── VectorUtil.cc │ │ ├── other │ │ │ ├── CodeCheck.cc │ │ │ ├── DrawingLayer.cc │ │ │ ├── ImageDrawingLayer.cc │ │ │ ├── Plot.cc │ │ │ ├── SVG.cc │ │ │ ├── Scripting.cc │ │ │ ├── TaggedFile.cc │ │ │ ├── sbl.py │ │ │ └── test.py │ │ └── system │ │ │ ├── FileSystem.cc │ │ │ ├── Microcontroller.cc │ │ │ ├── SerialPort.cc │ │ │ ├── Signal.cc │ │ │ ├── Socket.cc │ │ │ ├── TimeUtil.cc │ │ │ └── Timer.cc │ └── version.txt ├── bak_makefile ├── history │ └── history.txt ├── path.conf ├── prep │ ├── BlockPrep.cc │ ├── BlockPrep.h │ ├── HistoPrep.cc │ ├── HistoPrep.h │ ├── HistoStats.cc │ ├── HistoStats.h │ ├── HistoStitch.cc │ ├── HistoStitch.h │ ├── MPrep.cc │ ├── MPrep.h │ ├── Polarization.cc │ ├── Polarization.h │ ├── Prediction.cc │ ├── Prediction.h │ ├── StitchNode.cc │ ├── StitchNode.h │ ├── VolumeFile.cc │ ├── VolumeFile.h │ ├── VolumeUtil.cc │ └── VolumeUtil.h ├── registration │ ├── BlockRegister.cc │ ├── BlockRegister.h │ ├── CorresField3D.cc │ ├── CorresField3D.h │ ├── HistoRegister.cc │ ├── HistoRegister.h │ ├── HistoTransform.cc │ ├── HistoTransform.h │ ├── ImageSetSeq.cc │ ├── ImageSetSeq.h │ ├── Normalization.cc │ ├── Normalization.h │ ├── TestCorres3D.cc │ ├── TestCorres3D.h │ ├── VarCorres3D.cc │ ├── VarCorres3D.h │ ├── VarCorres3DUtil.cc │ └── VarCorres3DUtil.h ├── varCorres3D.conf └── varMotion.conf ├── histo_register_block ├── CMakeLists.txt ├── Makefile.am └── histo_register_block.c ├── histo_segment ├── Makefile.am └── histo_segment.c ├── histo_synthesize ├── Makefile.am └── histo_synthesize.c ├── images ├── Makefile.am ├── icon_analysis_open.gif ├── icon_analysis_open.tif ├── icon_arrow_ccw.gif ├── icon_arrow_cw.gif ├── icon_arrow_down.gif ├── icon_arrow_expand_x.gif ├── icon_arrow_expand_y.gif ├── icon_arrow_left.gif ├── icon_arrow_right.gif ├── icon_arrow_rot_x_neg.gif ├── icon_arrow_rot_x_neg.tif ├── icon_arrow_rot_x_pos.gif ├── icon_arrow_rot_x_pos.tif ├── icon_arrow_rot_y_neg.gif ├── icon_arrow_rot_y_neg.tif ├── icon_arrow_rot_y_pos.gif ├── icon_arrow_rot_y_pos.tif ├── icon_arrow_rot_z_neg.gif ├── icon_arrow_rot_z_neg.tif ├── icon_arrow_rot_z_pos.gif ├── icon_arrow_rot_z_pos.tif ├── icon_arrow_shrink_x.gif ├── icon_arrow_shrink_y.gif ├── icon_arrow_up.gif ├── icon_aux_volume.gif ├── icon_brush_3d.gif ├── icon_brush_circle.gif ├── icon_brush_square.gif ├── icon_camera.gif ├── icon_camera.tif ├── icon_color_label.gif ├── icon_color_picker.gif ├── icon_color_scalebar.gif ├── icon_colormap_grayscale.gif ├── icon_colormap_grayscale.tif ├── icon_colormap_lut.gif ├── icon_colormap_lut.tif ├── icon_control_point.gif ├── icon_cursor_goto.gif ├── icon_cursor_save.gif ├── icon_curv.gif ├── icon_curv_bw.gif ├── icon_curv_bw.tif ├── icon_cut_area.gif ├── icon_cut_clear.gif ├── icon_cut_closed_line.gif ├── icon_cut_line.gif ├── icon_cut_plane.gif ├── icon_disk.gif ├── icon_disk.tif ├── icon_disk_multiview.gif ├── icon_disk_multiview.tif ├── icon_disk_new_name.gif ├── icon_disk_new_name.tif ├── icon_draw_line.gif ├── icon_draw_line_closed.gif ├── icon_edit_ctrlpts.gif ├── icon_edit_custom.gif ├── icon_edit_label.gif ├── icon_edit_parc.gif ├── icon_edit_volume.gif ├── icon_erase_label.gif ├── icon_erase_line.gif ├── icon_fill.gif ├── icon_fill_label.gif ├── icon_fill_roi.gif ├── icon_fill_roi.png ├── icon_fill_volume.gif ├── icon_fill_volume.png ├── icon_folder.gif ├── icon_folder.tif ├── icon_home.gif ├── icon_home.tif ├── icon_label_filled.gif ├── icon_label_list.gif ├── icon_label_list.xpm ├── icon_label_off.gif ├── icon_label_open.gif ├── icon_label_open.tif ├── icon_label_outline.gif ├── icon_label_save.gif ├── icon_label_save.tif ├── icon_label_table.gif ├── icon_label_table.xpm ├── icon_label_to_marked.gif ├── icon_line_tool.gif ├── icon_linked_cursors.gif ├── icon_main_volume.gif ├── icon_marked_to_label.gif ├── icon_marker_crosshair.gif ├── icon_marker_crosshair.tif ├── icon_marker_diamond.gif ├── icon_matrix_erase.gif ├── icon_matrix_erase.tif ├── icon_matrix_write.gif ├── icon_matrix_write.tif ├── icon_navigate.gif ├── icon_orientation_coronal.gif ├── icon_orientation_coronal_pdm.gif ├── icon_orientation_horizontal.gif ├── icon_orientation_horizontal_pdm.gif ├── icon_orientation_sagittal.gif ├── icon_orientation_sagittal_pdm.gif ├── icon_orientation_x.gif ├── icon_orientation_y.gif ├── icon_orientation_z.gif ├── icon_overlay.gif ├── icon_redraw.gif ├── icon_redraw.tif ├── icon_rotate_plane.gif ├── icon_seg_volume.gif ├── icon_selection_add.gif ├── icon_selection_add.tif ├── icon_selection_subtract.gif ├── icon_selection_subtract.tif ├── icon_snapshot_load.gif ├── icon_snapshot_save.gif ├── icon_stopwatch.gif ├── icon_surface_inflated.gif ├── icon_surface_main.gif ├── icon_surface_original.gif ├── icon_surface_pial.gif ├── icon_surface_white.gif ├── icon_table_open.gif ├── icon_table_open.tif ├── icon_view_31.gif ├── icon_view_mosaic.gif ├── icon_view_mosaic_pdm.gif ├── icon_view_multiple.gif ├── icon_view_multiple.tif ├── icon_view_multiple_pdm.gif ├── icon_view_single.gif ├── icon_view_single.tif ├── icon_view_single_pdm.gif ├── icon_zoom_in.gif ├── icon_zoom_in.tif ├── icon_zoom_out.gif ├── icon_zoom_out.png └── icon_zoom_out.tif ├── include ├── AFNI.h ├── Bruker.h ├── CMakeLists.txt ├── DICOMRead.h ├── FsgdfPlot.h ├── MARS_DT_Boundary.h ├── MC.h ├── MRISOBBTree.h ├── MRISdistancefield.h ├── MRIio_old.h ├── Makefile.am ├── NrrdIO │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── NrrdIO.h │ ├── privateAir.h │ ├── privateNrrd.h │ ├── teem32bit.h │ ├── teemDio.h │ ├── teemEndian.h │ ├── teemPng.h │ └── teemQnanhibit.h ├── TexFont.h ├── affine.h ├── affine.hpp ├── affinegpu.hpp ├── analyze.h ├── annotation.h ├── art1.h ├── artmap.h ├── aseg_edit_svm.h ├── autoencoder.h ├── backprop.h ├── bfileio.h ├── box.h ├── canny.h ├── cdflib.h ├── cephes.h ├── chklc.h ├── chronometer.h ├── chronometer.hpp ├── class_array.h ├── classify.h ├── cluster.h ├── cma.h ├── cmat.h ├── cmdargs.h ├── colortab.h ├── congraph.h ├── connect.h ├── connectcomp.h ├── const.h ├── corio.h ├── cpputils.h ├── ctfactory.hpp ├── ctrpoints.h ├── cudacheck.h ├── cudatypeutils.hpp ├── cvector.h ├── dct.h ├── density.h ├── devicemanagement.h ├── diag.h ├── dicom │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── condition.h │ ├── ctn_os.h │ ├── ctnthread.h │ ├── dcmprivate.h │ ├── dicom.h │ ├── dicom_objects.h │ ├── dicom_platform.h │ ├── dicom_uids.h │ ├── lst.h │ └── lstprivate.h ├── dti.h ├── dtk.fs.h ├── error.h ├── evschutils.h ├── fastmarching.h ├── fcd.h ├── fexterns.h ├── fftutils.h ├── fgutil.h ├── field_code.h ├── filecode.h ├── filter.h ├── fio.h ├── fixedmap.hpp ├── flash.h ├── fmarchmesh.h ├── fmriutils.h ├── fs_vnl │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── fs_cost_function.h │ ├── fs_lbfgs.h │ ├── fs_lbfgs_observer.h │ ├── fs_lbfgs_subject.h │ └── fs_powell.h ├── fsenv.h ├── fsgdf.h ├── fsgdf_wrap.h ├── fsglm.h ├── fsinit.h ├── gca.h ├── gcaboundary.h ├── gcalinearnode.hpp ├── gcalinearprior.hpp ├── gcamcomputegradient_cuda.hpp ├── gcamfots_cuda.h ├── gcamfots_cuda.hpp ├── gcamorph.h ├── gcamorphcpu.hpp ├── gcamorphenergy.hpp ├── gcamorphgpu.hpp ├── gcamorphtermgpu.hpp ├── gcamorphtestutils.h ├── gcamorphtestutils.hpp ├── gcamregisterlevel_cuda.hpp ├── gcamremovenegativenodes_cuda.hpp ├── gcanodegpu.hpp ├── gcapriorgpu.hpp ├── gcarray.h ├── gcasgpu.hpp ├── gcautils.hpp ├── gclass.h ├── gcsa.h ├── general.h ├── generators.hpp ├── getdelim.h ├── getline.h ├── gifti_io.h ├── gifti_local.h ├── gifti_xml.h ├── gmm │ ├── gmm.h │ ├── gmm_MUMPS_interface.h │ ├── gmm_algobase.h │ ├── gmm_blas.h │ ├── gmm_blas_interface.h │ ├── gmm_condition_number.h │ ├── gmm_conjugated.h │ ├── gmm_def.h │ ├── gmm_dense_Householder.h │ ├── gmm_dense_lu.h │ ├── gmm_dense_qr.h │ ├── gmm_dense_sylvester.h │ ├── gmm_domain_decomp.h │ ├── gmm_except.h │ ├── gmm_inoutput.h │ ├── gmm_interface.h │ ├── gmm_interface_bgeot.h │ ├── gmm_iter.h │ ├── gmm_iter_solvers.h │ ├── gmm_kernel.h │ ├── gmm_lapack_interface.h │ ├── gmm_least_squares_cg.h │ ├── gmm_matrix.h │ ├── gmm_modified_gram_schmidt.h │ ├── gmm_opt.h │ ├── gmm_precond.h │ ├── gmm_precond_diagonal.h │ ├── gmm_precond_ildlt.h │ ├── gmm_precond_ildltt.h │ ├── gmm_precond_ilu.h │ ├── gmm_precond_ilut.h │ ├── gmm_precond_ilutp.h │ ├── gmm_precond_mr_approx_inverse.h │ ├── gmm_real_part.h │ ├── gmm_ref.h │ ├── gmm_scaled.h │ ├── gmm_solver_Newton.h │ ├── gmm_solver_Schwarz_additive.h │ ├── gmm_solver_bfgs.h │ ├── gmm_solver_bicgstab.h │ ├── gmm_solver_cg.h │ ├── gmm_solver_constrained_cg.h │ ├── gmm_solver_gmres.h │ ├── gmm_solver_idgmres.h │ ├── gmm_solver_qmr.h │ ├── gmm_std.h │ ├── gmm_sub_index.h │ ├── gmm_sub_matrix.h │ ├── gmm_sub_vector.h │ ├── gmm_superlu_interface.h │ ├── gmm_transposed.h │ ├── gmm_tri_solve.h │ ├── gmm_vector.h │ └── gmm_vector_to_matrix.h ├── gtm.h ├── gw_utils.h ├── h_logz.h ├── handle.h ├── heap.h ├── hip_brf.h ├── hipl_for.h ├── hipl_format.h ├── hippo.h ├── hips.h ├── hips_basic.h ├── hips_error.h ├── hips_header.h ├── hips_parser.h ├── hipsext.h ├── hipsh.h ├── hipspub.h ├── hipsu.h ├── histo.h ├── hmem.h ├── icosahedron.h ├── image.h ├── imautils.h ├── intensity_eig.h ├── inverse.h ├── iutils.h ├── kernel.h ├── kinput.h ├── label.h ├── ldtmplt.h ├── lpafile.h ├── machine.h ├── macros.h ├── mailbox.h ├── map.h ├── matfile.h ├── matrix.h ├── mconf.h ├── mgh_filter.h ├── mgh_matrix.h ├── mghendian.h ├── min_heap.h ├── minc_volume_io.h ├── mincutils.h ├── minmax.hpp ├── minmaxrc.h ├── mosaic.h ├── mri.h ├── mri2.h ├── mriBSpline.h ├── mriFunctionalDataAccess.h ├── mriHeadPointList.h ├── mriROI.h ├── mriSurface.h ├── mriTransform.h ├── mriTypes.h ├── mriVolume.h ├── mri_ca_configFile.h ├── mri_ca_gausDist.h ├── mri_ca_labelLUT.h ├── mri_ca_labelMapper.h ├── mri_ca_labelingParameters.h ├── mri_ca_measMapper.h ├── mri_ca_measure.h ├── mri_ca_measureVolume.h ├── mri_ca_sparse2DGausDistMatrix.h ├── mri_ca_sparse2DMatrix.h ├── mri_ca_sparse3DMatrix.h ├── mri_ca_statisticsVolumeHeader.h ├── mri_ca_trainingParameters.h ├── mri_ca_util.h ├── mri_circulars.h ├── mri_conform.h ├── mri_identify.h ├── mri_tess.h ├── mri_topology.h ├── mri_transform.h ├── mriclass.h ├── mriconvolve_cuda.h ├── mriconvolve_cuda.hpp ├── mricurv.h ├── mriframegpu.hpp ├── mrilabels_cuda.hpp ├── mrimean_cuda.h ├── mrimean_cuda.hpp ├── mrimorph.h ├── mrinorm.h ├── mris_compVolFrac.h ├── mris_expand.h ├── mris_topology.h ├── mrisbiorthogonalwavelets.h ├── mrisegment.h ├── mrishash.h ├── mrisurf.h ├── mrisurf_cuda.h ├── mrisutils.h ├── mrivol2vol_cuda.h ├── mrivol2vol_cuda.hpp ├── mthread.h ├── nifti1.h ├── nifti1_io.h ├── numerics.h ├── path.h ├── pbm.h ├── pbmplus.h ├── pdf.h ├── pgm.h ├── pixrect │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── bw2var.h │ ├── cg12_var.h │ ├── cg2reg.h │ ├── cg2var.h │ ├── cg3var.h │ ├── cg4var.h │ ├── cg8var.h │ ├── cg9var.h │ ├── gp1cmds.h │ ├── gp1reg.h │ ├── gp1var.h │ ├── gt_fbi.h │ ├── gt_rp.h │ ├── gtvar.h │ ├── mem32_var.h │ ├── mem_rop_impl_ops.h │ ├── mem_rop_impl_util.h │ ├── memreg.h │ ├── memvar.h │ ├── pixfont.h │ ├── pixrect.h │ ├── pixrect_hs.h │ ├── pr_dblbuf.h │ ├── pr_impl_make.h │ ├── pr_impl_util.h │ ├── pr_io.h │ ├── pr_line.h │ ├── pr_planegroups.h │ ├── pr_util.h │ ├── traprop.h │ └── tv1var.h ├── pnm.h ├── ppm.h ├── prime.h ├── proto.h ├── qdecutils.h ├── queue.h ├── randomfields.h ├── rbf.h ├── rbm.h ├── rec.h ├── region.h ├── registerio.h ├── resample.h ├── rescale.h ├── retinotopy.h ├── rfa.h ├── rforest.h ├── rfutils.h ├── rgb_image.h ├── rgb_utils.h ├── runfuncs.h ├── selxavgio.h ├── sig.h ├── signa.h ├── sse_mathfun.h ├── stats.h ├── stc.h ├── struct.h ├── surfcluster.h ├── svm.h ├── sys │ ├── CMakeLists.txt │ ├── Makefile.am │ └── timeb.h ├── tags.h ├── talairachex.h ├── testgpu.h ├── thread.h ├── thrust │ ├── CHANGELOG │ ├── adjacent_difference.h │ ├── advance.h │ ├── binary_search.h │ ├── copy.h │ ├── count.h │ ├── detail │ │ ├── adjacent_difference.inl │ │ ├── advance.inl │ │ ├── binary_search.inl │ │ ├── casts.h │ │ ├── config.h │ │ ├── config │ │ │ ├── compiler.h │ │ │ ├── config.h │ │ │ ├── debug.h │ │ │ ├── device_backend.h │ │ │ ├── host_device.h │ │ │ └── simple_defines.h │ │ ├── contiguous_storage.h │ │ ├── contiguous_storage.inl │ │ ├── copy.inl │ │ ├── count.inl │ │ ├── cstdint.h │ │ ├── destroy.h │ │ ├── device │ │ │ ├── adjacent_difference.h │ │ │ ├── binary_search.h │ │ │ ├── copy.h │ │ │ ├── cuda │ │ │ │ ├── arch.h │ │ │ │ ├── arch.inl │ │ │ │ ├── block │ │ │ │ │ ├── copy.h │ │ │ │ │ ├── inclusive_scan.h │ │ │ │ │ ├── merging_sort.h │ │ │ │ │ ├── odd_even_sort.h │ │ │ │ │ └── reduce.h │ │ │ │ ├── copy.h │ │ │ │ ├── copy_cross_space.h │ │ │ │ ├── copy_device_to_device.h │ │ │ │ ├── copy_if.h │ │ │ │ ├── copy_if.inl │ │ │ │ ├── detail │ │ │ │ │ ├── b40c │ │ │ │ │ │ ├── kernel_utils.h │ │ │ │ │ │ ├── radixsort_api.h │ │ │ │ │ │ ├── radixsort_kernel_common.h │ │ │ │ │ │ ├── radixsort_key_conversion.h │ │ │ │ │ │ ├── radixsort_reduction_kernel.h │ │ │ │ │ │ ├── radixsort_scanscatter_kernel.h │ │ │ │ │ │ ├── radixsort_spine_kernel.h │ │ │ │ │ │ └── vector_types.h │ │ │ │ │ ├── fast_scan.h │ │ │ │ │ ├── fast_scan.inl │ │ │ │ │ ├── safe_scan.h │ │ │ │ │ ├── safe_scan.inl │ │ │ │ │ ├── stable_merge_sort.h │ │ │ │ │ ├── stable_merge_sort.inl │ │ │ │ │ ├── stable_radix_sort.h │ │ │ │ │ ├── stable_radix_sort.inl │ │ │ │ │ ├── stable_radix_sort_bits.h │ │ │ │ │ ├── stable_radix_sort_key.inl │ │ │ │ │ ├── stable_radix_sort_key_value.inl │ │ │ │ │ ├── stable_radix_sort_merrill.inl │ │ │ │ │ ├── stable_radix_sort_util.h │ │ │ │ │ └── trivial_copy.h │ │ │ │ ├── dispatch │ │ │ │ │ ├── copy.h │ │ │ │ │ ├── reduce.h │ │ │ │ │ ├── reduce.inl │ │ │ │ │ └── scan.h │ │ │ │ ├── extern_shared_ptr.h │ │ │ │ ├── fill.h │ │ │ │ ├── fill.inl │ │ │ │ ├── for_each.h │ │ │ │ ├── for_each.inl │ │ │ │ ├── free.h │ │ │ │ ├── free.inl │ │ │ │ ├── launch_closure.h │ │ │ │ ├── launch_closure.inl │ │ │ │ ├── malloc.h │ │ │ │ ├── malloc.inl │ │ │ │ ├── no_throw_free.h │ │ │ │ ├── no_throw_free.inl │ │ │ │ ├── partition.h │ │ │ │ ├── reduce.h │ │ │ │ ├── reduce.inl │ │ │ │ ├── scalar │ │ │ │ │ ├── binary_search.h │ │ │ │ │ └── rotate.h │ │ │ │ ├── scan.h │ │ │ │ ├── scan.inl │ │ │ │ ├── segmented_scan.h │ │ │ │ ├── segmented_scan.inl │ │ │ │ ├── set_operations.h │ │ │ │ ├── set_operations.inl │ │ │ │ ├── sort.h │ │ │ │ ├── sort.inl │ │ │ │ ├── synchronize.h │ │ │ │ ├── synchronize.inl │ │ │ │ ├── trivial_copy.h │ │ │ │ ├── trivial_copy.inl │ │ │ │ └── warp │ │ │ │ │ ├── any.h │ │ │ │ │ └── scan.h │ │ │ ├── dereference.h │ │ │ ├── dispatch │ │ │ │ ├── copy.h │ │ │ │ ├── fill.h │ │ │ │ ├── for_each.h │ │ │ │ ├── free.h │ │ │ │ ├── malloc.h │ │ │ │ ├── no_throw_free.h │ │ │ │ ├── reduce.h │ │ │ │ ├── scan.h │ │ │ │ ├── set_operations.h │ │ │ │ ├── sort.h │ │ │ │ └── uninitialized_copy.h │ │ │ ├── extrema.h │ │ │ ├── fill.h │ │ │ ├── fill.inl │ │ │ ├── find.h │ │ │ ├── for_each.h │ │ │ ├── for_each.inl │ │ │ ├── generic │ │ │ │ ├── adjacent_difference.h │ │ │ │ ├── adjacent_difference.inl │ │ │ │ ├── binary_search.h │ │ │ │ ├── binary_search.inl │ │ │ │ ├── copy.h │ │ │ │ ├── copy_if.h │ │ │ │ ├── copy_if.inl │ │ │ │ ├── extrema.h │ │ │ │ ├── extrema.inl │ │ │ │ ├── fill.h │ │ │ │ ├── find.h │ │ │ │ ├── find.inl │ │ │ │ ├── free.h │ │ │ │ ├── malloc.h │ │ │ │ ├── no_throw_free.h │ │ │ │ ├── partition.h │ │ │ │ ├── partition.inl │ │ │ │ ├── reduce.h │ │ │ │ ├── reduce.inl │ │ │ │ ├── reduce_by_key.h │ │ │ │ ├── reduce_by_key.inl │ │ │ │ ├── remove.h │ │ │ │ ├── remove.inl │ │ │ │ ├── scan_by_key.h │ │ │ │ ├── scan_by_key.inl │ │ │ │ ├── set_operations.h │ │ │ │ ├── unique.h │ │ │ │ └── unique.inl │ │ │ ├── internal_allocator.h │ │ │ ├── no_throw_free.h │ │ │ ├── omp │ │ │ │ ├── copy.h │ │ │ │ ├── copy_device_to_device.h │ │ │ │ ├── copy_device_to_device.inl │ │ │ │ ├── copy_device_to_host_or_any.h │ │ │ │ ├── copy_device_to_host_or_any.inl │ │ │ │ ├── copy_host_or_any_to_device.h │ │ │ │ ├── copy_host_or_any_to_device.inl │ │ │ │ ├── detail │ │ │ │ │ ├── stable_merge_sort.h │ │ │ │ │ └── stable_merge_sort.inl │ │ │ │ ├── dispatch │ │ │ │ │ ├── copy.h │ │ │ │ │ └── sort.h │ │ │ │ ├── for_each.h │ │ │ │ ├── for_each.inl │ │ │ │ ├── reduce.h │ │ │ │ ├── reduce.inl │ │ │ │ ├── scan.h │ │ │ │ ├── scan.inl │ │ │ │ ├── sort.h │ │ │ │ └── sort.inl │ │ │ ├── partition.h │ │ │ ├── reduce.h │ │ │ ├── reduce.inl │ │ │ ├── remove.h │ │ │ ├── scan.h │ │ │ ├── scan.inl │ │ │ ├── set_operations.h │ │ │ ├── sort.h │ │ │ ├── sort.inl │ │ │ ├── uninitialized_copy.h │ │ │ └── unique.h │ │ ├── device_delete.inl │ │ ├── device_free.inl │ │ ├── device_malloc.inl │ │ ├── device_new.inl │ │ ├── device_ptr.inl │ │ ├── device_ptr_traits.h │ │ ├── device_reference.inl │ │ ├── device_vector.inl │ │ ├── diagnostic.h │ │ ├── dispatch │ │ │ ├── adjacent_difference.h │ │ │ ├── advance.h │ │ │ ├── binary_search.h │ │ │ ├── copy.h │ │ │ ├── destroy.h │ │ │ ├── distance.h │ │ │ ├── extrema.h │ │ │ ├── fill.h │ │ │ ├── find.h │ │ │ ├── for_each.h │ │ │ ├── is_trivial_copy.h │ │ │ ├── partition.h │ │ │ ├── reduce.h │ │ │ ├── remove.h │ │ │ ├── scan.h │ │ │ ├── set_operations.h │ │ │ ├── sort.h │ │ │ ├── uninitialized_copy.h │ │ │ ├── uninitialized_fill.h │ │ │ └── unique.h │ │ ├── distance.inl │ │ ├── equal.inl │ │ ├── extrema.inl │ │ ├── fill.inl │ │ ├── find.inl │ │ ├── for_each.inl │ │ ├── functional.inl │ │ ├── gather.inl │ │ ├── generate.inl │ │ ├── host │ │ │ ├── adjacent_difference.h │ │ │ ├── binary_search.h │ │ │ ├── copy.h │ │ │ ├── detail │ │ │ │ ├── copy_backward.h │ │ │ │ ├── general_copy.h │ │ │ │ ├── insertion_sort.h │ │ │ │ ├── merge.h │ │ │ │ ├── merge.inl │ │ │ │ ├── stable_merge_sort.h │ │ │ │ ├── stable_merge_sort.inl │ │ │ │ └── trivial_copy.h │ │ │ ├── dispatch │ │ │ │ └── copy.h │ │ │ ├── extrema.h │ │ │ ├── fill.h │ │ │ ├── find.h │ │ │ ├── for_each.h │ │ │ ├── for_each.inl │ │ │ ├── partition.h │ │ │ ├── reduce.h │ │ │ ├── remove.h │ │ │ ├── scan.h │ │ │ ├── set_operations.h │ │ │ ├── sort.h │ │ │ ├── sort.inl │ │ │ └── unique.h │ │ ├── host_vector.inl │ │ ├── inner_product.inl │ │ ├── integer_traits.h │ │ ├── internal_functional.h │ │ ├── logical.inl │ │ ├── mismatch.inl │ │ ├── move.h │ │ ├── mpl │ │ │ └── math.h │ │ ├── numeric_traits.h │ │ ├── pair.inl │ │ ├── partition.inl │ │ ├── raw_buffer.h │ │ ├── raw_buffer.inl │ │ ├── reduce.inl │ │ ├── remove.inl │ │ ├── replace.inl │ │ ├── reverse.inl │ │ ├── scan.inl │ │ ├── scatter.inl │ │ ├── sequence.inl │ │ ├── set_operations.inl │ │ ├── sort.inl │ │ ├── static_assert.h │ │ ├── swap.inl │ │ ├── swap_ranges.inl │ │ ├── transform.inl │ │ ├── transform_reduce.inl │ │ ├── transform_scan.inl │ │ ├── trivial_sequence.h │ │ ├── tuple.inl │ │ ├── tuple_meta_transform.h │ │ ├── tuple_transform.h │ │ ├── type_traits.h │ │ ├── type_traits │ │ │ └── has_trivial_assign.h │ │ ├── uninitialized_copy.inl │ │ ├── uninitialized_fill.inl │ │ ├── unique.inl │ │ ├── util │ │ │ ├── align.h │ │ │ └── blocking.h │ │ ├── vector_base.h │ │ └── vector_base.inl │ ├── device_allocator.h │ ├── device_delete.h │ ├── device_free.h │ ├── device_malloc.h │ ├── device_malloc_allocator.h │ ├── device_new.h │ ├── device_new_allocator.h │ ├── device_ptr.h │ ├── device_reference.h │ ├── device_vector.h │ ├── distance.h │ ├── equal.h │ ├── experimental │ │ └── cuda │ │ │ ├── detail │ │ │ └── ogl_interop_allocator.inl │ │ │ ├── ogl_interop_allocator.h │ │ │ └── pinned_allocator.h │ ├── extrema.h │ ├── fill.h │ ├── find.h │ ├── for_each.h │ ├── functional.h │ ├── gather.h │ ├── generate.h │ ├── host_vector.h │ ├── inner_product.h │ ├── is_sorted.h │ ├── iterator │ │ ├── constant_iterator.h │ │ ├── counting_iterator.h │ │ ├── detail │ │ │ ├── any_space_tag.h │ │ │ ├── backend_iterator_categories.h │ │ │ ├── backend_iterator_spaces.h │ │ │ ├── constant_iterator.inl │ │ │ ├── constant_iterator_base.h │ │ │ ├── counting_iterator.inl │ │ │ ├── device_iterator_category_to_backend_space.h │ │ │ ├── distance_from_result.h │ │ │ ├── forced_iterator.h │ │ │ ├── is_iterator_category.h │ │ │ ├── iterator_adaptor.inl │ │ │ ├── iterator_category_to_space.h │ │ │ ├── iterator_category_to_traversal.h │ │ │ ├── iterator_facade.inl │ │ │ ├── iterator_traits.inl │ │ │ ├── minimum_category.h │ │ │ ├── minimum_space.h │ │ │ ├── normal_iterator.h │ │ │ ├── permutation_iterator.inl │ │ │ ├── permutation_iterator_base.h │ │ │ ├── placement │ │ │ │ └── is_placed.h │ │ │ ├── reverse_iterator.inl │ │ │ ├── reverse_iterator_base.h │ │ │ ├── transform_iterator.inl │ │ │ ├── universal_categories.h │ │ │ ├── zip_iterator.inl │ │ │ └── zip_iterator_base.h │ │ ├── iterator_adaptor.h │ │ ├── iterator_categories.h │ │ ├── iterator_facade.h │ │ ├── iterator_traits.h │ │ ├── permutation_iterator.h │ │ ├── reverse_iterator.h │ │ ├── transform_iterator.h │ │ └── zip_iterator.h │ ├── logical.h │ ├── mismatch.h │ ├── pair.h │ ├── partition.h │ ├── random.h │ ├── random │ │ ├── detail │ │ │ ├── discard_block_engine.inl │ │ │ ├── linear_congruential_engine.inl │ │ │ ├── linear_congruential_engine_discard.h │ │ │ ├── linear_feedback_shift_engine.inl │ │ │ ├── linear_feedback_shift_engine_wordmask.h │ │ │ ├── mod.h │ │ │ ├── normal_distribution.inl │ │ │ ├── random_core_access.h │ │ │ ├── subtract_with_carry_engine.inl │ │ │ ├── uniform_int_distribution.inl │ │ │ ├── uniform_real_distribution.inl │ │ │ ├── xor_combine_engine.inl │ │ │ └── xor_combine_engine_max.h │ │ ├── discard_block_engine.h │ │ ├── linear_congruential_engine.h │ │ ├── linear_feedback_shift_engine.h │ │ ├── normal_distribution.h │ │ ├── subtract_with_carry_engine.h │ │ ├── uniform_int_distribution.h │ │ ├── uniform_real_distribution.h │ │ └── xor_combine_engine.h │ ├── reduce.h │ ├── remove.h │ ├── replace.h │ ├── reverse.h │ ├── scan.h │ ├── scatter.h │ ├── sequence.h │ ├── set_intersection.h │ ├── set_operations.h │ ├── sort.h │ ├── swap.h │ ├── system │ │ ├── cuda_error.h │ │ ├── detail │ │ │ ├── cuda_error.inl │ │ │ ├── errno.h │ │ │ ├── error_category.inl │ │ │ ├── error_code.inl │ │ │ ├── error_condition.inl │ │ │ └── system_error.inl │ │ ├── error_code.h │ │ └── system_error.h │ ├── system_error.h │ ├── transform.h │ ├── transform_reduce.h │ ├── transform_scan.h │ ├── tuple.h │ ├── uninitialized_copy.h │ ├── uninitialized_fill.h │ ├── unique.h │ ├── utility.h │ └── version.h ├── timer.h ├── topology │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── face.h │ ├── fastloop.h │ ├── globals.h │ ├── loop.h │ ├── patchdisk.h │ ├── segment.h │ ├── surface.h │ ├── topo_parms.h │ └── vertex.h ├── transform.h ├── trig512.h ├── tritri.h ├── tukey.h ├── typedefs.h ├── utils.h ├── utilsmath.h ├── vecvolgpu.hpp ├── version.h ├── vlabels.h ├── volcluster.h ├── volumecpu.hpp ├── volumegpu.hpp ├── volumegpu_impl.hpp ├── volumegpucompare.hpp ├── voxlist.h ├── windiag.h ├── x3DList.h ├── xDebug.h ├── xGLutWindow.h ├── xGrowableArray.h ├── xList.h ├── xSparseVolume.h ├── xTypes.h ├── xUndoList.h ├── xUtilities.h ├── xVoxel.h ├── xview │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── alert.h │ ├── attr.h │ ├── attrol.h │ ├── base.h │ ├── canvas.h │ ├── cms.h │ ├── cms_grays.h │ ├── cms_mono.h │ ├── cms_rgb.h │ ├── cmsrainbow.h │ ├── cursor.h │ ├── db.h │ ├── defaults.h │ ├── dragdrop.h │ ├── drawable.h │ ├── expandname.h │ ├── font.h │ ├── frame.h │ ├── fullscreen.h │ ├── generic.h │ ├── icon.h │ ├── icon_load.h │ ├── notice.h │ ├── notify.h │ ├── openmenu.h │ ├── openwin.h │ ├── panel.h │ ├── pixwin.h │ ├── pkg.h │ ├── pkg_public.h │ ├── rect.h │ ├── rectlist.h │ ├── screen.h │ ├── scrollbar.h │ ├── sel_attrs.h │ ├── sel_compat.h │ ├── sel_pkg.h │ ├── sel_svc.h │ ├── selection.h │ ├── seln.h │ ├── server.h │ ├── str_utils.h │ ├── sun.h │ ├── svrimage.h │ ├── termsw.h │ ├── text.h │ ├── textsw.h │ ├── tty.h │ ├── ttysw.h │ ├── win_enum.h │ ├── win_env.h │ ├── win_event.h │ ├── win_input.h │ ├── win_notify.h │ ├── win_screen.h │ ├── win_struct.h │ ├── window.h │ ├── window_hs.h │ ├── wmgr.h │ ├── xv_c_types.h │ ├── xv_error.h │ ├── xv_i18n.h │ ├── xv_version.h │ ├── xv_xrect.h │ ├── xview.h │ └── xview_xvin.h └── znzlib.h ├── itkio ├── CMakeLists.txt ├── Makefile.am ├── itkMGHImageIO.cxx ├── itkMGHImageIO.h ├── itkMGHImageIOFactory.cxx └── itkMGHImageIOFactory.h ├── itkutils ├── CMakeLists.txt ├── Makefile.am ├── bspline │ ├── itkBSplineDataPointSetToImageFilter.h │ ├── itkBSplineDataPointSetToImageFilter.txx │ ├── itkBSplineKernelFunction.h │ ├── itkBSplineKernelFunction.txx │ ├── itkPointSetToImageFilter.h │ └── itkPointSetToImageFilter.txx ├── itkOrientedVectorImage.h ├── itkOrientedVectorImage.txx └── ui │ ├── CommandParser.cxx │ ├── CommandParser.h │ ├── FreeSurferExecutable.cxx │ └── FreeSurferExecutable.h ├── jpeg ├── Makefile.am ├── README ├── cderror.h ├── cdjpeg.c ├── cdjpeg.h ├── cjpeg.c ├── coderules.doc ├── djpeg.c ├── filelist.doc ├── install.doc ├── jcapimin.c ├── jcapistd.c ├── jccoefct.c ├── jccolor.c ├── jcdctmgr.c ├── jchuff.c ├── jchuff.h ├── jcinit.c ├── jcmainct.c ├── jcmarker.c ├── jcmaster.c ├── jcomapi.c ├── jconfig.doc ├── jconfig.h ├── jcparam.c ├── jcphuff.c ├── jcprepct.c ├── jcsample.c ├── jctrans.c ├── jdapimin.c ├── jdapistd.c ├── jdatadst.c ├── jdatasrc.c ├── jdcoefct.c ├── jdcolor.c ├── jdct.h ├── jddctmgr.c ├── jdhuff.c ├── jdhuff.h ├── jdinput.c ├── jdmainct.c ├── jdmarker.c ├── jdmaster.c ├── jdmerge.c ├── jdphuff.c ├── jdpostct.c ├── jdsample.c ├── jdtrans.c ├── jerror.c ├── jerror.h ├── jfdctflt.c ├── jfdctfst.c ├── jfdctint.c ├── jidctflt.c ├── jidctfst.c ├── jidctint.c ├── jidctred.c ├── jinclude.h ├── jmemmgr.c ├── jmemnobs.c ├── jmemsys.h ├── jmorecfg.h ├── jpegint.h ├── jpeglib.h ├── jpegtran.c ├── jquant1.c ├── jquant2.c ├── jutils.c ├── jversion.h ├── libjpeg.doc ├── license.jpeg.txt ├── rdbmp.c ├── rdcolmap.c ├── rdgif.c ├── rdjpgcom.c ├── rdppm.c ├── rdrle.c ├── rdswitch.c ├── rdtarga.c ├── structure.doc ├── test_jpeg ├── testimg.bmp ├── testimg.jpg ├── testimg.ppm ├── testimgp.jpg ├── testorig.jpg ├── testprog.jpg ├── transupp.c ├── transupp.h ├── usage.doc ├── wizard.doc ├── wrbmp.c ├── wrgif.c ├── wrjpgcom.c ├── wrppm.c ├── wrrle.c └── wrtarga.c ├── label2flat ├── CMakeLists.txt ├── Makefile.am └── label2flat.c ├── label2patch ├── CMakeLists.txt ├── Makefile.am └── label2patch.c ├── label_area ├── CMakeLists.txt ├── Makefile.am └── label_area.c ├── label_border ├── Makefile.am └── label_border.c ├── lineprof ├── LineProf.cpp ├── LineProf.h ├── LineProfTest.cpp ├── Makefile.am ├── PetscSolver.cpp ├── PetscSolver.h ├── Preprocessor.cpp ├── Preprocessor.h ├── README.txt ├── Tracer.cpp ├── Tracer.h └── testLineProf ├── log ├── CMakeLists.txt ├── Makefile.am ├── congraph.c ├── connect.c ├── h_logz.c ├── lmedian.c ├── map.c └── runfuncs.c ├── lta_convert ├── Makefile.am ├── lta_convert.cpp └── lta_convert.help.xml ├── m4 └── autotroll.m4 ├── matlab ├── CMakeLists.txt ├── MRIangles2RotMat.m ├── MRIeuler2Mdc.m ├── MRIextractImage.m ├── MRIfspec.m ├── MRIisBHDR.m ├── MRIisMGH.m ├── MRImdc2euler.m ├── MRIread.m ├── MRIrotMat2angles.m ├── MRIseg2labelxyz.m ├── MRIsegReg.m ├── MRIvol2vol.m ├── MRIvote.m ├── MRIwrite.m ├── Makefile.am ├── README_TalairachingADF.txt ├── ReadSiemensPhysio.m ├── RgAdjMtx.m ├── Survival │ ├── README.md │ ├── SStat_lmeX_ext.m │ ├── ex_data │ │ ├── Qdec_addicts.dat │ │ ├── addicts.dat │ │ ├── addicts.mat │ │ ├── vets.dat │ │ └── vets.mat │ ├── mass_univariate │ │ ├── SStat_mass_CoxExt.m │ │ ├── SStat_mass_CoxPH.m │ │ ├── SStat_mass_CoxStratPH.m │ │ ├── SStat_mass_FDR.m │ │ ├── SStat_mass_FDR2.m │ │ ├── SStat_mass_HR.m │ │ ├── SStat_mass_PHTest.m │ │ └── parfor_progress.m │ └── univariate │ │ ├── SStat_CoxExt.m │ │ ├── SStat_CoxPH.m │ │ ├── SStat_CoxStratPH.m │ │ ├── SStat_HR.m │ │ ├── SStat_KM.m │ │ ├── SStat_PHTest.m │ │ └── SStat_X_ext.m ├── angles2rotmat.m ├── barsegstats.m ├── bmm_mcvect.m ├── bmm_mcvhist.m ├── bmmcost.m ├── bmmroc.m ├── cc_cut_afd.m ├── cc_cut_dir_afd.m ├── cc_cut_table.m ├── close3d.m ├── colprintf.m ├── combine_labels.m ├── convert_fieldsign.m ├── convert_unwarp_resample.m ├── cortical_labeling_afd_txt.m ├── cortical_labeling_dir_afd_txt.m ├── cortical_labeling_table.m ├── dMRIangles2RotMat.m ├── dice_labels.m ├── dijkstra.m ├── dilate3d.m ├── dtifa.m ├── dtimatrix.m ├── erode3d.m ├── fisher_twoclass.m ├── fread3.m ├── fs_ranksum.m ├── fs_signrank.m ├── fs_spmreg.m ├── fsgettmppath.m ├── fwrite3.m ├── gc_classify.m ├── gc_pvalue.m ├── gc_synth_data.m ├── gc_synth_params.m ├── gc_train.m ├── histo_smooth.m ├── irepierr.m ├── irepifit.m ├── irepifitvol.m ├── irepistructure.m ├── irepisynth.m ├── irepitiming.m ├── isdicomfile.m ├── juelichmat2mat.m ├── labelic.m ├── llbmm.m ├── lme │ ├── Qdec │ │ ├── Qdec2num.m │ │ ├── fReadQdec.m │ │ ├── fWriteQdec.m │ │ ├── findQdecVar.m │ │ ├── getQdecVarData.m │ │ ├── getQdecVars.m │ │ ├── num2Qdec.m │ │ └── rmQdecCol.m │ ├── README.md │ ├── fs_read_Y.m │ ├── fs_read_label.m │ ├── fs_read_surf.m │ ├── fs_write_Y.m │ ├── fs_write_fstats.m │ ├── geodesic │ │ ├── create_flat_triangular_mesh.m │ │ ├── create_hedgehog_mesh.m │ │ ├── create_subdivision_pattern.m │ │ ├── example1.m │ │ ├── example2.m │ │ ├── example3.m │ │ ├── example4.m │ │ ├── example5.m │ │ ├── extract_coordinates_from_path.m │ │ ├── geodesic_convert_surface_points.m │ │ ├── geodesic_create_surface_point.m │ │ ├── geodesic_delete.m │ │ ├── geodesic_distance_and_source.m │ │ ├── geodesic_license.txt │ │ ├── geodesic_matlab_api.h │ │ ├── geodesic_new_algorithm.m │ │ ├── geodesic_new_mesh.m │ │ ├── geodesic_propagate.m │ │ ├── geodesic_readme.txt │ │ ├── geodesic_src.tar.gz │ │ └── geodesic_trace_back.m │ ├── mass_univariate │ │ ├── AdjMtx.m │ │ ├── lme_FSfit.m │ │ ├── lme_RgFSfit.m │ │ ├── lme_mass_F.m │ │ ├── lme_mass_FDR.m │ │ ├── lme_mass_FDR2.m │ │ ├── lme_mass_LR.m │ │ ├── lme_mass_RgDist.m │ │ ├── lme_mass_RgEI.m │ │ ├── lme_mass_RgEI1.m │ │ ├── lme_mass_RgFSfit.m │ │ ├── lme_mass_RgGradient.m │ │ ├── lme_mass_RgGradient1.m │ │ ├── lme_mass_RgGrow.m │ │ ├── lme_mass_RgMean.m │ │ ├── lme_mass_fit.m │ │ ├── lme_mass_fit_EMinit.m │ │ ├── lme_mass_fit_Rgw.m │ │ ├── lme_mass_fit_init.m │ │ ├── lme_mass_fit_vw.m │ │ ├── lme_mass_rfx.m │ │ ├── parfor_progress.m │ │ └── sphCoord.m │ ├── sortData.m │ ├── univariate │ │ ├── lme_EI.m │ │ ├── lme_F.m │ │ ├── lme_Gradient.m │ │ ├── lme_Hessian.m │ │ ├── lme_LR.m │ │ ├── lme_fit_EM.m │ │ ├── lme_fit_EMinit.m │ │ ├── lme_fit_FS.m │ │ ├── lme_fit_FSinit.m │ │ ├── lme_fit_NR.m │ │ ├── lme_fit_init.m │ │ ├── lme_lowessPlot.m │ │ ├── lme_plannedPower.m │ │ ├── lme_plannedSampleSize.m │ │ ├── lme_realizedPower.m │ │ ├── lme_timePlot.m │ │ └── vec.m │ └── usage.txt ├── load_analyze.m ├── load_analyze_hdr.m ├── load_cor.m ├── load_csd.m ├── load_dicom_fl.m ├── load_dicom_series.m ├── load_gca.m ├── load_ima.m ├── load_mgh.m ├── load_mgh2.m ├── load_nifti.m ├── load_nifti_hdr.m ├── load_segstats.m ├── lta_read.m ├── mksubfov.m ├── mri_cdf2p.m ├── mri_glmfit_pcc.m ├── mri_kurtosis.m ├── mri_qoutlier.m ├── mri_surfrft_jlbr.m ├── mri_zcdf.m ├── mris_XYZdiff.m ├── mris_circleROI.m ├── mris_colorTableMake.m ├── mris_display.m ├── open3d.m ├── peakfinder.m ├── pearsoncc.m ├── plot_2dhisto.m ├── pons_cut_afd.m ├── pons_cut_dir_afd.m ├── pons_cut_table.m ├── randb.m ├── read_all.m ├── read_annotation.m ├── read_asc.m ├── read_ascii_curv.m ├── read_cor.m ├── read_csf_patch.m ├── read_curv.m ├── read_eccen_patch.m ├── read_freq_patch.m ├── read_fscolorlut.m ├── read_genesis_image.m ├── read_label.m ├── read_label_old.m ├── read_meas_dat.m ├── read_meas_prot.m ├── read_meas_prot__struct.m ├── read_moviebyu.m ├── read_patch.m ├── read_patch_asc.m ├── read_siemens_header.m ├── read_siemens_image.m ├── read_smooth_eccen.m ├── read_surf.m ├── read_type.m ├── read_vf.m ├── read_wfile.m ├── readrec.m ├── remove_spaces.m ├── ribbon_afd.m ├── ribbon_dir_afd.m ├── ribbon_table.m ├── roiname2hemi.m ├── rotmat.m ├── rotmat2angles.m ├── sampleSize.m ├── save_cor.m ├── save_mgh.m ├── save_mgh2.m ├── save_nifti.m ├── soap_bubble.m ├── ssbloch.m ├── ssblochgrad.m ├── stringunique.m ├── striphemi.m ├── strlen.m ├── subcortical_labeling_afd.m ├── subcortical_labeling_dir_afd.m ├── subcortical_labeling_table.m ├── surf_registration_afd.m ├── surf_registration_stats.m ├── surf_registration_table.m ├── sys_printf.m ├── syslog_prefix.m ├── talairaching_afd.m ├── talairaching_dir_afd.m ├── talairaching_stats.m ├── talairaching_table.m ├── threshold_label.m ├── triggerfinder.m ├── unwarp_init_globals.m ├── unwarp_resample.m ├── unwarp_scanners_table.m ├── vox2rasToQform.m ├── vox2ras_0to1.m ├── vox2ras_1to0.m ├── vox2ras_dfmeas.m ├── vox2ras_ksolve.m ├── vox2ras_rsolve.m ├── vox2ras_rsolveAA.m ├── vox2ras_tkreg.m ├── wm_seg_afd.m ├── wm_seg_dir_afd.m ├── wm_seg_table.m ├── write_analyze_hdr.m ├── write_annotation.m ├── write_ascii_curv.m ├── write_curv.m ├── write_label.m ├── write_surf.m ├── write_wfile.m ├── x2fsgd.m ├── xfm_read.m └── zeropad.m ├── minc.cmake ├── mkxsubjreg ├── CMakeLists.txt ├── Makefile.am └── mkxsubjreg.c ├── mri_add_xform_to_header ├── CMakeLists.txt ├── Makefile.am ├── mri_add_xform_to_header.c └── mri_add_xform_to_header.help.xml ├── mri_and ├── Makefile.am ├── mri_and.c └── mri_or.c ├── mri_annotation2label ├── CMakeLists.txt ├── Makefile.am ├── mri_annotation2label.c └── runit ├── mri_aparc2aseg ├── CMakeLists.txt ├── Makefile.am ├── mri_aparc2aseg.c ├── mri_aparc2aseg.help.xml ├── test_mri_aparc2aseg ├── testdata.tar.gz └── testdata2.tar.gz ├── mri_aparc2wmseg ├── CMakeLists.txt ├── Makefile.am └── mri_aparc2wmseg.c ├── mri_apply_inu_correction ├── CMakeLists.txt ├── Makefile.am └── mri_apply_inu_correction.c ├── mri_aseg_edit_reclassify ├── Makefile.am └── mri_aseg_edit_reclassify.c ├── mri_aseg_edit_train ├── Makefile.am └── mri_aseg_edit_train.c ├── mri_auto_fill ├── CMakeLists.txt ├── Makefile.am └── mri_auto_fill.c ├── mri_average ├── CMakeLists.txt ├── Makefile.am └── mri_average.c ├── mri_bc_sc_bias_correct ├── CMakeLists.txt ├── Makefile.am └── mri_bc_sc_bias_correct.c ├── mri_bias ├── CMakeLists.txt ├── Makefile.am ├── mri_apply_bias.c └── mri_compute_bias.c ├── mri_binarize ├── CMakeLists.txt ├── Makefile.am └── mri_binarize.c ├── mri_build_priors ├── CMakeLists.txt ├── Makefile.am └── mri_build_priors.c ├── mri_ca_label ├── CMakeLists.txt ├── Makefile.am ├── callgrind.cpu ├── mri_ca_label.c ├── mri_ca_label.help.xml ├── test_mri_ca_label └── testdata.tar.gz ├── mri_ca_normalize ├── CMakeLists.txt ├── Makefile.am ├── mri_ca_normalize.c ├── mri_ca_normalize.help.xml ├── mri_cal_normalize.c ├── test_mri_ca_normalize └── testdata.tar.gz ├── mri_ca_register ├── CMakeLists.txt ├── Makefile.am ├── mri_ca_register.c ├── mri_ca_register.help.xml ├── mri_ca_register_cuda.help.xml ├── test_mri_ca_register └── testdata.tar.gz ├── mri_ca_tissue_parms ├── CMakeLists.txt ├── Makefile.am └── mri_ca_tissue_parms.c ├── mri_ca_train ├── CMakeLists.txt ├── Makefile.am └── mri_ca_train.c ├── mri_cal_renormalize_gca ├── Makefile.am ├── mri_cal_renormalize_gca.c └── mri_cal_renormalize_gca.help.xml ├── mri_cc ├── CMakeLists.txt ├── Makefile.am ├── mri_cc.c └── mri_cc.help.xml ├── mri_cc_ma_fill ├── CMakeLists.txt └── mri_cc_ma_fill.c ├── mri_cc_medial_axis ├── CMakeLists.txt └── mri_cc_medial_axis.c ├── mri_cht2p ├── CMakeLists.txt ├── Makefile.am └── mri_cht2p.c ├── mri_classify ├── Makefile.am └── mri_classify.c ├── mri_cnr ├── CMakeLists.txt ├── Makefile.am └── mri_cnr.c ├── mri_compile_edits ├── Makefile.am └── mri_compile_edits.c ├── mri_compute_change_map ├── Makefile.am └── mri_compute_change_map.c ├── mri_compute_overlap ├── CMakeLists.txt ├── Makefile.am └── mri_compute_overlap.c ├── mri_compute_seg_overlap ├── CMakeLists.txt ├── Makefile.am ├── mri_compute_seg_overlap.c └── mri_compute_seg_overlap.help.xml ├── mri_compute_structure_transforms ├── Makefile.am └── mri_compute_structure_transforms.c ├── mri_compute_volume_fractions ├── Makefile.am ├── mri_compute_layer_fractions.c ├── mri_compute_volume_fractions.c ├── mri_compute_volume_intensities.c └── mris_compute_layer_intensities.c ├── mri_concat ├── CMakeLists.txt ├── Makefile.am └── mri_concat.c ├── mri_concatenate_gcam ├── Makefile.am └── mri_concatenate_gcam.c ├── mri_concatenate_lta ├── CMakeLists.txt ├── Makefile.am ├── mri_concatenate_lta.c ├── test_mri_concatenate_lta └── testdata.tar.gz ├── mri_convert ├── CMakeLists.txt ├── Makefile.am ├── mri_convert.c ├── mri_convert.help.xml ├── mri_make_uchar.c ├── test_mri_convert └── testdata.tar.gz ├── mri_convert_mdh ├── CMakeLists.txt ├── Makefile.am └── mri_convert_mdh.c ├── mri_copy_values ├── CMakeLists.txt ├── Makefile.am └── mri_copy_values.c ├── mri_cor2label ├── CMakeLists.txt ├── Makefile.am └── mri_cor2label.c ├── mri_coreg ├── Makefile.am └── mri_coreg.c ├── mri_correct_segmentations ├── Makefile.am └── mri_correct_segmentations.c ├── mri_cvs_register ├── Makefile.am ├── id.xfm ├── mri_cvs_check ├── mri_cvs_data_copy ├── mri_cvs_register ├── mri_cvs_register.help.xml └── mri_cvs_requiredfiles.txt ├── mri_dct_align ├── CMakeLists.txt ├── Makefile.am ├── mri_dct_align.c └── mri_dct_align_binary.c ├── mri_deface ├── CMakeLists.txt ├── Makefile.am └── mri_deface.c ├── mri_diff ├── CMakeLists.txt ├── Makefile.am └── mri_diff.c ├── mri_distance_transform ├── CMakeLists.txt ├── Makefile.am └── mri_distance_transform.cpp ├── mri_divide_segmentation ├── Makefile.am └── mri_divide_segmentation.c ├── mri_edit_segmentation ├── CMakeLists.txt ├── Makefile.am └── mri_edit_segmentation.c ├── mri_edit_segmentation_with_surfaces ├── CMakeLists.txt ├── Makefile.am └── mri_edit_segmentation_with_surfaces.c ├── mri_edit_wm_with_aseg ├── CMakeLists.txt ├── Makefile.am ├── mri_edit_wm_with_aseg.c └── mri_edit_wm_with_aseg.help.xml ├── mri_elastic_energy ├── Makefile.am └── mri_elastic_energy.c ├── mri_em_register ├── CMakeLists.txt ├── Makefile.am ├── callgrind.cpu.out ├── em_register_cuda.cu ├── em_register_cuda.h ├── emregisterutils.cpp ├── emregisterutils.h ├── findtranslation.cpp ├── findtranslation.h ├── mri_em_register.c ├── mri_em_register.help.xml ├── mri_em_register_cuda.help.xml ├── test_mri_em_register └── testdata.tar.gz ├── mri_estimate_tissue_parms ├── CMakeLists.txt ├── Makefile.am └── mri_estimate_tissue_parms.c ├── mri_evaluate_morph ├── CMakeLists.txt ├── Makefile.am └── mri_evaluate_morph.c ├── mri_extract ├── CMakeLists.txt ├── Makefile.am └── mri_extract.c ├── mri_extract_conditions ├── CMakeLists.txt ├── Makefile.am └── mri_extract_conditions.c ├── mri_extract_label ├── CMakeLists.txt ├── Makefile.am └── mri_extract_label.c ├── mri_extract_largest_CC ├── CMakeLists.txt ├── Makefile.am ├── mri_extract_largest_CC.c ├── myutil.h ├── myutils.c ├── subroutines.c └── subroutines.h ├── mri_extract_ma_intensity ├── CMakeLists.txt └── mri_extract_ma_intensity.c ├── mri_fcili ├── Makefile.am └── mri_fcili.c ├── mri_fdr ├── Makefile.am └── mri_fdr.c ├── mri_fieldsign ├── Makefile.am └── mri_fieldsign.c ├── mri_fill ├── CMakeLists.txt ├── Makefile.am ├── mri_fill.c ├── mri_fill.help.xml ├── myutil.c ├── myutil.h ├── subroutines.c └── subroutines.h ├── mri_fit_bias ├── Makefile.am └── mri_fit_bias.c ├── mri_fslmat_to_lta ├── CMakeLists.txt ├── Makefile.am └── mri_fslmat_to_lta.c ├── mri_fuse_intensity_images ├── Makefile.am └── mri_fuse_intensity_images.c ├── mri_fuse_segmentations ├── Makefile.am └── mri_fuse_segmentations.c ├── mri_fwhm ├── CMakeLists.txt ├── Makefile.am └── mri_fwhm.c ├── mri_gca_ambiguous ├── CMakeLists.txt ├── Makefile.am └── mri_gca_ambiguous.c ├── mri_gcab_train ├── Makefile.am └── mri_gcab_train.c ├── mri_gcut ├── Makefile.am ├── gcut.h ├── graphcut.cpp ├── graphcut.h ├── mri_gcut.cpp ├── mri_gcut.help.xml └── pre_pro.cpp ├── mri_gdfglm ├── CMakeLists.txt ├── Makefile.am └── mri_gdfglm.c ├── mri_glmfit ├── CMakeLists.txt ├── Makefile.am ├── mri_glmfit.c ├── test_mri_glmfit └── teststats.tar.gz ├── mri_gtmpvc ├── Makefile.am └── mri_gtmpvc.c ├── mri_gtmseg ├── Makefile.am └── mri_gtmseg.c ├── mri_hausdorff_dist ├── Makefile.am └── mri_hausdorff_dist.c ├── mri_head ├── CMakeLists.txt ├── Makefile.am └── mri_head.c ├── mri_hires_register ├── CMakeLists.txt ├── Makefile.am ├── make_movie.tcl ├── mri_compute_distances.c ├── mri_hires_register.c ├── mri_linear_align.c ├── mri_linear_align_binary.c ├── mri_nl_align.c └── mri_nl_align_binary.c ├── mri_histo_eq ├── CMakeLists.txt ├── Makefile.am └── mri_histo_eq.c ├── mri_histo_normalize ├── Makefile.am └── mri_histo_normalize.c ├── mri_ibmc ├── Makefile.am └── mri_ibmc.c ├── mri_iic ├── Makefile.am ├── matrix3d.cpp ├── matrix3d.h ├── tensorCubicSmoothing.cpp ├── tensorCubicSmoothing.h ├── testMatrix.cpp ├── testMultiplication.cpp └── testTCS.cpp ├── mri_info ├── CMakeLists.txt ├── Makefile.am └── mri_info.c ├── mri_interpolate ├── CMakeLists.txt ├── Makefile.am └── mri_interpolate.c ├── mri_jacobian ├── CMakeLists.txt ├── Makefile.am └── mri_jacobian.c ├── mri_joint_density ├── CMakeLists.txt ├── Makefile.am └── mri_joint_density.c ├── mri_label2label ├── CMakeLists.txt ├── Makefile.am └── mri_label2label.c ├── mri_label2vol ├── CMakeLists.txt ├── Makefile.am └── mri_label2vol.c ├── mri_label_accuracy ├── CMakeLists.txt ├── Makefile.am └── mri_label_accuracy.c ├── mri_label_histo ├── CMakeLists.txt ├── Makefile.am └── mri_label_histo.c ├── mri_label_vals ├── CMakeLists.txt ├── Makefile.am └── mri_label_vals.c ├── mri_label_volume ├── CMakeLists.txt ├── Makefile.am └── mri_label_volume.c ├── mri_linear_register ├── CMakeLists.txt ├── Makefile.am └── mri_linear_register.c ├── mri_log_likelihood ├── CMakeLists.txt ├── Makefile.am └── mri_log_likelihood.c ├── mri_make_bem_surfaces ├── Makefile.am └── mri_make_bem_surfaces.c ├── mri_make_density_map ├── CMakeLists.txt ├── Makefile.am └── mri_make_density_map.c ├── mri_make_labels ├── Makefile.am └── mri_make_labels.c ├── mri_make_register ├── CMakeLists.txt ├── Makefile.am └── mri_make_register.c ├── mri_make_template ├── CMakeLists.txt ├── Makefile.am └── mri_make_template.c ├── mri_map_atrophy ├── CMakeLists.txt └── mri_map_atrophy.c ├── mri_map_cpdat ├── Makefile.am └── mri_map_cpdat.cpp ├── mri_mark_temporal_lobe ├── CMakeLists.txt ├── Makefile.am └── mri_mark_temporal_lobe.c ├── mri_mask ├── CMakeLists.txt ├── Makefile.am ├── mri_mask.c └── mri_mask.help.xml ├── mri_matrix_multiply ├── CMakeLists.txt ├── Makefile.am └── mri_matrix_multiply.c ├── mri_mc ├── CMakeLists.txt ├── Makefile.am ├── README ├── build_MC_table.c ├── build_test_volume.c ├── compare_test_volumes ├── mc_table.gif ├── mri_mc.c ├── mri_pretess.c ├── mri_pretess.help.xml ├── mris_extract_main_component.c ├── mris_extract_main_component.help.xml └── test_volume_reference.mgz ├── mri_mcsim ├── CMakeLists.txt ├── Makefile.am └── mri_mcsim.c ├── mri_modify ├── CMakeLists.txt ├── Makefile.am ├── mri_copy_params.cpp └── mri_modify.cpp ├── mri_morphology ├── CMakeLists.txt ├── Makefile.am └── mri_morphology.c ├── mri_mosaic ├── Makefile.am └── mri_mosaic.c ├── mri_ms_EM ├── CMakeLists.txt ├── Makefile.am ├── PoissonSolver.c ├── PoissonSolver.h ├── mri_ms_EM.c ├── myutil.h └── myutils.c ├── mri_ms_EM_with_atlas ├── CMakeLists.txt ├── Makefile.am ├── PoissonSolver.c ├── PoissonSolver.h ├── mri_ms_EM_with_atlas.c ├── myutil.h ├── myutils.c ├── subroutines.c └── subroutines.h ├── mri_ms_LDA ├── CMakeLists.txt ├── Makefile.am └── mri_ms_LDA.c ├── mri_ms_fitparms ├── CMakeLists.txt ├── Makefile.am ├── mri_ms_fitparms.c └── mri_ms_fitparms.help.xml ├── mri_multiscale_segment ├── Makefile.am └── mri_multiscale_segment.c ├── mri_multispectral_segment ├── CMakeLists.txt ├── Makefile.am └── mri_multispectral_segment.c ├── mri_nlfilter ├── CMakeLists.txt ├── Makefile.am └── mri_nlfilter.c ├── mri_normalize ├── CMakeLists.txt ├── Makefile.am ├── mri_long_normalize.c ├── mri_long_normalize.help.xml ├── mri_normalize.c └── mri_normalize.help.xml ├── mri_normalize_tp2 ├── CMakeLists.txt ├── Makefile.am └── mri_normalize_tp2.c ├── mri_otl ├── Makefile.am └── list_otl_labels.c ├── mri_paint ├── CMakeLists.txt ├── Makefile.am └── mri_paint.c ├── mri_parse_sdcmdir ├── 98915109 ├── CMakeLists.txt ├── Makefile.am ├── mri_parse_sdcmdir.c ├── test_dicomdir.sumfile └── test_mri_parse_sdcmdir ├── mri_parselabel ├── CMakeLists.txt ├── Makefile.am └── mri_parselabel.cpp ├── mri_partial_ribbon ├── CMakeLists.txt ├── Makefile.am └── mri_partial_ribbon.c ├── mri_path2label ├── CMakeLists.txt ├── Makefile.am └── mri_path2label.c ├── mri_polv ├── CMakeLists.txt ├── Makefile.am └── mri_polv.c ├── mri_probe_ima ├── CMakeLists.txt ├── Makefile.am └── mri_probe_ima.c ├── mri_probedicom ├── CMakeLists.txt ├── Makefile.am └── mri_probedicom.c ├── mri_rbvpvc ├── Makefile.am └── mri_rbvpvc.c ├── mri_reduce ├── CMakeLists.txt ├── Makefile.am └── mri_reduce.c ├── mri_register ├── CMakeLists.txt ├── Makefile.am └── mri_register.c ├── mri_relabel_hypointensities ├── CMakeLists.txt ├── Makefile.am └── mri_relabel_hypointensities.c ├── mri_relabel_nonwm_hypos ├── Makefile.am └── mri_relabel_nonwm_hypos.c ├── mri_remove_neck ├── CMakeLists.txt ├── Makefile.am ├── mri_remove_neck.c └── mri_remove_neck.help.xml ├── mri_rf_label ├── Makefile.am ├── mri_rf_label.c └── mri_rf_label.help.xml ├── mri_rf_long_label ├── Makefile.am └── mri_rf_long_label.c ├── mri_rf_long_train ├── Makefile.am └── mri_rf_long_train.c ├── mri_rf_train ├── Makefile.am └── mri_rf_train.c ├── mri_ribbon ├── CMakeLists.txt ├── Makefile.am └── mri_ribbon.c ├── mri_rigid_register ├── CMakeLists.txt ├── Makefile.am └── mri_rigid_register.c ├── mri_robust_register ├── CostFunctions.cpp ├── CostFunctions.h ├── Interpolator.h ├── JointHisto.cpp ├── JointHisto.h ├── Makefile.am ├── MultiRegistration.cpp ├── MultiRegistration.h ├── MyMRI.cpp ├── MyMRI.h ├── MyMatrix.cpp ├── MyMatrix.h ├── Quaternion.cpp ├── Quaternion.h ├── RegPowell.cpp ├── RegPowell.h ├── RegRobust.cpp ├── RegRobust.h ├── Registration.cpp ├── Registration.h ├── RegistrationStep.h ├── Regression.cpp ├── Regression.h ├── RobustGaussian.cpp ├── RobustGaussian.h ├── Transformation.h ├── callgrind.mri_robust_template.cpu.out ├── lta_diff.cpp ├── mri_create_tests.cpp ├── mri_gradient_info.cpp ├── mri_robust_register.cpp ├── mri_robust_register.help.xml ├── mri_robust_template.cpp ├── mri_robust_template.help.xml ├── test_libgfortran ├── test_mri_robust_template └── testdata.tar.gz ├── mri_seg_diff ├── Makefile.am └── mri_seg_diff.c ├── mri_seghead ├── CMakeLists.txt ├── Makefile.am └── mri_seghead.c ├── mri_segment ├── CMakeLists.txt ├── Makefile.am ├── mri_segment.c └── mri_segment.help.xml ├── mri_segment_tumor ├── Makefile.am ├── T1_PD_T2.gca ├── T1_T2.gca └── mri_segment_tumor.c ├── mri_segment_wm_damage ├── CMakeLists.txt ├── Makefile.am └── mri_segment_wm_damage.c ├── mri_segreg ├── Makefile.am └── mri_segreg.c ├── mri_segstats ├── CMakeLists.txt ├── Makefile.am ├── callgrind.cpu.out ├── mri_segstats.c ├── mri_segstats.help.xml ├── test_mri_segstats └── testdata.tar.gz ├── mri_simulate_atrophy ├── Makefile.am └── mri_simulate_atrophy.c ├── mri_stats2seg ├── CMakeLists.txt ├── Makefile.am └── mri_stats2seg.c ├── mri_strip_nonwhite ├── CMakeLists.txt ├── Makefile.am └── mri_strip_nonwhite.c ├── mri_strip_subject_info ├── CMakeLists.txt ├── Makefile.am └── mri_strip_subject_info.c ├── mri_surf2surf ├── CMakeLists.txt ├── Makefile.am └── mri_surf2surf.c ├── mri_surf2vol ├── CMakeLists.txt ├── Makefile.am └── mri_surf2vol.c ├── mri_surfacemask ├── CMakeLists.txt ├── Makefile.am └── mri_surfacemask.cpp ├── mri_surfcluster ├── CMakeLists.txt ├── Makefile.am └── mri_surfcluster.c ├── mri_synthesize ├── CMakeLists.txt ├── Makefile.am └── mri_synthesize.c ├── mri_tessellate ├── CMakeLists.txt ├── Makefile.am ├── ico_supersample.c ├── mri_tessellate.c ├── mri_tessellate.help.xml ├── systemid.h └── trilib.h ├── mri_threshold ├── CMakeLists.txt ├── Makefile.am └── mri_threshold.c ├── mri_topologycorrection ├── CMakeLists.txt ├── Makefile.am └── mri_topologycorrection.c ├── mri_train ├── CMakeLists.txt ├── Makefile.am └── mri_train.c ├── mri_train_autoencoder ├── Makefile.am ├── mri_apply_autoencoder.c ├── mri_train_autoencoder.c └── run.csh ├── mri_transform ├── CMakeLists.txt ├── Makefile.am └── mri_transform.c ├── mri_transform_to_COR ├── CMakeLists.txt ├── Makefile.am └── mri_transform_to_COR.c ├── mri_twoclass ├── CMakeLists.txt ├── Makefile.am └── mri_twoclass.c ├── mri_update_gca ├── Makefile.am └── mri_update_gca.c ├── mri_vol2roi ├── CMakeLists.txt ├── Makefile.am └── mri_vol2roi.c ├── mri_vol2surf ├── CMakeLists.txt ├── Makefile.am └── mri_vol2surf.c ├── mri_vol2vol ├── CMakeLists.txt ├── Makefile.am ├── callgrind.out.14787 └── mri_vol2vol.c ├── mri_volcluster ├── CMakeLists.txt ├── Makefile.am └── mri_volcluster.c ├── mri_voldiff ├── CMakeLists.txt ├── Makefile.am └── mri_voldiff.c ├── mri_volsynth ├── CMakeLists.txt ├── Makefile.am └── mri_volsynth.c ├── mri_warp_convert ├── Makefile.am └── mri_warp_convert.c ├── mri_watershed ├── CMakeLists.txt ├── Makefile.am ├── brain_volume │ ├── CMakeLists.txt │ ├── Makefile.am │ ├── TVector.h │ ├── mri_brain_volume.cpp │ ├── mrivariables.h │ └── test.cpp ├── callgrind.cpu.out ├── mri_validate_skull_stripped.cpp ├── mri_watershed.cpp └── mri_watershed.help.xml ├── mri_wbc ├── Makefile.am └── mri_wbc.c ├── mri_wmfilter ├── CMakeLists.txt ├── Makefile.am └── mri_wmfilter.c ├── mri_xcorr ├── Makefile.am └── mri_xcorr.c ├── mri_xvolavg ├── CMakeLists.txt ├── Makefile.am └── mri_xvolavg.c ├── mri_z2p ├── CMakeLists.txt ├── Makefile.am └── mri_z2p.c ├── mris2rgb ├── CMakeLists.txt ├── Makefile.am └── mris2rgb.c ├── mris_BA_segment ├── Makefile.am └── mris_BA_segment.c ├── mris_add_template ├── CMakeLists.txt ├── Makefile.am └── mris_add_template.c ├── mris_anatomical_stats ├── CMakeLists.txt ├── Makefile.am ├── mris_anatomical_stats.c ├── mris_anatomical_stats.help.xml ├── test1.expected ├── test2.expected ├── test2_logfile.expected ├── test3.expected ├── test4.expected ├── test6.expected └── test_mris_anatomical_stats ├── mris_annot_to_segmentation ├── CMakeLists.txt ├── Makefile.am └── mris_annot_to_segmentation.c ├── mris_apply_reg ├── Makefile.am ├── mris_apply_reg.c └── mris_apply_reg.help.xml ├── mris_aseg_distance ├── CMakeLists.txt ├── Makefile.am └── mris_aseg_distance.c ├── mris_average_curvature ├── CMakeLists.txt ├── Makefile.am └── mris_average_curvature.c ├── mris_average_parcellation ├── CMakeLists.txt ├── Makefile.am └── mris_average_parcellation.c ├── mris_ca_label ├── CMakeLists.txt ├── Makefile.am ├── mris_ca_label.c ├── mris_ca_label.help.xml ├── test_mris_ca_label └── testdata.tar.gz ├── mris_ca_train ├── CMakeLists.txt ├── Makefile.am └── mris_ca_train.c ├── mris_calc ├── CMakeLists.txt ├── Makefile.am ├── help.txt ├── makehelp.sh ├── mris_calc.c └── mris_calc.help.xml ├── mris_classify_thickness ├── CMakeLists.txt ├── Makefile.am └── mris_classify_thickness.c ├── mris_compute_acorr ├── CMakeLists.txt ├── Makefile.am └── mris_compute_acorr.c ├── mris_compute_lgi ├── ComputeGeodesicProjection.m ├── MakeGeodesicOuterROI.m ├── Makefile.am ├── PropagateGeodesic.m ├── SearchProjectionOnPial.m ├── compute_lgi.m ├── createMeshFacesOfVertex.m ├── dijk.m ├── find_corresponding_center_FSformat.m ├── freesurfer_fread3.m ├── freesurfer_read_surf.m ├── getFaceArea.m ├── getFacesArea.m ├── getMeshArea.m ├── getOrthogonalVector.m ├── getVerticesAndFacesInSphere.m ├── isInGeodesicROI.m ├── isVertexInRadius.m ├── make_outer_surface.m ├── make_roi_paths.m ├── mesh_adjacency.m ├── mesh_vertex_nearest.m ├── mris_compute_lgi ├── pred2path.m ├── read_ROIlabel.m ├── read_normals.m ├── redo_lgi.m ├── reorganize_verticeslist.m ├── transVertexToNormalAxisBase.m ├── write_lgi.m └── write_path.m ├── mris_compute_optimal_kernel ├── CMakeLists.txt ├── Makefile.am └── mris_compute_optimal_kernel.c ├── mris_compute_overlap ├── CMakeLists.txt ├── Makefile.am └── mris_compute_overlap.c ├── mris_compute_parc_overlap ├── CMakeLists.txt ├── Makefile.am └── mris_compute_parc_overlap.c ├── mris_compute_volume_fractions ├── Makefile.am ├── mris_compute_volume_fractions.c └── myown.c ├── mris_congeal ├── Makefile.am ├── make_movie.csh ├── mris_congeal.c └── render_surface.tcl ├── mris_convert ├── CMakeLists.txt ├── Makefile.am ├── giftidata.tar.gz ├── mris_convert.c ├── test_gifti └── test_mris_convert ├── mris_copy_header ├── Makefile.am └── mris_copy_header.c ├── mris_curvature ├── CMakeLists.txt ├── Makefile.am ├── mris_curvature.c └── mris_curvature.help.xml ├── mris_curvature_stats ├── CMakeLists.txt ├── Makefile.am ├── help.txt ├── makehelp.sh └── mris_curvature_stats.c ├── mris_curvature_vectors ├── Makefile.am └── mris_curvature_vectors.c ├── mris_decimate ├── Makefile.am ├── main.cpp ├── mris_decimate.cpp ├── mris_decimate.h └── mris_decimate.help.xml ├── mris_decimate_gui ├── DecimatePanel.cpp ├── DecimatePanel.h ├── Info.plist ├── MainApp.cpp ├── MainApp.h ├── MainWindow.cpp ├── MainWindow.h ├── Makefile.am ├── MyCmdLineParser.cpp ├── MyCmdLineParser.h ├── RenderPanel.cpp ├── RenderPanel.h ├── res │ ├── DecimatePanelBase.cpp │ ├── DecimatePanelBase.fbp │ ├── DecimatePanelBase.h │ ├── MainWindowBase.cpp │ ├── MainWindowBase.fbp │ └── MainWindowBase.h ├── wxVTKRenderWindowInteractor.cpp └── wxVTKRenderWindowInteractor.h ├── mris_deform ├── CMakeLists.txt ├── Makefile.am ├── mris_ca_deform.c ├── mris_deform.c └── mris_nudge.c ├── mris_density ├── CMakeLists.txt ├── Makefile.am └── mris_density.c ├── mris_diff ├── CMakeLists.txt ├── Makefile.am └── mris_diff.c ├── mris_distance_map ├── CMakeLists.txt ├── Makefile.am └── mris_distance_map.c ├── mris_distance_to_label ├── CMakeLists.txt ├── Makefile.am └── mris_distance_to_label.cpp ├── mris_distance_transform ├── Makefile.am └── mris_distance_transform.c ├── mris_divide_parcellation ├── CMakeLists.txt ├── Makefile.am └── mris_divide_parcellation.c ├── mris_entropy ├── CMakeLists.txt ├── Makefile.am └── mris_entropy.c ├── mris_errors ├── CMakeLists.txt ├── Makefile.am └── mris_errors.c ├── mris_euler_number ├── CMakeLists.txt ├── Makefile.am ├── mris_euler_number.c └── mris_euler_number.help.xml ├── mris_expand ├── CMakeLists.txt ├── Makefile.am ├── mris_expand.c ├── test_mris_expand └── testdata.tar.gz ├── mris_fbirn_annot ├── CMakeLists.txt ├── Makefile.am └── mris_fbirn_annot.c ├── mris_fill ├── CMakeLists.txt ├── Makefile.am └── mris_fill.c ├── mris_find_flat_regions ├── CMakeLists.txt ├── Makefile.am └── mris_find_flat_regions.c ├── mris_fix_topology ├── CMakeLists.txt ├── Makefile.am ├── mris_fix_topology.c ├── mris_fix_topology.help.xml ├── mris_remove_intersection.c └── mris_remove_intersection.help.xml ├── mris_flatten ├── CMakeLists.txt ├── Makefile.am ├── make_mris_flatten_movie.tcl └── mris_flatten.c ├── mris_fwhm ├── CMakeLists.txt ├── Makefile.am └── mris_fwhm.c ├── mris_glm ├── CMakeLists.txt ├── Makefile.am └── mris_glm.c ├── mris_hausdorff_dist ├── Makefile.am └── mris_hausdorff_dist.c ├── mris_inflate ├── CMakeLists.txt ├── Makefile.am ├── mris_inflate.c └── mris_inflate.help.xml ├── mris_info ├── CMakeLists.txt ├── Makefile.am └── mris_info.cpp ├── mris_init_global_tractography ├── Makefile.am └── mris_init_global_tractography.c ├── mris_interpolate_warp ├── Makefile.am └── mris_interpolate_warp.c ├── mris_jacobian ├── CMakeLists.txt ├── Makefile.am ├── mris_jacobian.c └── mris_jacobian.help.xml ├── mris_label2annot ├── CMakeLists.txt ├── Makefile.am ├── mris_label2annot.c └── runit ├── mris_label_area ├── CMakeLists.txt ├── Makefile.am └── mris_label_area.c ├── mris_label_calc ├── Makefile.am └── mris_label_calc.cpp ├── mris_label_mode ├── CMakeLists.txt ├── Makefile.am └── mris_label_mode.c ├── mris_left_right_register ├── Makefile.am ├── make_mris_register_movie.tcl └── mris_left_right_register.c ├── mris_longitudinal_surfaces ├── CMakeLists.txt ├── Makefile.am └── mris_longitudinal_surfaces.c ├── mris_make_average_surface ├── CMakeLists.txt ├── Makefile.am └── mris_make_average_surface.c ├── mris_make_face_parcellation ├── Makefile.am └── mris_make_face_parcellation.c ├── mris_make_map_surfaces ├── Makefile.am ├── mris_make_map_surfaces.c └── mris_make_map_surfaces.help.xml ├── mris_make_surfaces ├── CMakeLists.txt ├── Makefile.am ├── mris_exvivo_surfaces.c ├── mris_make_surfaces.c ├── mris_make_surfaces.help.xml ├── mris_mef_surfaces.c └── mris_refine_surfaces.c ├── mris_make_template ├── CMakeLists.txt ├── Makefile.am └── mris_make_template.c ├── mris_map_cuts ├── Makefile.am └── mris_map_cuts.c ├── mris_merge_parcellations ├── Makefile.am └── mris_merge_parcellations.c ├── mris_mesh_subdivide ├── Makefile.am └── mris_mesh_subdivide.cxx ├── mris_morph_stats ├── CMakeLists.txt ├── Makefile.am └── mris_morph_stats.c ├── mris_ms_refine ├── CMakeLists.txt ├── Makefile.am └── mris_ms_refine.c ├── mris_ms_surface_CNR ├── CMakeLists.txt ├── Makefile.am └── mris_ms_surface_CNR.c ├── mris_multiscale_stats ├── CMakeLists.txt ├── Makefile.am └── mris_multiscale_stats.c ├── mris_niters2fwhm ├── CMakeLists.txt ├── Makefile.am └── mris_niters2fwhm.c ├── mris_parcellate_connectivity ├── Makefile.am └── mris_parcellate_connectivity.c ├── mris_pmake ├── C_mpmOverlay.cpp ├── C_mpmOverlay.h ├── C_mpmProg.cpp ├── C_mpmProg.h ├── Makefile.am ├── abs2rel.c ├── asynch.cpp ├── asynch.h ├── c_SMessage.cpp ├── c_SMessage.h ├── c_SSocket.cpp ├── c_SSocket.h ├── c_label.cpp ├── c_label.h ├── c_surface.cpp ├── c_surface.h ├── c_vertex.cpp ├── c_vertex.h ├── dijkstra.cpp ├── dijkstra.h ├── env.cpp ├── env.h ├── general.cpp ├── general.h ├── help.cpp ├── help.h ├── legacy.cpp ├── legacy.h ├── mris_pmake.cpp ├── mris_pmake.help.xml ├── pathconvert.h ├── pstream.h ├── rel2abs.c ├── scanopt.cpp ├── scanopt.h ├── surface.cpp ├── surface.h └── test_mris_pmake ├── mris_pval_fill ├── CMakeLists.txt └── mris_pval_fill.c ├── mris_register ├── CMakeLists.txt ├── Makefile.am ├── callgrind.cpu.out ├── make_mris_register_movie.tcl ├── mris_register.c └── mris_register.help.xml ├── mris_register_label_map ├── Makefile.am └── mris_register_label_map.c ├── mris_register_to_volume ├── Makefile.am ├── mris_register_to_label.c └── mris_register_to_volume.c ├── mris_remove_variance ├── CMakeLists.txt ├── Makefile.am └── mris_remove_variance.c ├── mris_resample ├── Makefile.am └── mris_resample.cpp ├── mris_rescale ├── CMakeLists.txt ├── Makefile.am └── mris_rescale.c ├── mris_reverse ├── CMakeLists.txt ├── Makefile.am └── mris_reverse.c ├── mris_rf_label ├── Makefile.am └── mris_rf_label.c ├── mris_rf_train ├── Makefile.am └── mris_rf_train.c ├── mris_rotate ├── CMakeLists.txt ├── Makefile.am └── mris_rotate.c ├── mris_sample_label ├── CMakeLists.txt ├── Makefile.am └── mris_sample_label.c ├── mris_sample_parc ├── CMakeLists.txt ├── Makefile.am └── mris_sample_parc.c ├── mris_seg2annot ├── CMakeLists.txt ├── Makefile.am └── mris_seg2annot.c ├── mris_segment ├── Makefile.am └── mris_segment.c ├── mris_segment_vals ├── CMakeLists.txt ├── Makefile.am └── mris_segment_vals.c ├── mris_segmentation_stats ├── Makefile.am └── mris_segmentation_stats.c ├── mris_show ├── CMakeLists.txt ├── Makefile.am └── mris_show.c ├── mris_shrinkwrap ├── CMakeLists.txt ├── Makefile.am ├── mris_AA_shrinkwrap.c └── mris_shrinkwrap.c ├── mris_simulate_atrophy ├── Makefile.am └── mris_simulate_atrophy.c ├── mris_smooth ├── CMakeLists.txt ├── Makefile.am ├── mris_smooth.c └── mris_smooth.help.xml ├── mris_spharm ├── CMakeLists.txt └── mris_spharm.c ├── mris_sphere ├── CMakeLists.txt ├── Makefile.am ├── make_mris_sphere_movie.tcl ├── mris_remove_negative_vertices.c ├── mris_sphere.c ├── mris_sphere.help.xml ├── test_mris_sphere └── testdata.tar.gz ├── mris_spherical_average ├── CMakeLists.txt ├── Makefile.am └── mris_spherical_average.c ├── mris_spherical_wavelets ├── CMakeLists.txt └── mris_spherical_wavelets.c ├── mris_surface_change ├── Makefile.am └── mris_surface_change.c ├── mris_surface_stats ├── CMakeLists.txt ├── Makefile.am └── mris_surface_stats.c ├── mris_surface_to_vol_distances ├── CMakeLists.txt ├── Makefile.am └── mris_surface_to_vol_distances.c ├── mris_svm_classify ├── Makefile.am └── mris_svm_classify.c ├── mris_svm_train ├── Makefile.am └── mris_svm_train.c ├── mris_talairach ├── CMakeLists.txt ├── Makefile.am └── mris_talairach.c ├── mris_thickness ├── CMakeLists.txt ├── Makefile.am ├── mris_cluster_profiles.c ├── mris_intensity_profile.c └── mris_thickness.c ├── mris_thickness_comparison ├── CMakeLists.txt ├── Makefile.am └── mris_thickness_comparison.c ├── mris_thickness_diff ├── CMakeLists.txt ├── Makefile.am └── mris_thickness_diff.c ├── mris_topo_fixer ├── CMakeLists.txt ├── Makefile.am └── mris_topo_fixer.cpp ├── mris_transform ├── CMakeLists.txt ├── Makefile.am └── mris_transform.c ├── mris_translate_annotation ├── CMakeLists.txt ├── Makefile.am └── mris_translate_annotation.c ├── mris_transmantle_dysplasia_paths ├── Makefile.am └── mris_transmantle_dysplasia_paths.c ├── mris_twoclass ├── CMakeLists.txt ├── Makefile.am └── mris_twoclass.c ├── mris_volmask ├── CMakeLists.txt ├── Makefile.am ├── TestMRISDistanceField.cpp ├── TestMRISOBBTree.cpp ├── cmd_line_interface.cpp ├── cmd_line_interface.h ├── mris_volmask.cpp ├── mris_volmask.help.xml ├── mris_volmask_old.cpp └── test_mris_volmask ├── mris_volume ├── CMakeLists.txt ├── Makefile.am ├── mris_volume.c └── mris_wm_volume.c ├── mris_w_to_curv ├── CMakeLists.txt ├── Makefile.am └── mris_w_to_curv.c ├── mris_warp ├── Makefile.am └── mris_warp.c ├── mrisp_paint ├── CMakeLists.txt ├── Makefile.am ├── mrisp_paint.c └── mrisp_paint.help.xml ├── nmovie ├── CMakeLists.txt ├── Makefile.am └── nmovie.c ├── nmovie_qt ├── MainWindow.cpp ├── MainWindow.h ├── MainWindow.ui ├── Makefile.am ├── RenderWidget.cpp ├── RenderWidget.h ├── main.cpp └── nmovie.pro ├── oct_register_mosaic ├── Makefile.am └── oct_register_mosaic.c ├── oct_train ├── Makefile.am ├── oct_rf_train.c ├── oct_train.c └── segment_oct.m ├── opencl_algorithms ├── Makefile.am ├── dijkstra.cl ├── dijkstra.cl.h ├── make_cl_header.sh ├── oclCommon.cpp ├── oclCommon.h ├── oclDijkstraKernel.cpp └── oclDijkstraKernel.h ├── optseq2 ├── CMakeLists.txt ├── Makefile.am ├── optseq2.c ├── test_data.tar.gz └── test_optseq2.csh ├── orient_mri ├── CMakeLists.txt ├── Makefile.am ├── OrientMRIEvents.h ├── OrientMRIIcons.txt ├── OrientMRILibInit.data ├── OrientMRIMain.cxx ├── vtkKWOrientMRIApp.cxx ├── vtkKWOrientMRIApp.h ├── vtkKWOrientMRIView2D.cxx ├── vtkKWOrientMRIView2D.h ├── vtkKWOrientMRIView3D.cxx ├── vtkKWOrientMRIView3D.h ├── vtkKWOrientMRIWindow.cxx ├── vtkKWOrientMRIWindow.h ├── vtkOrientMRIInteractorStyleView2D.cxx ├── vtkOrientMRIInteractorStyleView2D.h ├── vtkOrientMRIInteractorStyleView3D.cxx └── vtkOrientMRIInteractorStyleView3D.h ├── pyScout ├── CMakeCache.txt ├── CMakeLists.txt ├── CrossHair.py ├── DlgImageContrast.py ├── DlgPreferences.py ├── DlgProfileInspector.py ├── DlgRegionAddInfo.py ├── DlgRegionHighlights.py ├── FindPetscNoMPI.cmake ├── Globals.py ├── ImagePipeline.py ├── Laplace.py ├── Mode.py ├── ProfileExport.py ├── Region.py ├── RenderingProperties.py ├── Spline.py ├── SplineDlgLabels.py ├── SplineDlgPreferences.py ├── SplineExport.py ├── SplineMode.py ├── SplineSet.py ├── SplineStateManager.py ├── StateManager.py ├── WrapperPolyData.cpp ├── WrapperPolyData.h ├── bgDlg.py ├── laplace2.cpp ├── laplace2.h ├── laplace2.i ├── locator.cpp ├── locator.h ├── preprocessor.cpp ├── preprocessor.h ├── pyScout.py ├── solver.cpp ├── solver.h ├── tracer.cpp ├── tracer.h └── vtkProbe.py ├── qdec ├── CMakeLists.txt ├── Makefile.am ├── QdecEvents.h ├── QdecIcons.txt ├── QdecLibInit.data ├── QdecMain.cxx ├── QdecUtilities.cxx ├── QdecUtilities.h ├── QdecVertexAnnotationLookup.h ├── development_notes.txt ├── qdec-boad-wink.wnk ├── qdec.ppt ├── qdec2.table.dat ├── qdec_splash.png ├── run_mris_preproc ├── vtkKWQdecApp.cxx ├── vtkKWQdecApp.h ├── vtkKWQdecAppTcl.cxx ├── vtkKWQdecView.cxx ├── vtkKWQdecView.h ├── vtkKWQdecViewTcl.cxx ├── vtkKWQdecWindow.cxx ├── vtkKWQdecWindow.h └── vtkKWQdecWindowTcl.cxx ├── qdec_glmfit ├── CMakeLists.txt ├── Makefile.am └── qdec_glmfit.cxx ├── qdecproject ├── CMakeLists.txt ├── Makefile.am ├── ProgressUpdateGUI.h ├── QdecContrast.cxx ├── QdecContrast.h ├── QdecDataTable.cxx ├── QdecDataTable.h ├── QdecFactor.cxx ├── QdecFactor.h ├── QdecGlmDesign.cxx ├── QdecGlmDesign.h ├── QdecGlmFit.cxx ├── QdecGlmFit.h ├── QdecGlmFitResults.cxx ├── QdecGlmFitResults.h ├── QdecProject.cxx ├── QdecProject.h ├── QdecSubject.cxx ├── QdecSubject.h └── umbrello.xmi ├── rbftest ├── CMakeLists.txt ├── Makefile.am └── rbftest.c ├── references.txt ├── regdat2xfm ├── CMakeLists.txt ├── Makefile.am └── regdat2xfm.cpp ├── repair_siemens_file ├── CMakeLists.txt ├── Makefile.am └── repair_siemens_file.c ├── rgb ├── CMakeLists.txt ├── Makefile.am ├── close.c ├── filbuf.c ├── flsbuf.c ├── name.c ├── open.c ├── pix.c ├── rdwr.c ├── rgbutils.c ├── rle.c └── row.c ├── scripts ├── CMakeLists.txt ├── FT4MRI_Reorient ├── IsLTA ├── LongQdecTable.py ├── Makefile.am ├── Python_Development_Readme.txt ├── UpdateNeeded ├── allisons_surfaces.tcl ├── annot2std ├── aparc2feat ├── aparcstats2table ├── aparcstatsdiff ├── apas2aseg ├── aseg2feat ├── asegstats2table ├── asegstatsdiff ├── avg-surf-label ├── avi2talxfm ├── bblabel ├── bbmask ├── bbregister ├── bbregister.help.xml ├── bedpostx_mgh ├── beta2sxa ├── biasfield ├── birn-glm-demo ├── bmedits2surf ├── bmh.tcl ├── browse-minc-header.tcl ├── bugr ├── build_desikan_killiany_gcs.csh ├── cblumwmgyri ├── check_func_ras_coords.tcl ├── check_subject ├── clear_fs_env.csh ├── compute_interrater_variability.csh ├── compute_label_volumes.csh ├── copyfreesurfer.csh ├── cor_to_minc ├── cp-dicom ├── cuda_setup ├── curv-flat.tcl ├── curv-views.tcl ├── dara_data.tcl ├── datastruct_utils.py ├── dcmdir-info-mgh ├── dcmunpack ├── deface_subject ├── defect-seg ├── dgmsocket.py ├── dicom-rename ├── dipmovie-flat.tcl ├── dmrirc.example ├── dmrirc.long.example ├── dsh ├── dt_recon ├── eccen-flat.tcl ├── eccen-views.tcl ├── epidewarp.fsl ├── extract_talairach_avi_QA.awk ├── feat2segstats ├── feat2surf ├── findsession ├── fix_subject ├── fix_subject-lh ├── fix_subject-rh ├── fix_subject_corrected ├── fix_subject_corrected-lh ├── fix_subject_corrected-rh ├── fix_subject_on_seychelles ├── fixup_mni_paths ├── flip4fsl ├── fname2ext ├── fname2stem ├── freesurfer ├── fs-flat.tcl ├── fs-make.tcl ├── fs-views.tcl ├── fs_lib_check ├── fs_spmreg.glnxa64 ├── fs_time ├── fs_tutorial_data ├── fs_update ├── fscalc ├── fscalc.fsl ├── fsfget ├── fsgd_parser.py ├── fsgdfPlot.tcl ├── fsl.5.0.2.xyztrans.sch ├── fsl_rigid_register ├── fsl_sub_mgh ├── fslregister ├── fsr-checkxopts ├── fsr-getxopts ├── fsralpha.tmp ├── fsutils.py ├── fvcompare ├── gca-apply ├── gcainit ├── gcaprepone ├── gcatrain ├── get_label_thickness ├── getfullpath ├── gnuplot.freesurfer ├── grad_unwarp ├── groupstats ├── groupstatsdiff ├── gtmseg ├── help_xml_validate ├── hgoutgoing.bash ├── inflate_subject ├── inflate_subject-lh ├── inflate_subject-rh ├── inflate_subject3 ├── inflate_subject_new ├── inflate_subject_new-lh ├── inflate_subject_new-rh ├── inflate_subject_sc ├── intcapseg ├── inu_correct_vol.csh ├── irepifitvol ├── irepifitvol.glnx64 ├── is-surface ├── isanalyze ├── isnewer ├── isnifti ├── isolate_labels.csh ├── jkgcatrain ├── kww_setup ├── label_child ├── label_elderly_subject ├── label_subject ├── label_subject_flash ├── label_subject_mixed ├── labels_disjoint ├── labels_intersect ├── labels_union ├── long_create_base_sigma ├── long_create_orig ├── long_mris_slopes ├── long_qdec_table ├── long_stats_combine ├── long_stats_slopes ├── long_stats_tps ├── long_submit_jobs ├── long_submit_postproc ├── lpcregister ├── make-segvol-table ├── make_average_subcort ├── make_average_subject ├── make_average_surface ├── make_average_volume ├── make_cortex_label ├── make_etiv ├── make_final_surfaces_corrected_subject ├── make_final_surfaces_subject ├── make_final_surfaces_subject-lh ├── make_final_surfaces_subject-rh ├── make_final_surfaces_subject_on_seychelles ├── make_final_surfaces_subject_richard ├── make_hemi_mask ├── make_quick_surfaces_subject ├── make_symmetric ├── make_upright ├── map_all_labels ├── map_all_labels-lh ├── map_central_sulcus ├── map_to_base ├── mcparams2reg ├── meanval ├── merge-labels ├── merge_stats_tables ├── mergeseg ├── minc2seqinfo ├── misc.py ├── mk-fieldsign.tcl ├── mkdefectlut ├── mkfsdist ├── mkfsdistall ├── mkfssnapshot ├── mkheadsurf ├── mkima_index.tcl ├── mkmnc_index.tcl ├── mksubjdirs ├── mksurfatlas ├── mni152reg ├── morph_only_subject ├── morph_only_subject-lh ├── morph_only_subject-rh ├── morph_rgb-lh ├── morph_rgb-rh ├── morph_subject ├── morph_subject-lh ├── morph_subject-rh ├── morph_subject_on_seychelles ├── morph_tables-lh ├── morph_tables-rh ├── morph_tables-rh.bak ├── mri-func2sph ├── mri-funcvits ├── mri-sph2surf ├── mri-structvits ├── mri_add_new_tp ├── mri_align_long.csh ├── mri_create_t2combined ├── mri_glmfit-sim ├── mri_mergelabels ├── mri_motion_correct ├── mri_motion_correct.fsl ├── mri_motion_correct.fsl.help.xml ├── mri_motion_correct2 ├── mri_nu_correct.mni ├── mri_nu_correct.mni.help.xml ├── mri_reorient_LR.csh ├── mris_preproc ├── mris_roiCircle ├── mris_volsmooth ├── ms_refine_subject ├── nmr-std-env-dev.bash ├── nmr-std-env.bash ├── nu_correct_one.csh ├── nu_correct_subject ├── numaris4-protocols.unpackcfg ├── offsetmovie.tcl ├── orientLAS ├── overlapstats2table ├── parc_atlas_jackknife_test ├── parcellate_subject ├── parcellate_subject-lh ├── parcellate_subject-rh ├── pctsurfcon ├── petsc_setup ├── phasemovie.tcl ├── plot_structure_stats.tcl ├── polar-flat.tcl ├── polar-views.tcl ├── polyorder ├── print_unique_labels.csh ├── progressbar.tcl ├── qt_setup ├── rbbr ├── rcbf-prep ├── readenv.tcl ├── real-flat.tcl ├── real-views.tcl ├── rebuild_gca_atlas.csh ├── recon-all ├── recon-all.makefile ├── reconbatchjobs ├── reg-feat2anat ├── reg-mni305.2mm ├── reg2subject ├── register.csh ├── register_child ├── register_elderly_subject ├── register_subject ├── register_subject_flash ├── register_subject_mixed ├── reinflate_subject ├── reinflate_subject-lh ├── reinflate_subject-rh ├── remove_talairach ├── renormalize_T1_subject ├── renormalize_subject ├── renormalize_subject_keep_editting ├── reregister_subject_mixed ├── rmcr ├── rtview ├── run-qdec-glm ├── saveflat.tcl ├── saveviews.tcl ├── scanseq.unpackinfo ├── segment_monkey ├── segment_subject ├── segment_subject_notal ├── segment_subject_notal2 ├── segment_subject_old_skull_strip ├── segment_subject_sc ├── segment_subject_talmgh ├── segpons ├── setdefpatchview.tcl ├── setlabelstat ├── sfa2fieldsign ├── show_tal ├── skip_long_make_checks ├── slicedelay ├── solmovie-flat.tcl ├── sphere_subject ├── sphere_subject-lh ├── sphere_subject-rh ├── spm_t_to_b ├── spmmat2register ├── spmregister ├── spmseg ├── sratio ├── stattablediff ├── stem2fname ├── subject_info.py ├── surfreg ├── tal_compare ├── talairach ├── talairach2 ├── talairach_mgh ├── talsegprob ├── tcl_setup ├── template.help.xml ├── test_fs_tutorial.csh ├── test_recon-all.csh ├── thickdiffmap ├── tkUtils.tcl ├── tkanalyse.tcl ├── tkm_common.tcl ├── tkm_dialog.tcl ├── tkm_functional.tcl ├── tkm_graph.tcl ├── tkm_wrappers.tcl ├── tkmedit.tcl ├── tkmeditfv ├── tkregister.tcl ├── tkregister2.tcl ├── tkregisterfv ├── tksurfer.tcl ├── tksurferfv ├── trac-all ├── trac-paths ├── trac-preproc ├── tractstats2table ├── twocond-flat.tcl ├── twocond-masked-views.tcl ├── twocond-views.tcl ├── unpack_ima.tcl ├── unpack_ima1.tcl ├── unpack_mnc.tcl ├── unpackimadir ├── unpackimadir2 ├── unpackmincdir ├── unpacksdcmdir ├── usbtree ├── vertexvol ├── vno_match_check ├── vol2segavg ├── vol2symsurf ├── vsm-smooth ├── vtk_setup ├── wfilemask ├── wm-anat-snr ├── wmedits2surf ├── wmsaseg ├── wrappers.tcl ├── xcerebralseg ├── xcorr ├── xfmrot ├── xhemi-tal ├── xhemireg └── xsanatreg ├── scuba ├── Array2.cpp ├── Array2.h ├── Broadcaster.cpp ├── Broadcaster.h ├── CMakeLists.txt ├── ChartWindow.cpp ├── ChartWindow.h ├── DataCollection.cpp ├── DataCollection.h ├── DataManager.cpp ├── DataManager.h ├── DebugReporter.cpp ├── DebugReporter.h ├── IDTracker.h ├── InputState.cpp ├── InputState.h ├── Layer.cpp ├── Layer.h ├── Listener.cpp ├── Listener.h ├── Makefile.am ├── Matrix44.cpp ├── Matrix44.h ├── Path.cpp ├── Path.h ├── PathManager.cpp ├── PathManager.h ├── Point2.h ├── Point3.h ├── PreferencesManager.cpp ├── PreferencesManager.h ├── ProgressDisplayManager.cpp ├── ProgressDisplayManager.h ├── Scuba-impl.h ├── ScubaColorLUT.cpp ├── ScubaColorLUT.h ├── ScubaDataCollectionFactory.cpp ├── ScubaDataCollectionFactory.h ├── ScubaFrame.cpp ├── ScubaFrame.h ├── ScubaGlobalPreferences.cpp ├── ScubaGlobalPreferences.h ├── ScubaKeyCombo.cpp ├── ScubaKeyCombo.h ├── ScubaLayer2DMRI.cpp ├── ScubaLayer2DMRI.h ├── ScubaLayer2DMRIS.cpp ├── ScubaLayer2DMRIS.h ├── ScubaLayerFactory.cpp ├── ScubaLayerFactory.h ├── ScubaMultiFrameVolumeChart.cpp ├── ScubaMultiFrameVolumeChart.h ├── ScubaROI.cpp ├── ScubaROI.h ├── ScubaROIVolume.cpp ├── ScubaROIVolume.h ├── ScubaToolState.cpp ├── ScubaToolState.h ├── ScubaTransform.cpp ├── ScubaTransform.h ├── ScubaView.cpp ├── ScubaView.h ├── ScubaVolumeROIIntensityChart.cpp ├── ScubaVolumeROIIntensityChart.h ├── ScubaWindowToRASTranslator.cpp ├── ScubaWindowToRASTranslator.h ├── SegmentationVolumeReport.cpp ├── SegmentationVolumeReport.h ├── ShortestPathFinder.cpp ├── ShortestPathFinder.h ├── SurfaceCollection.cpp ├── SurfaceCollection.h ├── TclChartWindow.cpp ├── TclChartWindow.h ├── TclChartWindow.tcl ├── TclCommandManager.cpp ├── TclCommandManager.h ├── TclProgressDisplayManager.cpp ├── TclProgressDisplayManager.h ├── TclScubaKeyCombo.cpp ├── TclScubaKeyCombo.h ├── Timer.cpp ├── Timer.h ├── ToglManager.cpp ├── ToglManager.h ├── Transform44.cpp ├── Transform44.h ├── UndoManager.cpp ├── UndoManager.h ├── Utilities.cpp ├── Utilities.h ├── VectorOps.cpp ├── VectorOps.h ├── View.cpp ├── View.h ├── ViewState.cpp ├── ViewState.h ├── Volume3.cpp ├── Volume3.h ├── VolumeCollection.cpp ├── VolumeCollection.h ├── WindowFrame.cpp ├── WindowFrame.h ├── development_notes.txt ├── histolabel.tcl ├── makeoprofile.sh ├── makeprofile.sh ├── notes.txt ├── scuba.cpp ├── scuba.tcl ├── scuba_glut.tcl ├── string_fixed.h ├── testCleanup.csh ├── testLUT.lut ├── testSegmentationVolumeReport-correct.txt ├── testSegmentationVolumeReportIntReport-correct.txt ├── testSetup.csh ├── test_Broadcaster.cpp ├── test_CoordTimer.cpp ├── test_DataCollection.cpp ├── test_DataManager.cpp ├── test_IDTracker.cpp ├── test_Matrix44.cpp ├── test_Path.cpp ├── test_PreferencesManager.cpp ├── test_RASToVoxel.cpp ├── test_ScubaColorLUT.cpp ├── test_ScubaDataCollections.cpp ├── test_ScubaFrame.cpp ├── test_ScubaFrame.tcl ├── test_ScubaKeyCombo.cpp ├── test_ScubaLayer2DMRI.cpp ├── test_ScubaLayers.cpp ├── test_ScubaLayers.tcl ├── test_ScubaROI.cpp ├── test_ScubaROIVolume.cpp ├── test_ScubaTransform.cpp ├── test_ScubaView.cpp ├── test_SegmentationVolumeReport.cpp ├── test_ShortestPathFinder.cpp ├── test_SurfaceCollection.cpp ├── test_TclChartWindow.cpp ├── test_TclCommandManager.cpp ├── test_TclCommandManager.tcl ├── test_TclScubaKeyCombo.cpp ├── test_ToglManager.cpp ├── test_ToglManager.tcl ├── test_Transform44.cpp ├── test_UndoManager.cpp ├── test_Utilities.cpp ├── test_VectorOps.cpp ├── test_Volume3.cpp ├── test_VolumeCollection.cpp ├── test_VolumeHistogram.cpp ├── test_VolumeHistogram.mak ├── test_data.tar.gz ├── test_gltexture.cpp ├── test_gltexture2d.cpp ├── test_layers.tcl ├── test_tkUtils.tcl ├── test_view.tcl ├── tkcon.tcl ├── togl.c ├── togl.h ├── wiki-ScubaGuide-ControlPoints.txt ├── wiki-ScubaGuide-GUI.txt ├── wiki-ScubaGuide-Segmentations.txt ├── wiki-ScubaGuide-Transforms.txt ├── wiki-ScubaGuide.txt ├── wiki_Scuba2DSurfaces.txt ├── wiki_ScubaAnatomicalVolumes.txt ├── wiki_ScubaControlPoints.txt ├── wiki_ScubaFunctionalVolumes.txt ├── wiki_ScubaScripting.txt ├── wiki_ScubaSegmentationVolumes.txt ├── wiki_ScubaTools.txt └── wiki_ScubaVolumeROIs.txt ├── scuba2 ├── Broadcaster.cxx ├── Broadcaster.h ├── CMakeLists.txt ├── IDTracker.cxx ├── IDTracker.h ├── Listener.cxx ├── Listener.h ├── Makefile.am ├── ScubaCollectionProperties.h ├── ScubaCollectionPropertiesDTI.h ├── ScubaCollectionPropertiesMRI.h ├── ScubaCollectionPropertiesMRIS.h ├── ScubaCollectionPropertiesODF.h ├── ScubaCollectionPropertiesPath.h ├── ScubaIcons.txt ├── ScubaInfoItem.cxx ├── ScubaInfoItem.h ├── ScubaLibInit.cxx ├── ScubaLibInit.data ├── ScubaMain.cxx ├── ScubaViewProperties.h ├── development_notes.txt ├── string_fixed.h ├── vtkKWScubaApp.cxx ├── vtkKWScubaApp.h ├── vtkKWScubaApplicationSettingsInterface.cxx ├── vtkKWScubaApplicationSettingsInterface.h ├── vtkKWScubaLayer.cxx ├── vtkKWScubaLayer.h ├── vtkKWScubaLayer2DDTI.cxx ├── vtkKWScubaLayer2DDTI.h ├── vtkKWScubaLayer2DMRI.cxx ├── vtkKWScubaLayer2DMRI.h ├── vtkKWScubaLayer2DMRIS.cxx ├── vtkKWScubaLayer2DMRIS.h ├── vtkKWScubaLayer2DPath.cxx ├── vtkKWScubaLayer2DPath.h ├── vtkKWScubaLayer3DDTI.cxx ├── vtkKWScubaLayer3DDTI.h ├── vtkKWScubaLayer3DMRI.cxx ├── vtkKWScubaLayer3DMRI.h ├── vtkKWScubaLayer3DMRIS.cxx ├── vtkKWScubaLayer3DMRIS.h ├── vtkKWScubaLayer3DODF.cxx ├── vtkKWScubaLayer3DODF.h ├── vtkKWScubaLayer3DPath.cxx ├── vtkKWScubaLayer3DPath.h ├── vtkKWScubaLayerCollection.cxx ├── vtkKWScubaLayerCollection.h ├── vtkKWScubaLayerCollectionDTI.cxx ├── vtkKWScubaLayerCollectionDTI.h ├── vtkKWScubaLayerCollectionMRI.cxx ├── vtkKWScubaLayerCollectionMRI.h ├── vtkKWScubaLayerCollectionMRIS.cxx ├── vtkKWScubaLayerCollectionMRIS.h ├── vtkKWScubaLayerCollectionODF.cxx ├── vtkKWScubaLayerCollectionODF.h ├── vtkKWScubaLayerCollectionPath.cxx ├── vtkKWScubaLayerCollectionPath.h ├── vtkKWScubaTool.cxx ├── vtkKWScubaTool.h ├── vtkKWScubaToolEdit2DMRI.cxx ├── vtkKWScubaToolEdit2DMRI.h ├── vtkKWScubaToolNavigate.cxx ├── vtkKWScubaToolNavigate.h ├── vtkKWScubaView.cxx ├── vtkKWScubaView.h ├── vtkKWScubaWindow.cxx ├── vtkKWScubaWindow.h ├── vtkScubaInteractorStyle.cxx ├── vtkScubaInteractorStyle.h └── vtkScubaInteractorStyleTcl.cxx ├── setup_configure ├── spherical_stats ├── CMakeLists.txt ├── Makefile.am └── spherical_stats.c ├── spline3 ├── Makefile.am ├── README.txt ├── Spline3.h └── Spline3_test.cpp ├── stat_normalize ├── CMakeLists.txt ├── Makefile.am └── stat_normalize.c ├── stim_polar ├── CMakeLists.txt ├── Makefile.am └── stim_polar.c ├── svm-lib ├── CMakeLists.txt ├── INSTALL_README.txt ├── Makefile.am ├── README.txt ├── classification_setup.example ├── svm-data-param.cpp ├── svm-data-param.h ├── svm-element-type.h ├── svm-element-types.h ├── svm-io-format.h ├── svm-kernel-param.h ├── svm-kernel.cpp ├── svm-kernel.h ├── svm-lib-c.cpp ├── svm-lib-c.h ├── svm-lib.cpp ├── svm-lib.h ├── svm-matrix.h ├── svm-model.cpp ├── svm-model.h ├── svm-param.cpp ├── svm-param.h ├── svm-pr-loqo.c ├── svm-pr-loqo.h ├── svm-similarity.cpp ├── svm-similarity.h ├── svm-sketch.cpp ├── svm-sketch.h ├── svm-vector-types.h └── svm-vector.h ├── swi_processing ├── Makefile.am ├── Readme.md ├── cmd_line_interface.cpp ├── cmd_line_interface.h ├── meta_process_swi.sh ├── process_swi.sh ├── swi_preprocess.cpp └── swi_process.cpp ├── talairach_afd ├── CMakeLists.txt ├── Makefile.am ├── bad_tal.txt ├── bad_tal.xfm ├── good_tal.txt ├── good_tal.xfm ├── talairach_afd.c ├── talairach_afd.help.xml └── test_tal_afd ├── talairach_avi ├── 3T18yoSchwartzReactN32_as_orig.4dfp.hdr ├── 3T18yoSchwartzReactN32_as_orig.4dfp.ifh ├── 3T18yoSchwartzReactN32_as_orig.4dfp.img ├── 3T18yoSchwartzReactN32_as_orig.4dfp.img.rec ├── 3T18yoSchwartzReactN32_as_orig.4dfp.mat ├── 3T18yoSchwartzReactN32_as_orig.lst ├── 4dfptoanalyze.c ├── 711-2B_as_mni_average_305.4dfp.hdr ├── 711-2B_as_mni_average_305.4dfp.ifh ├── 711-2B_as_mni_average_305.4dfp.img ├── 711-2B_as_mni_average_305.4dfp.img.rec ├── 711-2B_as_mni_average_305_mask.4dfp.hdr ├── 711-2B_as_mni_average_305_mask.4dfp.ifh ├── 711-2B_as_mni_average_305_mask.4dfp.img ├── 711-2B_as_mni_average_305_mask.4dfp.img.rec ├── 711-2C_as_mni_average_305.4dfp.hdr ├── 711-2C_as_mni_average_305.4dfp.ifh ├── 711-2C_as_mni_average_305.4dfp.img ├── 711-2C_as_mni_average_305.4dfp.img.rec ├── 711-2C_as_mni_average_305.4dfp.mat ├── ANALYZE.h ├── CMakeLists.txt ├── Getifh.c ├── Getifh.h ├── Inithdr.c ├── Makefile.am ├── RLB700_atlas_as_orig.4dfp.hdr ├── RLB700_atlas_as_orig.4dfp.ifh ├── RLB700_atlas_as_orig.4dfp.img ├── RLB700_atlas_as_orig.4dfp.img.rec ├── RLB700_preprocessing_statistics.pdf ├── SVIP_Adult_Comp_N24_as_orig.4dfp.hdr ├── SVIP_Adult_Comp_N24_as_orig.4dfp.ifh ├── SVIP_Adult_Comp_N24_as_orig.4dfp.img ├── SVIP_Adult_Comp_N24_as_orig.4dfp.img.rec ├── SVIP_Adult_Control_N12_as_orig.4dfp.hdr ├── SVIP_Adult_Control_N12_as_orig.4dfp.ifh ├── SVIP_Adult_Control_N12_as_orig.4dfp.img ├── SVIP_Adult_Control_N12_as_orig.4dfp.img.rec ├── SVIP_Adult_Patient_N12_as_orig.4dfp.hdr ├── SVIP_Adult_Patient_N12_as_orig.4dfp.ifh ├── SVIP_Adult_Patient_N12_as_orig.4dfp.img ├── SVIP_Adult_Patient_N12_as_orig.4dfp.img.rec ├── SVIP_Child_Comp_N24_as_orig.4dfp.hdr ├── SVIP_Child_Comp_N24_as_orig.4dfp.ifh ├── SVIP_Child_Comp_N24_as_orig.4dfp.img ├── SVIP_Child_Comp_N24_as_orig.4dfp.img.rec ├── SVIP_Full_Comp_N48_as_orig.4dfp.hdr ├── SVIP_Full_Comp_N48_as_orig.4dfp.ifh ├── SVIP_Full_Comp_N48_as_orig.4dfp.img ├── SVIP_Full_Comp_N48_as_orig.4dfp.img.rec ├── SVIP_Young_Control_N12_as_orig.4dfp.hdr ├── SVIP_Young_Control_N12_as_orig.4dfp.ifh ├── SVIP_Young_Control_N12_as_orig.4dfp.img ├── SVIP_Young_Control_N12_as_orig.4dfp.img.rec ├── SVIP_Young_Patient_N12_as_orig.4dfp.hdr ├── SVIP_Young_Patient_N12_as_orig.4dfp.ifh ├── SVIP_Young_Patient_N12_as_orig.4dfp.img ├── SVIP_Young_Patient_N12_as_orig.4dfp.img.rec ├── analyzeto4dfp.c ├── brec ├── brec.awk ├── cflip.c ├── cgauss3d.c ├── cgauss3dd.c ├── compute_vox2vox.c ├── conc.c ├── conc.h ├── eigen.f ├── endianio.c ├── endianio.h ├── ffind.f ├── fftsol.f ├── fimgreg.f ├── flip_4dfp.c ├── ft4imgn.f ├── ft4imgo.f ├── ft4ixyz.f ├── gauss_4dfp.c ├── ifh.h ├── ifh2hdr.c ├── imgpad.f ├── imgreg_4dfp.c ├── imgvalm.f ├── imgvalx.f ├── librms.h ├── matopr.f ├── mni_average_305.4dfp.hdr ├── mni_average_305.4dfp.ifh ├── mni_average_305.4dfp.img ├── mni_average_305.4dfp.img.rec ├── mpr2mni305 ├── nu.mgz ├── param6opr.f ├── polfit.f ├── rec.c ├── rec.h ├── reference-tal.lta ├── reference-tal.xfm ├── set_rnan.f ├── spline3dvgh.f ├── t4_sub.f ├── t4img_4dfp ├── t4imgs_4dfp.c ├── t4scale.c ├── tal_QC_AZS ├── talairach_avi ├── talairach_avi.help.xml ├── test_libg2c ├── test_talairach_avi ├── to_711-2B.f └── zero_lt_4dfp.c ├── template ├── CMakeLists.txt ├── Makefile.am ├── main_template.c ├── mri_elastic_energy.c ├── mri_multiscale_segment.c └── template.c ├── test_makevol ├── CMakeLists.txt ├── Makefile.am └── main.c ├── test_tm ├── BatchSystem.lua ├── Hermes.db ├── Info.txt ├── nightly.bash ├── regressiontests │ ├── conv1d │ │ ├── conv1d.lua │ │ ├── float.tdesc │ │ ├── short.tdesc │ │ └── uchar.tdesc │ ├── convgauss │ │ ├── convgauss.tdesc │ │ ├── float.tdesc │ │ ├── gauss.lua │ │ ├── short.tdesc │ │ └── uchar.tdesc │ ├── gcam │ │ ├── NetCDF-IO │ │ │ ├── ncio.tdesc │ │ │ └── writetest.config │ │ ├── addstatus │ │ │ ├── addstatus.config │ │ │ └── gcamaddstatus.tdesc │ │ ├── applygradient │ │ │ ├── applygradient.config │ │ │ └── gcamapplygradient.tdesc │ │ ├── clear │ │ │ ├── clear.config │ │ │ └── gcamclear.tdesc │ │ ├── computemetricproperties │ │ │ ├── cmp.config │ │ │ └── gcamcmp.tdesc │ │ ├── jacobenergy │ │ │ └── gcamjacobenergy.tdesc │ │ ├── jacobterm │ │ │ ├── gcamjacobterm.tdesc │ │ │ └── jacobterm.config │ │ ├── labelenergy │ │ │ └── gcamlabelenergy.tdesc │ │ ├── labelterm │ │ │ ├── copydeltas │ │ │ │ ├── gcamlabeltermcopydeltas.tdesc │ │ │ │ └── labelcopydeltas.config │ │ │ ├── finalupdate │ │ │ │ ├── gcamlabeltermfinal.tdesc │ │ │ │ └── labelfinal.config │ │ │ ├── full │ │ │ │ ├── gcamlabelterm.tdesc │ │ │ │ └── labelterm.config │ │ │ ├── mainloop │ │ │ │ ├── gcamlabeltermmainloop.tdesc │ │ │ │ └── labelmainloop.config │ │ │ ├── postantconsist │ │ │ │ ├── gcamlabeltermpostantconsist.tdesc │ │ │ │ └── labelpostantconsist.config │ │ │ └── removeoutliers │ │ │ │ ├── gcamlabeltermremoveoutliers.tdesc │ │ │ │ └── labelremoveoutliers.config │ │ ├── loglikelihoodenergy │ │ │ └── gcamlle.tdesc │ │ ├── loglikelihoodterm │ │ │ ├── gcamllterm.tdesc │ │ │ └── llterm.config │ │ ├── removesingularities │ │ │ ├── gcamremovesingularities.tdesc │ │ │ └── removesingularities.config │ │ ├── removestatus │ │ │ ├── gcamremovestatus.tdesc │ │ │ └── removestatus.config │ │ ├── smoothgradient │ │ │ ├── gcamsmoothgradient.tdesc │ │ │ └── smoothgradient.config │ │ ├── smoothnessenergy │ │ │ └── gcamsmoothnessenergy.tdesc │ │ ├── smoothnessterm │ │ │ ├── gcamsmoothnessterm.tdesc │ │ │ └── smoothnessterm.config │ │ └── undogradient │ │ │ ├── gcamundogradient.tdesc │ │ │ └── undogradient.config │ ├── mrilabel │ │ ├── MarkLabelBorderVoxels │ │ │ └── mlbv.tdesc │ │ └── VoxInLabelPartialVolume │ │ │ └── vilpv.tdesc │ ├── mrimean │ │ ├── float.tdesc │ │ ├── mean.lua │ │ ├── mean.tdesc │ │ ├── short.tdesc │ │ └── uchar.tdesc │ ├── mrivol2vol │ │ ├── float.tdesc │ │ ├── identity.fsl │ │ ├── identity.tdesc │ │ ├── short.tdesc │ │ ├── transform1.fsl │ │ ├── translation1.fsl │ │ ├── translation2.fsl │ │ ├── uchar.tdesc │ │ └── vol2vol.lua │ ├── registration │ │ └── linear │ │ │ ├── linearreg.tdesc │ │ │ ├── lta.norm.config │ │ │ └── lta.nu.config │ └── volumegpu │ │ └── copy │ │ ├── volumecopy.tdesc │ │ └── volumediff.pl ├── scripts │ ├── build.bash │ ├── cvsupdate.bash │ └── inputs.bash └── tools │ ├── doubleFileDiff.pl │ ├── freesurfer.lua │ ├── gcamMultiDiff.pl │ ├── ltaMultiDiff.pl │ ├── mridiff.pl │ └── mripairdiff.pl ├── test_window_env ├── CMakeLists.txt ├── Makefile.am └── test_window_env.c ├── tetgen ├── CMakeLists.txt ├── LICENSE ├── Makefile.am ├── README ├── README-MGH ├── example.poly ├── predicates.cxx ├── test_tetgen ├── tetgen.cxx ├── tetgen.h ├── x86_64-example.1.ele ├── x86_64-example.1.face └── x86_64-example.1.node ├── tiff ├── Makefile.am ├── VERSION ├── icon_folder.tif ├── license.tiff.txt ├── port.h ├── t4.h ├── test_tiff.c ├── tif_aux.c ├── tif_close.c ├── tif_codec.c ├── tif_color.c ├── tif_compress.c ├── tif_dir.c ├── tif_dir.h ├── tif_dirinfo.c ├── tif_dirread.c ├── tif_dirwrite.c ├── tif_dumpmode.c ├── tif_error.c ├── tif_extension.c ├── tif_flush.c ├── tif_getimage.c ├── tif_jpeg.c ├── tif_luv.c ├── tif_lzw.c ├── tif_next.c ├── tif_ojpeg.c ├── tif_open.c ├── tif_packbits.c ├── tif_pixarlog.c ├── tif_predict.c ├── tif_predict.h ├── tif_print.c ├── tif_read.c ├── tif_strip.c ├── tif_swab.c ├── tif_thunder.c ├── tif_tile.c ├── tif_unix.c ├── tif_version.c ├── tif_warning.c ├── tif_write.c ├── tif_zip.c ├── tiff.h ├── tiff_test ├── tiffcomp.h ├── tiffconf.h ├── tiffio.h ├── tiffiop.h ├── tiffvers.h └── uvcode.h ├── tkmedit ├── CMakeLists.txt ├── Makefile.am ├── development_notes.txt ├── tkmDisplayArea.c ├── tkmDisplayArea.h ├── tkmFunctionalVolume.c ├── tkmFunctionalVolume.h ├── tkmMeditWindow.c ├── tkmMeditWindow.h ├── tkmedit.c └── tkmedit.h ├── tkregister2 ├── CMakeLists.txt ├── Makefile.am ├── cmdl │ ├── CMakeLists.txt │ └── Makefile.am └── tkregister2.c ├── tksurfer ├── CMakeLists.txt ├── Makefile.am ├── development_notes.txt └── tksurfer.c ├── travis_make.sh ├── trc ├── ByteSwap.h ├── ErrorCode.h ├── Makefile.am ├── TrackExporter.h ├── TrackIO.cxx ├── TrackIO.h ├── bite.cxx ├── bite.h ├── blood.cxx ├── blood.h ├── coffin.cxx ├── coffin.h ├── dmri_forrest.cxx ├── dmri_group.cxx ├── dmri_mergepaths.cxx ├── dmri_motion.cxx ├── dmri_paths.cxx ├── dmri_pathstats.cxx ├── dmri_spline.cxx ├── dmri_train.cxx ├── dmri_trk2trk.cxx ├── dmri_vox2vox.cxx ├── forrest.cxx ├── forrest.h ├── spline.cxx ├── spline.h ├── vial.cxx └── vial.h ├── tridec ├── CMakeLists.txt ├── Makefile.am └── tridec.c ├── unix ├── CMakeLists.txt ├── Makefile.am ├── cuserid.c ├── ftime.c ├── glStub.c ├── lwpproto.h ├── oglutil.c ├── oglutil.h ├── texfont.c ├── unix_thread.c ├── windiag.c ├── xvmri.c ├── xvmri.h ├── xvutil.c ├── xvutil.h ├── xwin.c ├── xwin.h ├── xwindow.c └── xwindow.h ├── utils ├── Bruker.c ├── DICOMRead.c ├── MARS_DT_Boundary.c ├── MRIio_old.c ├── Makefile.am ├── NrrdIO │ ├── 754.c │ ├── Makefile.am │ ├── accessors.c │ ├── array.c │ ├── arraysNrrd.c │ ├── axis.c │ ├── biffbiff.c │ ├── comment.c │ ├── copyright.NrrdIO │ ├── defaultsNrrd.c │ ├── dio.c │ ├── encoding.c │ ├── encodingAscii.c │ ├── encodingBzip2.c │ ├── encodingGzip.c │ ├── encodingHex.c │ ├── encodingRaw.c │ ├── endianAir.c │ ├── endianNrrd.c │ ├── enum.c │ ├── enumsNrrd.c │ ├── format.c │ ├── formatEPS.c │ ├── formatNRRD.c │ ├── formatPNG.c │ ├── formatPNM.c │ ├── formatText.c │ ├── formatVTK.c │ ├── gzio.c │ ├── keyvalue.c │ ├── methodsNrrd.c │ ├── miscAir.c │ ├── mop.c │ ├── parseAir.c │ ├── parseNrrd.c │ ├── qnanhibit.c │ ├── read.c │ ├── reorder.c │ ├── sampleIO.c │ ├── sane.c │ ├── simple.c │ ├── string.c │ ├── subset.c │ └── write.c ├── Progname.c ├── affinegpu.cu ├── afni.c ├── annotation.c ├── art1.c ├── artmap.c ├── aseg_edit_svm.c ├── autoencoder.c ├── backprop.c ├── bfileio.c ├── box.c ├── cephes │ ├── Makefile.am │ ├── bdtr.c │ ├── chdtr.c │ ├── const.c │ ├── fdtr.c │ ├── gamma.c │ ├── igam.c │ ├── igami.c │ ├── incbet.c │ ├── incbi.c │ ├── mtherr.c │ ├── ndtr.c │ ├── ndtri.c │ ├── polevl.c │ └── stdtr.c ├── chklc.c ├── chronometer.c ├── chronometerpp.cpp ├── class_array.c ├── cluster.c ├── cma.c ├── cmat.c ├── cmdargs.c ├── colortab.c ├── connectcomp.c ├── corio.c ├── cpputils.cpp ├── ctrpoints.c ├── cudatypeutils.cu ├── cvector.c ├── dcdflib.c ├── dct.c ├── density.c ├── devicemanagement.cu ├── diag.c ├── diffuse.c ├── dti.c ├── dtk.fs.c ├── error.c ├── evschutils.c ├── fcd.c ├── fftutils.c ├── field_code.c ├── filter.c ├── fio.c ├── flash.c ├── fmarchmesh.c ├── fmriutils.c ├── fsPrintHelp.c ├── fs_cost_function.cpp ├── fs_lbfgs.cpp ├── fs_lbfgs_observer.cpp ├── fs_lbfgs_subject.cpp ├── fs_powell.cpp ├── fsenv.c ├── fsglm.c ├── fsinit.c ├── gca.c ├── gcaboundary.c ├── gcalinearnode.cpp ├── gcalinearprior.cpp ├── gcamcomputegradient_cuda.cu ├── gcamfots_cuda.cu ├── gcamorph.c ├── gcamorphcpu.cpp ├── gcamorphenergygpu.cu ├── gcamorphgpu.cu ├── gcamorphtermgpu.cu ├── gcamorphtestutils.cpp ├── gcamregisterlevel_cuda.cu ├── gcamregisterpipeline_cuda.cu ├── gcanodegpu.cu ├── gcapriorgpu.cu ├── gcarray.c ├── gcasgpu.cu ├── gcautils.cpp ├── gclass.c ├── gcsa.c ├── getdelim.c ├── getline.c ├── gifti_io.c ├── gifti_local.c ├── gifti_test.c ├── gifti_test.h ├── gifti_tool.c ├── gifti_tool.h ├── gifti_xml.c ├── gtm.c ├── gw_ic2562.c ├── gw_utils.c ├── handle.c ├── heap.c ├── hippo.c ├── histo.c ├── ic12.c ├── ic163842.c ├── ic2562.c ├── ic42.c ├── ic642.c ├── icosahedron.c ├── image.c ├── imageio.c ├── imautils.c ├── intensity_eig.c ├── inverse.c ├── ipmpar.c ├── kernel.c ├── kinput.c ├── label.c ├── lpafile.c ├── machine.c ├── matfile.c ├── matrix.c ├── mgh_filter.c ├── mgh_matrix.c ├── min_heap.c ├── mincutils.c ├── minmaxrc.c ├── morph.c ├── mosaic.c ├── mri.c ├── mri2.c ├── mriBSpline.c ├── mriFunctionalDataAccess.c ├── mriHeadPointList.c ├── mriSurface.c ├── mriTransform.c ├── mriVolume.c ├── mri_conform.c ├── mri_fastmarching.cpp ├── mri_identify.c ├── mri_level_set.c ├── mri_tess.c ├── mri_topology.c ├── mri_transform.c ├── mriclass.c ├── mriconvolve_cuda.cu ├── mricurv.c ├── mrifilter.c ├── mriflood.c ├── mriframegpu.cu ├── mrihisto.c ├── mriio.c ├── mriio_nrrd.c ├── mriio_nrrd_itk.cpp ├── mrilabels_cuda.cu ├── mrimean_cuda.cu ├── mrimorph.c ├── mrinorm.c ├── mripolv.c ├── mriprob.c ├── mris_compVolFrac.c ├── mrisbiorthogonalwavelets.c ├── mrisegment.c ├── mriset.c ├── mrishash.c ├── mrisp.c ├── mrisurf.c ├── mrisurf_cuda.cu ├── mrisutils.c ├── mrivol2vol_cuda.cu ├── mrivoxel.c ├── nifti1_io.c ├── numerics.cpp ├── offset.c ├── path.c ├── pdf.c ├── pgmstubs.c ├── prime.c ├── queue.c ├── randomfields.c ├── rbf.c ├── rbm.c ├── rec.c ├── region.c ├── registerio.c ├── resample.c ├── rescale.c ├── retinotopy.c ├── rfa.c ├── rforest.c ├── rfutils.c ├── selxavgio.c ├── sig.c ├── signa.c ├── sse_mathfun_test.c ├── stats.c ├── stc.c ├── surfcluster.c ├── svm.c ├── tags.c ├── talairachex.c ├── test │ ├── ANN.h │ ├── ANNperf.h │ ├── ANNx.h │ ├── MRISresampleOntoSphere.cpp │ ├── MRISwaveletsTransform.cpp │ ├── Makefile.am │ ├── checkanalyze.cpp │ ├── cleanup_test_data │ ├── difftool.cpp │ ├── extest.cpp │ ├── fmarching3dnband.c │ ├── fmarching3dnband.h │ ├── gcaread.cpp │ ├── heap_mesh.c │ ├── heap_mesh.h │ ├── i2rtest.cpp │ ├── icotest.cpp │ ├── inftest.cpp │ ├── mghxform.cpp │ ├── mnitest.cpp │ ├── mri_apply_EM_mask.c │ ├── mri_apply_INU.c │ ├── mri_compute_all_CNR.c │ ├── mri_compute_stats.c │ ├── mri_concatenate_lta.c │ ├── mri_copy_params.cpp │ ├── mri_edit_wm.c │ ├── mri_extract.c │ ├── mri_flip2analyze.cpp │ ├── mri_fslmat_to_lta.c │ ├── mri_ms_LDA.c │ ├── mri_ms_compute_CNR.c │ ├── mri_ms_gca_EM.c │ ├── mri_remove.cpp │ ├── mri_transform_to_COR.c │ ├── mri_uchar.cpp │ ├── mris_compute_thickness.cpp │ ├── mris_diff.cpp │ ├── mris_diff_on_surface.c │ ├── mris_gethires.cpp │ ├── mris_indirect_morph.cpp │ ├── mrishash │ │ ├── Makefile.am │ │ ├── mrishash_demo_100_find_coverage.c │ │ ├── mrishash_demo_200_mht_hatch.c │ │ ├── mrishash_test_100_find_tests.c │ │ └── mrishash_test_200_intersect.c │ ├── rastest.cpp │ ├── sc_test.c │ ├── setup_test_data │ ├── surf2surf.cpp │ ├── surftest.cpp │ ├── test_c_nr_wrapper.c │ ├── test_data.tar.gz │ ├── test_matrix.cpp │ ├── test_mri_identify.cpp │ ├── test_mriio.cpp │ ├── test_nr_wrapper.cpp │ ├── testcolortab.c │ ├── testcras.cpp │ ├── testm3d.cpp │ ├── tiff_write_image.c │ ├── tixtest.c │ ├── vltest.cpp │ └── xtqli.c ├── thread.c ├── timer.c ├── transform.c ├── tritri.c ├── tukey.c ├── utils.c ├── vecvolgpu.cu ├── version.c ├── vlabels.c ├── volcluster.c ├── voxlist.c ├── x3DList.c ├── xDebug.c ├── xGLutWindow.c ├── xGrowableArray.c ├── xList.c ├── xSparseVolume.c ├── xTypes.c ├── xUndoList.c ├── xUtilities.c ├── xVoxel.c ├── xmlToHtml.c └── znzlib.c ├── utilscpp ├── CMakeLists.txt ├── Makefile.am ├── face.cpp ├── fastloop.cpp ├── globals.cpp ├── loop.cpp ├── mris_fastmarching.cpp ├── mris_topology.cpp ├── patchdisk.cpp ├── segment.cpp ├── surface.cpp ├── test │ ├── CMakeLists.txt │ ├── Makefile.am │ └── ctest.c └── vertex.cpp ├── vtkfsio ├── CMakeLists.txt ├── Makefile.am ├── lh.vtkFSSurfaceWriterTestFile ├── vtkFSSurfaceLabelSource.cxx ├── vtkFSSurfaceLabelSource.h ├── vtkFSSurfaceScalarsReader.cxx ├── vtkFSSurfaceScalarsReader.h ├── vtkFSSurfaceSource.cxx ├── vtkFSSurfaceSource.h ├── vtkFSSurfaceWriter.cxx ├── vtkFSSurfaceWriter.h ├── vtkFSSurfaceWriterTester.cxx ├── vtkFSVolumeSource.cxx └── vtkFSVolumeSource.h ├── vtkutils ├── CMakeLists.txt ├── IconLoader.cxx ├── IconLoader.h ├── IconLoaderTest.cxx ├── IconLoaderTest.h ├── IconLoaderTestIcons.txt ├── Makefile.am ├── RgbatransferfunctioneditortesterLibInit.data ├── testIconLoader ├── vtkArrowPipeline.cxx ├── vtkArrowPipeline.h ├── vtkArrowPipelineTester.cxx ├── vtkFDTensorGlyph.cxx ├── vtkFDTensorGlyph.h ├── vtkFreesurferLookupTable.cxx ├── vtkFreesurferLookupTable.h ├── vtkInflatePolyData.cxx ├── vtkInflatePolyData.h ├── vtkKWBltGraph.cxx ├── vtkKWBltGraph.h ├── vtkKWProgressDialog.cxx ├── vtkKWProgressDialog.h ├── vtkKWRGBATransferFunctionEditor.cxx ├── vtkKWRGBATransferFunctionEditor.h ├── vtkKWRGBATransferFunctionEditorTester-scalars.mgh ├── vtkKWRGBATransferFunctionEditorTester.cxx ├── vtkKWRGBATransferFunctionEditorTester.h ├── vtkODFGlyph.cxx ├── vtkODFGlyph.h ├── vtkRGBAColorTransferFunction.cxx ├── vtkRGBAColorTransferFunction.h ├── vtkRGBATransferFunction.cxx └── vtkRGBATransferFunction.h ├── vxl.cmake ├── x86cpucaps └── cpucaps └── xml2 ├── DOCBparser.c ├── HTMLparser.c ├── HTMLtree.c ├── Makefile.am ├── SAX.c ├── SAX2.c ├── acconfig.h ├── c14n.c ├── catalog.c ├── chvalid.c ├── config.h ├── debugXML.c ├── dict.c ├── elfgcchack.h ├── encoding.c ├── entities.c ├── error.c ├── globals.c ├── hash.c ├── legacy.c ├── libxml.h ├── libxml ├── DOCBparser.h ├── HTMLparser.h ├── HTMLtree.h ├── SAX.h ├── SAX2.h ├── c14n.h ├── catalog.h ├── chvalid.h ├── debugXML.h ├── dict.h ├── encoding.h ├── entities.h ├── globals.h ├── hash.h ├── list.h ├── nanoftp.h ├── nanohttp.h ├── parser.h ├── parserInternals.h ├── pattern.h ├── relaxng.h ├── schemasInternals.h ├── schematron.h ├── threads.h ├── tree.h ├── uri.h ├── valid.h ├── xinclude.h ├── xlink.h ├── xmlIO.h ├── xmlautomata.h ├── xmlerror.h ├── xmlexports.h ├── xmlmemory.h ├── xmlmodule.h ├── xmlreader.h ├── xmlregexp.h ├── xmlsave.h ├── xmlschemas.h ├── xmlschemastypes.h ├── xmlstring.h ├── xmlunicode.h ├── xmlversion.h ├── xmlwriter.h ├── xpath.h ├── xpathInternals.h └── xpointer.h ├── license.xml2.txt ├── list.c ├── nanoftp.c ├── nanohttp.c ├── parser.c ├── parserInternals.c ├── pattern.c ├── relaxng.c ├── runtest.c ├── schematron.c ├── test └── threads │ ├── a.example.org.xml 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