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Generating docs for compound anatomist::CommandContext...
Generating docs for compound anatomist::ErrorMessage...
Generating docs for compound anatomist::OutputEvent...
Generating docs for compound anatomist::OutputEventFilter...
Generating docs for compound anatomist::EventHandler...
Generating docs for compound anatomist::APipeReader...
Generating docs for compound anatomist::Unserializer...
Generating docs for compound anatomist::CommandServer...
Generating docs for compound anatomist::Command...
Generating docs for compound anatomist::RegularCommand...
Generating docs for compound anatomist::SerializingCommand...
Generating docs for compound anatomist::WaitCommand...
Generating docs for compound anatomist::Processor...
Generating docs for nested compound anatomist::Processor::Memo...
Generating docs for compound anatomist::Registry...
Generating docs for compound anatomist::CommandReader...
Generating docs for compound anatomist::CommandWriter...
Generating docs for compound anatomist::Serializer...
Generating docs for compound anatomist::Fusion2dMethod...
Generating docs for compound anatomist::Fusion3dMethod...
Generating docs for compound anatomist::PlanarFusion3dMethod...
Generating docs for compound anatomist::FusionTextureMethod...
Generating docs for compound anatomist::FusionMultiTextureMethod...
Generating docs for compound anatomist::FusionCutMeshMethod...
Generating docs for compound anatomist::Fusion2DMeshMethod...
Generating docs for compound anatomist::FusionSliceMethod...
Generating docs for compound anatomist::FusionRGBAVolumeMethod...
Generating docs for compound anatomist::FusionClipMethod...
Generating docs for compound anatomist::FusionTesselationMethod...
Generating docs for compound anatomist::ConnectivityMatrixFusionMethod...
Generating docs for compound anatomist::VectorFieldFusionMethod...
Generating docs for compound anatomist::FusionMethod...
Generating docs for compound anatomist::FusionFactory...
Generating docs for compound anatomist::StdModule...
Generating docs for compound anatomist::AConnectivityMatrix...
Generating docs for compound anatomist::ASparseMatrix...
Generating docs for compound anatomist::GLItem...
Generating docs for compound anatomist::Primitive...
Generating docs for compound anatomist::GLList...
Generating docs for compound anatomist::GLTexture...
Generating docs for compound anatomist::GLItemList...
Generating docs for compound anatomist::GLNoExecItemList...
Generating docs for compound anatomist::ConstraintEditorWindow...
Generating docs for compound anatomist::NodeSelectionAction...
Generating docs for compound anatomist::NodeSelectionControl...
Generating docs for compound anatomist::HierarchyEditor...
Generating docs for compound anatomist::ErpReader...
Generating docs for compound anatomist::AInterpolerMethod...
Generating docs for compound anatomist::AInterpoler...
Generating docs for compound anatomist::ALandmarkFactory...
Generating docs for compound anatomist::PlaneFusionMethod...
Generating docs for compound anatomist::CylinderFusionMethod...
Generating docs for compound anatomist::ASurfMatchMethod...
Generating docs for compound anatomist::ASurfMatcher...
Generating docs for compound anatomist::AnaSurfMatch...
Generating docs for compound anatomist::SurfpaintModule...
Generating docs for compound anatomist::SurfpaintTools...
Generating docs for compound anatomist::SurfpaintToolsAction...
Generating docs for compound anatomist::SurfpaintToolsControl...
Generating docs for compound anatomist::VolRenderFusionMethod...
Generating docs for compound anatomist::Vo[ 92%] Create "share/doc/5.2"
[ 92%] Built target aims-free-devdoc
/casa/host/build/include/anatomist/action/levelsetaction.h:64: warning: The following parameter of anatomist::RoiLevelSetActionSharedData::update(const Observable *observable, void *arg) is not documented:
  parameter 'arg'
/casa/host/build/include/anatomist/action/paintaction.h:124: warning: The following parameters of anatomist::PaintStrategy::paint(AWindow3D *win, Transformation *transf, const Point3df &point, const AObject *originalLabel, AObject *finalLabel, float brushSize, bool lineMode, carto::VolumeRef< AObject * > &volumeOfLabels, const Point3df &vlOffset, aims::BucketMap< Void >::Bucket &deltaModifications, std::list< std::pair< Point3d, ChangesItem > > &changes, const Point3df &voxelSize, bool line, bool replace, bool mm)=0 are not documented:
  parameter 'win'
  parameter 'transf'
  parameter 'point'
  parameter 'originalLabel'
  parameter 'finalLabel'
  parameter 'brushSize'
  parameter 'lineMode'
  parameter 'volumeOfLabels'
  parameter 'deltaModifications'
  parameter 'changes'
  parameter 'voxelSize'
  parameter 'line'
  parameter 'replace'
  parameter 'mm'
/casa/host/build/include/anatomist/action/paintaction.h:177: warning: The following parameters of anatomist::PointPaintStrategy::paint(AWindow3D *win, Transformation *transf, const Point3df &point, const AObject *originalLabel, AObject *finalLabel, float brushSize, bool lineMode, carto::VolumeRef< AObject * > &volumeOfLabels, const Point3df &vlOffset, aims::BucketMap< Void >::Bucket &deltaModifications, std::list< std::pair< Point3d, ChangesItem > > &changes, const Point3df &voxelSize, bool line, bool replace, bool mm) are not documented:
  parameter 'win'
  parameter 'transf'
  parameter 'point'
  parameter 'originalLabel'
  parameter 'finalLabel'
  parameter 'brushSize'
  parameter 'lineMode'
  parameter 'volumeOfLabels'
  parameter 'deltaModifications'
  parameter 'changes'
  parameter 'voxelSize'
  parameter 'line'
  parameter 'replace'
  parameter 'mm'
/casa/host/build/include/anatomist/action/paintaction.h:200: warning: The following parameters of anatomist::SquarePaintStrategy::paint(AWindow3D *win, Transformation *transf, const Point3df &point, const AObject *originalLabel, AObject *finalLabel, float brushSize, bool lineMode, carto::VolumeRef< AObject * > &volumeOfLabels, const Point3df &vlOffset, aims::BucketMap< Void >::Bucket &deltaModifications, std::list< std::pair< Point3d, ChangesItem > > &changes, const Point3df &voxelSize, bool line, bool replace, bool mm) are not documented:
  parameter 'win'
  parameter 'transf'
  parameter 'point'
  parameter 'originalLabel'
  parameter 'finalLabel'
  parameter 'brushSize'
  parameter 'lineMode'
  parameter 'volumeOfLabels'
  parameter 'deltaModifications'
  parameter 'changes'
  parameter 'voxelSize'
  parameter 'line'
  parameter 'replace'
  parameter 'mm'
/casa/host/build/include/anatomist/action/paintaction.h:224: warning: The following parameters of anatomist::DiskPaintStrategy::paint(AWindow3D *win, Transformation *transf, const Point3df &point, const AObject *originalLabel, AObject *finalLabel, float brushSize, bool lineMode, carto::VolumeRef< AObject * > &volumeOfLabels, const Point3df &vlOffset, aims::BucketMap< Void >::Bucket &deltaModifications, std::list< std::pair< Point3d, ChangesItem > > &changes, const Point3df &voxelSize, bool line, bool replace, bool mm) are not documented:
  parameter 'win'
  parameter 'transf'
  parameter 'point'
  parameter 'originalLabel'
  parameter 'finalLabel'
  parameter 'brushSize'
  parameter 'lineMode'
  parameter 'volumeOfLabels'
  parameter 'deltaModifications'
  parameter 'changes'
  parameter 'voxelSize'
  parameter 'line'
  parameter 'replace'
  parameter 'mm'
/casa/host/build/include/anatomist/action/paintaction.h:259: warning: The following parameters of anatomist::BallPaintStrategy::paint(AWindow3D *win, Transformation *transf, const Point3df &point, const AObject *originalLabel, AObject *finalLabel, float brushSize, bool lineMode, carto::VolumeRef< AObject * > &volumeOfLabels, const Point3df &vlOffset, aims::BucketMap< Void >::Bucket &deltaModifications, std::list< std::pair< Point3d, ChangesItem > > &changes, const Point3df &voxelSize, bool line, bool replace, bool mm) are not documented:
  parameter 'win'
  parameter 'transf'
  parameter 'point'
  parameter 'originalLabel'
  parameter 'finalLabel'
  parameter 'brushSize'
  parameter 'lineMode'
  parameter 'volumeOfLabels'
  parameter 'deltaModifications'
  parameter 'changes'
  parameter 'voxelSize'
  parameter 'line'
  parameter 'replace'
  parameter 'mm'
/casa/host/build/include/anatomist/action/paintaction.h:296: warning: The following parameter of anatomist::PaintActionSharedData::update(const Observable *observable, void *arg) is not documented:
  parameter 'arg'
[ 92%] Built target highres-cortex-doxygen
[ 92%] Generating AimsMeshCut help file ...
/casa/host/build/include/anatomist/action/roimanagementaction.h:203: warning: The following parameter of anatomist::RoiManagementActionSharedData::update(const Observable *observable, void *arg) is not documented:
  parameter 'arg'
/casa/host/build/include/anatomist/processor/Command.h:65: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:67: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:69: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:65: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:67: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:69: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/commands/cGetConnThres.h:58: warning: argument 'ref' of command @param is not found in the argument list of anatomist::GetConnThresholdCommand::GetConnThresholdCommand(AObject *image, AWindow *win, const std::string &requestid, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cGetConnThres.h:58: warning: argument 'obj' of command @param is not found in the argument list of anatomist::GetConnThresholdCommand::GetConnThresholdCommand(AObject *image, AWindow *win, const std::string &requestid, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cGetConnThres.h:58: warning: argument 'refId' of command @param is not found in the argument list of anatomist::GetConnThresholdCommand::GetConnThresholdCommand(AObject *image, AWindow *win, const std::string &requestid, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cGetConnThres.h:58: warning: argument 'unser' of command @param is not found in the argument list of anatomist::GetConnThresholdCommand::GetConnThresholdCommand(AObject *image, AWindow *win, const std::string &requestid, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cGetConnThres.h:68: warning: The following parameters of anatomist::GetConnThresholdCommand::GetConnThresholdCommand(AObject *image, AWindow *win, const std::string &requestid, CommandContext *context=0) are not documented:
  parameter 'image'
  parameter 'requestid'
  parameter 'context'
/casa/host/build/include/anatomist/processor/Command.h:65: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:67: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:69: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/commands/cSetConnThres.h:56: warning: argument 'ref' of command @param is not found in the argument list of anatomist::SetConnThresholdCommand::SetConnThresholdCommand(AObject *image, AWindow *win, bool assignLowThreshold, float lowThres, bool assignHighThreshold, float highThres, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cSetConnThres.h:56: warning: argument 'obj' of command @param is not found in the argument list of anatomist::SetConnThresholdCommand::SetConnThresholdCommand(AObject *image, AWindow *win, bool assignLowThreshold, float lowThres, bool assignHighThreshold, float highThres, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cSetConnThres.h:56: warning: argument 'refId' of command @param is not found in the argument list of anatomist::SetConnThresholdCommand::SetConnThresholdCommand(AObject *image, AWindow *win, bool assignLowThreshold, float lowThres, bool assignHighThreshold, float highThres, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cSetConnThres.h:56: warning: argument 'unser' of command @param is not found in the argument list of anatomist::SetConnThresholdCommand::SetConnThresholdCommand(AObject *image, AWindow *win, bool assignLowThreshold, float lowThres, bool assignHighThreshold, float highThres, CommandContext *context=0)
/casa/host/build/include/anatomist/commands/cSetConnThres.h:66: warning: The following parameters of anatomist::SetConnThresholdCommand::SetConnThresholdCommand(AObject *image, AWindow *win, bool assignLowThreshold, float lowThres, bool assignHighThreshold, float highThres, CommandContext *context=0) are not documented:
  parameter 'image'
  parameter 'assignLowThreshold'
  parameter 'lowThres'
  parameter 'assignHighThreshold'
  parameter 'highThres'
  parameter 'context'
/casa/host/build/include/anatomist/processor/Command.h:65: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:67: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:69: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:65: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:67: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/processor/Command.h:69: warning: Found unknown command '\tt'
/casa/host/build/include/anatomist/action/dynsegmentaction.h:65: warning: The following parameter of anatomist::RoiDynSegmentAction::update(const anatomist::Observable *observable, void *arg) is not documented:
  parameter 'arg'
[ 96%] Generating AimsMeshes2Graph help file ...
[ 96%] Generating AimsMeshGenerate help file ...
lRenderShaderFusionMethod...
Generating docs for compound anatomist::VolRenderModule...
Generating docs for compound anatomist::VolRender...
Generating docs for compound anatomist::VolRenderShader...
Generating docs for compound anatomist::ProfileModule...
Generating docs for compound anatomist::RoiLevelSetActionSharedData...
Generating docs for compound anatomist::RoiLevelSetAction...
Generating docs for compound anatomist::RoiLabelNamingAction...
Generating docs for compound anatomist::ChangesItem...
Generating docs for compound anatomist::ChangedBucketsItem...
Generating docs for compound anatomist::RoiChangeProcessor...
Generating docs for compound anatomist::PaintStrategy...
Generating docs for compound anatomist::PointPaintStrategy...
Generating docs for compound anatomist::SquarePaintStrategy...
Generating docs for compound anatomist::DiskPaintStrategy...
Generating docs for compound anatomist::BallPaintStrategy...
Generating docs for compound anatomist::PaintActionSharedData...
Generating docs for compound anatomist::PaintAction...
Generating docs for compound anatomist::RoiBlobSegmentationAction...
Generating docs for compound anatomist::PaintControl...
Generating docs for compound anatomist::RoiLevelSetControl...
Generating docs for compound anatomist::RoiLabelNamingControl...
Generating docs for compound anatomist::RoiManagementActionSharedData...
Generating docs for compound anatomist::RoiManagementAction...
Generating docs for compound anatomist::RoiBaseModule...
Generating docs for compound anatomist::CreateGraphCommand...
Generating docs for compound anatomist::GetConnThresholdCommand...
Generating docs for compound anatomist::SetConnThresholdCommand...
Generating docs for compound anatomist::AddNodeCommand...
Generating docs for compound anatomist::PaintParamsCommand...
Generating docs for compound anatomist::RoiDynSegmentAction...
Generating docs for compound anatomist::RoiMorphoMathAction...
Generating docs for compound anatomist::RoiDynSegmentControl...
Generating docs for compound anatomist::RoiAlgoModule...
Generating docs for compound anatomist::HistogramModule...
Generating docs for namespace anatomist::internal
Generating docs for compound anatomist::internal::ColorTraitsType...
Generating docs for compound anatomist::internal::PaletteWinExtensionActions...
Generating docs for compound anatomist::internal::VectorFieldCoordSpinBox...
Generating docs for compound anatomist::internal::AGraphicsView...
Generating docs for compound anatomist::internal::AGraphicsScene...
Generating docs for compound anatomist::internal::TransformerActionData...
Generating docs for compound anatomist::internal::NoDragSlider...
Generating docs for compound anatomist::internal::CommandReader_Bridge...
Generating docs for namespace carto
Generating docs for compound carto::GLWidget...
Generating docs for namespace Vr
Generating docs for compound Vr::Creator...
Generating docs for compound Vr::CubeZBuffer...
Generating docs for compound Vr::MIPShader...
Generating docs for compound Vr::MPVRShader...
Generating docs for compound Vr::RfmtShader...
Generating docs for compound Vr::Shader...
Generating docs for compound Vr::ShaderFactory...
Generating docs for compound Vr::Slicing...
Generating docs for compound Vr::SumShader...
Generating docs for compound Vr::Vector3d...
Generating docs for compound Vr::VRShader...
Generating docs for compound Vr::VrSingleton...
Generating graph info page...
Generating directory documentation...
Generating dependency graph for directory anatomist/action
Generating dependency graph for directory anatomist
Generating dependency graph for directory anatomist/application
Generating dependency graph for directory anatomist/browser
Generating dependency graph for directory anatomist/bucket
Generating dependency graph for directory anatomist/color
Generating dependency graph for directory anatomist/commands
Generating dependency graph for directory anatomist/constrainteditor
Generating dependency graph for directory anatomist/control
Generating dependency graph for directory anatomist/controler
Gener/casa/host/build/include/anatomist/application/anatomist_doc.h:41: warning: image file anatomist.png is not found in IMAGE_PATH: assuming external image.
/casa/host/build/include/anatomist/application/anatomist_doc.h:41: warning: image file anatomist.png is not found in IMAGE_PATH: assuming external image.
ating dependency graph for directory anatomist/erpio
Generating dependency graph for directory anatomist/graph
Generating dependency graph for directory anatomist/hierarchy
Generating dependency graph for directory anatomist/interface
Generating dependency graph for directory anatomist/interpoler
Generating dependency graph for directory anatomist/landmark
Generating dependency graph for directory anatomist/mobject
Generating dependency graph for directory anatomist/module
Generating dependency graph for directory anatomist/object
Generating dependency graph for directory anatomist/processor
Generating dependency graph for directory anatomist/reference
Generating dependency graph for directory anatomist/selection
Generating dependency graph for directory anatomist/sparsematrix
Generating dependency graph for directory anatomist/stdmod
Generating dependency graph for directory anatomist/surface
Generating dependency graph for directory anatomist/surfmatcher
Generating dependency graph for directory anatomist/volume
Generating dependency graph for directory anatomist/window
Generating dependency graph for directory anatomist/window3D
Generating dependency graph for directory anatomist/winhisto
Generating dependency graph for directory anatomist/winprof
Generating index page...
Generating page index...
Generating module index...
Generating namespace index...
Generating namespace member index...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating graphical class hierarchy...
Generating member index...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
writing tag file...
Running plantuml with JAVA...
Running dot...
lookup cache used 18418/65536 hits=112141 misses=22464
finished...
[ 96%] Built target anatomist-doxygen
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,810::INFO::Found '0' pipeline(s) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,810::INFO::Found '3' process(es) in 'deepsulci.sulci_labeling.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,810::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.error_computation.ErrorComputation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,811::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.labeling.SulciDeepLabeling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,812::INFO::Processing pipeline 'deepsulci.sulci_labeling.capsul.training.SulciDeepTraining'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,812::INFO::Writing index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,812::INFO::process: '3' files written for module 'sulci_labeling' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,813::INFO::Writing module 'sulci_labeling' index at location '/casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:47,813::INFO::Index: an index has been written for module 'sulci_labeling' at location /casa/host/src/morphologist/morpho-deepsulci/master/sphinx/process_docs/deepsulci/sulci_labeling.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:47,857::INFO::Pipeline 'morphologist.capsul.morphologist.Morphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.morphologist.Morphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:47,958::INFO::Pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,024::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.png'.
[ 96%] Generating AimsOverVolume help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,090::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLNormalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,212::INFO::Pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.brainorientation.BrainOrientation.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,617::INFO::Pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,668::INFO::Pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,734::INFO::Pipeline 'morphologist.capsul.spmnormalization.SPMNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.spmnormalization.SPMNormalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,784::INFO::Pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,851::INFO::Pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.png'.
[ 96%] Generating AimsMeshTransform help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:48,935::INFO::Pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:49,018::INFO::Pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabelling.SulciLabelling.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:49,019::INFO::Summary: '14' files written for module 'capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:49,647::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:49,647::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:49,647::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
[ 96%] Generating AimsRemoveNaN help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:49,976::INFO::Pipeline 'morphologist.capsul.morphologist.Morphologist' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.morphologist.Morphologist.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:50,060::INFO::Pipeline 'morphologist.capsul.fslnormalization.FSLNormalization' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.fslnormalization.FSLNormalization.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:50,131::INFO::Pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling' representation has been written at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/schema/morphologist.capsul.axon.sulcilabelling.SulciLabelling.png'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:50,131::INFO::Summary: '14' files written for module 'capsul'.
[ 96%] Generating AimsRoiFeatures help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:50,744::INFO::Found '14' pipeline(s) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:50,744::INFO::Found '40' process(es) in 'morphologist.capsul'.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:50,744::INFO::Processing pipeline 'morphologist.capsul.axon.axonmorphologist.AxonMorphologist'...
[ 96%] Generating AimsSelectLabel help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_view.py::2025-08-01 05:17:51,872::INFO::Found '0' pipeline(s) in 'deepsulci.pattern_classification.capsul'.
[ 96%] Generating AimsSetMinf help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,179::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,185::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,236::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,243::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,280::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,328::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,338::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,361::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,378::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,391::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:52,403::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
[ 96%] Generating AimsSplitRgb help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,078::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,091::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,106::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,106::INFO::pipeline: '14' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,107::INFO::Processing pipeline 'morphologist.capsul.axon.acpcorientation.AcpcOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,108::INFO::Processing pipeline 'morphologist.capsul.axon.aimsconverter.AimsConverter'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,109::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationtoaims.BaladinNormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,110::INFO::Processing pipeline 'morphologist.capsul.axon.brainsegmentation.BrainSegmentation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,111::INFO::Processing pipeline 'morphologist.capsul.axon.brainvolumes.brainvolumes'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,112::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationtoaims.FSLnormalizationToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,113::INFO::Processing pipeline 'morphologist.capsul.axon.greywhiteclassificationhemi.GreyWhiteClassificationHemi'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,114::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitemesh.GreyWhiteMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,115::INFO::Processing pipeline 'morphologist.capsul.axon.greywhitetopology.GreyWhiteTopology'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,115::INFO::Processing pipeline 'morphologist.capsul.axon.histoanalysis.HistoAnalysis'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,116::INFO::Processing pipeline 'morphologist.capsul.axon.importt1mri.ImportT1MRI'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,117::INFO::Processing pipeline 'morphologist.capsul.axon.morpho_report.morpho_report'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,119::INFO::Processing pipeline 'morphologist.capsul.axon.morphologistprocess.morphologistProcess'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,125::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_aimsmiregister.normalization_aimsmiregister'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,126::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_baladin.Normalization_Baladin'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,127::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_fsl_reinit.Normalization_FSL_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,128::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_spm_reinit.Normalization_SPM_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,129::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm12_reinit.normalization_t1_spm12_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,130::INFO::Processing pipeline 'morphologist.capsul.axon.normalization_t1_spm8_reinit.normalization_t1_spm8_reinit'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,130::INFO::Processing pipeline 'morphologist.capsul.axon.pialmesh.PialMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,131::INFO::Processing pipeline 'morphologist.capsul.axon.reorientanatomy.ReorientAnatomy'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,132::INFO::Processing pipeline 'morphologist.capsul.axon.scalpmesh.ScalpMesh'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,133::INFO::Processing pipeline 'morphologist.capsul.axon.skullstripping.skullstripping'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,134::INFO::Processing pipeline 'morphologist.capsul.axon.splitbrain.SplitBrain'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,135::INFO::Processing pipeline 'morphologist.capsul.axon.spmsn3dtoaims.SPMsn3dToAims'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,136::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraph.SulciGraph'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,137::INFO::Processing pipeline 'morphologist.capsul.axon.sulcigraphmorphometrybysubject.sulcigraphmorphometrybysubject'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,138::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingann.SulciLabellingANN'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,139::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamglobal.SulciLabellingSPAMGlobal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,140::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspamlocal.SulciLabellingSPAMLocal'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,142::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspammarkov.SulciLabellingSPAMMarkov'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,143::INFO::Processing pipeline 'morphologist.capsul.axon.sulciskeleton.SulciSkeleton'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,144::INFO::Processing pipeline 'morphologist.capsul.axon.t1biascorrection.T1BiasCorrection'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,146::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformation.TalairachTransformation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,146::INFO::Processing pipeline 'morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,147::INFO::Processing pipeline 'morphologist.capsul.import_t1_mri.ImportT1Mri'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,148::INFO::Processing pipeline 'morphologist.capsul.morphologist_simple.MorphologistSimple'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,155::INFO::Processing pipeline 'morphologist.capsul.morphologist_viewer.MorphologistView'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,156::INFO::Processing pipeline 'morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,157::INFO::Processing pipeline 'morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,158::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/process/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,159::INFO::process: '40' files written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/process.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,159::INFO::Writing module 'capsul' index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/index.rst'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,159::INFO::Index: an index has been written for module 'capsul' at location /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul.
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,364::INFO::Processing pipeline 'morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,369::INFO::Processing pipeline 'morphologist.capsul.axon.brainorientation.BrainOrientation'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,420::INFO::Processing pipeline 'morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,427::INFO::Processing pipeline 'morphologist.capsul.axon.normalization.Normalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,464::INFO::Processing pipeline 'morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,512::INFO::Processing pipeline 'morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,522::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabelling.SulciLabelling'...
[ 96%] Generating AimsSubVolume help file ...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,544::INFO::Processing pipeline 'morphologist.capsul.axon.sulcilabellingspam.SulciLabellingSPAM'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,555::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,563::INFO::Processing pipeline 'morphologist.capsul.fslnormalization.FSLnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:53,570::INFO::Processing pipeline 'morphologist.capsul.morphologist.Morphologist'...
generating CAPSUL processes docs...
['/usr/bin/python3.10', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'morphologist.capsul', '-o', '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist', '--schema']
loading pickled environment... done
loading intersphinx inventory from /casa/host/build/share/doc/soma-base-5.3/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/pyaims-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/pyanatomist-5.2/sphinx/objects.inv...
loading intersphinx inventory from /casa/host/build/share/doc/soma-workflow-3.3/sphinx/objects.inv...
loading intersphinx inventory from doc/morphologist-ui-5.2/objects.inv...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'doc/morphologist-ui-5.2/objects.inv' not fetchable due to <class 'FileNotFoundError'>: [Errno 2] No such file or directory: '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/doc/morphologist-ui-5.2/objects.inv'
[autosummary] generating autosummary for: index.rst, process_docs/morphologist/capsul/index.rst, process_docs/morphologist/capsul/pipeline/index.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.axonmorphologist.AxonMorphologist.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.baladinnormalizationpipeline.BaladinNormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.brainorientation.BrainOrientation.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalization.Normalization.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.normalizationskullstripped.NormalizationSkullStripped.rst, process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst, ..., process_docs/morphologist/capsul/process/morphologist.capsul.axon.sulciskeleton.SulciSkeleton.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.t1biascorrection.T1BiasCorrection.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformation.TalairachTransformation.rst, process_docs/morphologist/capsul/process/morphologist.capsul.axon.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst, process_docs/morphologist/capsul/process/morphologist.capsul.import_t1_mri.ImportT1Mri.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_simple.MorphologistSimple.rst, process_docs/morphologist/capsul/process/morphologist.capsul.morphologist_viewer.MorphologistView.rst, process_docs/morphologist/capsul/process/morphologist.capsul.sulci_manip.graph_pointcloud_label.GraphPointCloudLabel.rst, process_docs/morphologist/capsul/process/morphologist.capsul.talairachtransformationfromnormalization.TalairachTransformationFromNormalization.rst, sulpated.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 57 source files that are out of date
updating environment: 0 added, 57 changed, 0 removed
reading sources... [  1%] process_docs/morphologist/capsul/index
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:54,268::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMNormalization'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:54,280::INFO::Processing pipeline 'morphologist.capsul.spmnormalization.SPMnormalizationPipeline'...
/casa/host/src/capsul/master/capsul/sphinxext/capsul_pipeline_rst.py::2025-08-01 05:17:54,290::INFO::Writing index at location '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist/capsul/pipeline/index.rst'...
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['/usr/bin/python3.10', '-m', 'capsul.sphinxext.capsul_pipeline_rst', '-i', 'morphologist.capsul', '-o', '/casa/host/src/morphologist/morphologist-gpl/master/sphinx/dev_doc/process_docs/morphologist', '--schema']
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.fslnormalization.FSLnormalizationPipeline.rst:66: WARNING: duplicate label morphologist.capsul.axon.fslnormalizationpipeline.fslnormalizationpipeline_outputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.fslnormalizationpipeline.FSLnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst:30: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_inputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.spmnormalization.SPMnormalizationPipeline.rst:70: WARNING: duplicate label morphologist.capsul.axon.spmnormalizationpipeline.spmnormalizationpipeline_outputs, other instance in /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/process_docs/morphologist/capsul/pipeline/morphologist.capsul.axon.spmnormalizationpipeline.SPMnormalizationPipeline.rst
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checking consistency... /casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:10: WARNING: Citation [FISCHER2012] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:118: WARNING: Citation [PERROT2009] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:120: WARNING: Citation [PERROT2011] is not referenced.
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/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:134: WARNING: Citation [KELLER2009] is not referenced.
/casa/host/src/morphologist/morphologist-gpl/master/sphinx/user_doc/index.rst:139: WARNING: Citation [VAROQUAUX2010] is not referenced.
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[ 96%] Generating AimsRegisterFFDApply help file ...
[ 96%] Generating AimsReplaceLevel help file ...
[ 96%] Generating AimsSegmentsToMesh help file ...
[ 96%] Generating AimsSNR help file ...
[ 96%] Generating AimsSphereDistribution help file ...
[ 96%] Generating AimsMoment help file ...
[ 96%] Generating AimsMorphoMath help file ...
[ 96%] Generating AimsSplitArray help file ...
[ 96%] Generating AimsMIRegister help file ...
[ 96%] Generating AimsSubSampling help file ...
[ 96%] Generating AimsSubTensor help file ...
[ 96%] Generating AimsSulcusSPAM help file ...
[ 96%] Generating AimsSumFrame help file ...
[ 96%] Generating AimsTMStarget help file ...
[ 96%] Generating AimsTalairachTransform help file ...
[ 96%] Generating AimsMeshWhite help file ...
[ 96%] Generating AimsTensorExtract help file ...
[ 96%] Generating AimsMeshSmoothing help file ...
[ 96%] Generating AimsTensorSNR help file ...
[ 96%] Generating AimsTexture2Primal help file ...
[ 96%] Generating AimsTextureRegularization help file ...
[ 96%] Generating AimsTextureAverage help file ...
[ 96%] Generating AimsTextureDerivative help file ...
[ 96%] Generating AimsTextureErosion help file ...
[ 96%] Generating AimsMeshParcellation2VolumeParcellation help file ...
[ 96%] Generating AimsTextureDilation help file ...
[ 96%] Generating AimsTexturePrimalSketch help file ...
[ 96%] Generating AimsTextureScaleSpace help file ...
[ 96%] Generating AimsTextureSmoothing help file ...
[ 96%] Generating AimsTextureThreshold help file ...
[ 96%] Generating AimsMeshLineMeasurement help file ...
[ 96%] Generating AimsTopologicalClassification help file ...
[ 96%] Generating AimsTextureVoronoi help file ...
[ 96%] Generating AimsMeshGeodesicDepth help file ...
[ 96%] Generating AimsValidateFit help file ...
[ 96%] Generating AimsVFilter help file ...
[ 96%] Generating AimsVoiStat help file ...
[ 96%] Generating AimsVol2Tex help file ...
[ 96%] Generating AimsVoronoi help file ...
[ 96%] Generating AimsVeinExtraction help file ...
[ 96%] Generating AimsZCat help file ...
[ 96%] Generating AimsBundleSelectCenter help file ...
[ 96%] Generating AimsFovSplit help file ...
[ 96%] Generating AimsSumPETFrame help file ...
[ 96%] Generating AimsSiemensEPI2Volume help file ...
[ 96%] Generating AimsRegisterFFDEstimate help file ...
[ 96%] Generating AimsAttributedViewer help file ...
[ 96%] Generating AimsLabelSelector help file ...
[ 96%] Generating anatomist-bin help file ...
[ 96%] Generating mkhierarchy-anatomist help file ...
[ 96%] Generating ylLaplacian help file ...
[ 96%] Generating ylIsoCurvature help file ...
[ 96%] Generating ylAdvectPath help file ...
[ 96%] Generating ylAdvectTubes help file ...
[ 96%] Generating ylAdvectEuclidean help file ...
[ 96%] Generating ylAdvectValues help file ...
[ 96%] Generating ylPropagateAlongField help file ...
[ 96%] Generating ylLabelEachVoxel help file ...
[ 96%] Generating ylMergeCortexColumnRegions help file ...
[ 96%] Generating ylMakeTraversePseudoAreaMap help file ...
[ 96%] Generating ylUpwindDistance help file ...
[ 96%] Generating VipBiasCorrection help file ...
[ 96%] Generating VipClosing help file ...
[ 96%] Generating VipCovarianceMatrix help file ...
[ 96%] Generating VipDeriche help file ...
[ 96%] Generating VipDilation help file ...
[ 96%] Generating VipDistanceMap help file ...
[ 96%] Generating VipExtEdge help file ...
[ 96%] Generating VipFileDump help file ...
[ 96%] Generating VipErosion help file ...
[ 96%] Generating VipFoetusHomotopicSnake help file ...
[ 96%] Generating VipFoldArg help file ...
[ 96%] Generating VipFoldArgAtt help file ...
[ 96%] Generating VipGeometry help file ...
[ 96%] Generating VipGetBrain help file ...
[ 96%] Generating VipGetHead help file ...
[ 96%] Generating VipGreyStatFromClassif help file ...
[ 96%] Generating VipGreyWhiteClassif help file ...
[ 96%] Generating VipHistoAnalysis help file ...
[ 96%] Generating VipHomotopic help file ...
[ 96%] Generating VipHomotopicSnake help file ...
[ 96%] Generating VipHyste help file ...
[ 96%] Generating VipLabelContour help file ...
[ 96%] Generating VipLabelArg help file ...
[ 96%] Generating VipLabelMatching help file ...
[ 96%] Generating VipMatching help file ...
[ 96%] Generating VipLabelOverlap help file ...
[ 96%] Generating VipListLabel help file ...
[ 96%] Generating VipMerge help file ...
[ 96%] Generating VipMinimizeInformation help file ...
[ 96%] Generating VipMoment help file ...
[ 96%] Generating VipOpenFold help file ...
[ 96%] Generating VipOpening help file ...
[ 96%] Generating VipPca help file ...
[ 96%] Generating VipSkeleton help file ...
[ 96%] Generating VipSplitBrain help file ...
[ 96%] Generating VipSetPointValue help file ...
[ 96%] Generating VipTalairachCoordinates help file ...
[ 96%] Generating VipSwapEndian help file ...
[ 96%] Generating VipT1BiasCorrection help file ...
[ 96%] Generating VipTalairachTransform help file ...
[ 96%] Generating VipTopoClassifMeaning help file ...
[ 96%] Generating VipTopoClassification help file ...
[ 96%] Generating vip_test_well_composed_configurations help file ...
[ 96%] Generating vip_test_well_composed_topology help file ...
[ 96%] Generating readFolds help file ...
[ 96%] Generating siChangeModels help file ...
[ 96%] Generating siCopyNames help file ...
[ 96%] Generating siDomTrain help file ...
[ 96%] Generating siDivNameList help file ...
[ 96%] Generating siEnergy help file ...
[ 96%] Generating siError help file ...
[ 96%] Generating siErrorStats help file ...
[ 96%] Generating siFlip help file ...
[ 96%] Generating siFunctionalGraphs help file ...
[ 96%] Generating siGraph2Label help file ...
[ 96%] Generating sigraph-config help file ...
[ 96%] Generating siLearn help file ...
[ 96%] Generating siLyxErrors help file ...
[ 96%] Generating siMakeModel help file ...
[ 96%] Generating siMakeColoredHierarchy help file ...
[ 96%] Generating siMakeParcellationHierarchy help file ...
[ 96%] Generating siMergeModels help file ...
[ 96%] Generating siMeshSulciOperture help file ...
[ 96%] Generating siMkModelEdges help file ...
[ 96%] Generating siMeshSulciProjection help file ...
[ 96%] Generating siMorpho help file ...
[ 96%] Generating siMultilabelCompare help file ...
[ 96%] Generating siParcellation help file ...
[ 96%] Generating siPIDcommand help file ...
[ 96%] Generating siPutTextureInModel help file ...
[ 96%] Generating siRelax help file ...
[ 96%] Generating siRevert help file ...
[ 96%] Generating siSulcalParcellation help file ...
[ 96%] Generating siTestModels help file ...
[ 96%] Generating siTriangModel help file ...
[ 96%] Generating siTryGauss help file ...
[ 96%] Generating AimsReadDpy help file ...
[ 96%] Generating AimsAdaptiveSelVoxel help file ...
[ 96%] Generating bioReadDpy help file ...
[ 96%] Generating AimsBorderGenerate help file ...
[ 96%] Generating AimsAxialProjection help file ...
[ 96%] Generating AimsBorderInfo help file ...
[ 96%] Generating AimsCenterSlices help file ...
[ 96%] Generating AimsFeaturesExtraction help file ...
[ 96%] Generating AimsFovAdapt help file ...
[ 96%] Generating AimsGL2Activity help file ...
[ 96%] Generating AimsIndividStackSlices help file ...
[ 96%] Generating AimsInterSliceNormalize help file ...
[ 96%] Generating AimsManualRegistration help file ...
[ 96%] Generating AimsMidPlaneAlign help file ...
[ 96%] Generating bioDetectSlices help file ...
[ 96%] Generating bioModelClassify help file ...
[ 96%] Generating bioModelGenerate help file ...
[ 96%] Generating AimsAffineRegister help file ...
[ 96%] Generating AimsAmyloidDensity help file ...
[ 96%] Generating AimsAmyloidLoadAvgDistNeigh help file ...
[ 96%] Generating AimsAmyloidLoadInvSurfVor help file ...
[ 96%] Generating AimsAmyloidDetection help file ...
[ 96%] Generating AimsAmyloidFiltering help file ...
[ 96%] Generating AimsAmyloidMRIDetection help file ...
[ 96%] Generating AimsAreaNbConnectCompRatio help file ...
[ 96%] Generating AimsBorderCrop help file ...
[ 96%] Generating AimsBorderLineProj help file ...
[ 96%] Generating AimsBinaryBoundingBox help file ...
[ 96%] Generating AimsBinaryBorder help file ...
[ 96%] Generating AimsBoundingBoxCalculation help file ...
[ 96%] Generating AimsBoundingBoxExtraction help file ...
[ 96%] Generating AimsComponentFeaturesProcess help file ...
[ 96%] Generating AimsComponentFeaturesVisualize help file ...
[ 96%] Generating AimsComponentFeaturesMapGenerate help file ...
[ 96%] Generating AimsCorrectImages help file ...
[ 96%] Generating AimsChannelProcess help file ...
[ 96%] Generating AimsCreateFieldsFromMotion help file ...
[ 96%] Generating AimsEntropicThresholding help file ...
[ 96%] Generating AimsEqualizer help file ...
[ 96%] Generating AimsFovCentering help file ...
[ 96%] Generating AimsGenerateVolume help file ...
[ 96%] Generating AimsGridCalibrate help file ...
[ 96%] Generating AimsGridGenerate help file ...
[ 96%] Generating AimsHeightFiltering help file ...
[ 96%] Generating AimsIndexCluster help file ...
[ 96%] Generating AimsIndividSlices help file ...
[ 96%] Generating AimsInterlaceVolumes help file ...
[ 96%] Generating AimsInterpolate help file ...
[ 96%] Generating AimsLabelReorder help file ...
[ 96%] Generating AimsMaskContour help file ...
[ 96%] Generating AimsMergeFFDLabels help file ...
[ 96%] Generating AimsMeshMatching help file ...
[ 96%] Generating AimsMIBucketRegister help file ...
[ 96%] Generating AimsMidPlaneMask help file ...
[ 96%] Generating AimsMosaic help file ...
[ 96%] Generating AimsSeparateComp help file ...
[ 96%] Generating AimsStereologySampling help file ...
[ 96%] Generating AimsStereotaxy help file ...
[ 96%] Generating AimsSubSamplingConservative help file ...
[ 96%] Generating AimsWatershed help file ...
[ 96%] Generating AimsSeededWatershed help file ...
[ 96%] Generating bioCellBoundingBoxesGenerate help file ...
[ 96%] Generating bioCellEvaluate help file ...
[ 96%] Generating bioClusterStatistics help file ...
[ 96%] Generating bioComponentConnexe help file ...
[ 96%] Generating bioCorrectMissingLabels help file ...
[ 96%] Generating bioExtractAmyloidLoad help file ...
[ 96%] Generating bioExtractDice help file ...
[ 96%] Generating bioFindCellSeeds help file ...
[ 96%] Generating bioMacGetSingleBrain help file ...
[ 96%] Generating bioPrepareData4DlIndiv help file ...
[ 96%] Generating bioRenumberConnectComp help file ...
[ 96%] Generating bioStatDominanceAppli help file ...
[ 96%] Generating bioVoxelFeatures help file ...
[ 96%] Generating AimsAdaptiveGaussianSmoothing help file ...
[ 96%] Generating AimsEdgeExtract help file ...
[ 96%] Generating AimsExtremaMap help file ...
[ 96%] Generating AimsRegionGrowingExtrema help file ...
[ 96%] Generating AimsSigmaImageCalculate help file ...
[ 96%] Generating bioVoxelWiseStatistics help file ...
[ 96%] Generating AimsSegmentationEM help file ...
[ 96%] Generating AimsSelectGradPoints help file ...
[ 96%] Generating AimsRegisterQNEstimate help file ...
[ 96%] Generating bioKMeans help file ...
[ 96%] Generating AimsSparseMatrixSmoothing help file ...
[ 96%] Generating constelBundlesFiltering help file ...
[ 96%] Generating constelConnectionDensityTexture help file ...
[ 96%] Generating constelConnectivityMatrix help file ...
[ 96%] Generating constelFibersLengths help file ...
[ 96%] Generating constelMeanConnectivityProfileFromMatrix help file ...
[ 96%] Generating constelSelectBundlesFromNames help file ...
[ 96%] Generating constelSelectFibersFromMesh help file ...
[ 96%] Generating AimsSegment2Modes help file ...
[ 96%] Generating AimsRoiOverlap help file ...
[ 96%] Generating AimsSamplingInfo help file ...
[ 96%] Generating AimsRgbToHsv help file ...
[ 96%] Generating AimsConstraintCleaner help file ...
[ 96%] Generating AimsGyriStuff help file ...
[ 96%] Generating AimsCorticalReferential help file ...
[ 96%] Generating AimsRebuildComp help file ...
[ 96%] Generating AimsResampleFromFieldsData help file ...
[ 96%] Generating AimsMeshIsoLine help file ...
[ 96%] Generating AimsCorticalThickness help file ...
[ 96%] Generating AimsFunctionProjection help file ...
[100%] Generating AimsMeshMedianSurface help file ...
[100%] Generating AimsOverlapInfo help file ...
[100%] Generating AimsCoordinateGridMesh help file ...
[100%] Generating AimsCoordinatesToTexture help file ...
[100%] Generating AimsMultiRecal help file ...
[100%] Generating AimsCoordinatesTextureToMesh help file ...
[100%] Generating AimsParameterizeGyri help file ...
[100%] Generating AimsParameterizeSulcus help file ...
[100%] Generating AimsPlotOnSPhericalAtlas help file ...
[100%] Generating AimsSulcusCorticalSnake help file ...
[100%] Generating AimsFlattenCortex help file ...
[100%] Generating surfTexActivationSimulation help file ...
[100%] Generating AimsTextureToAtlas help file ...
[100%] Generating AimsCheck2DCoordinates help file ...
[100%] Generating AimsMeshToAtlas help file ...
[100%] Generating AimsSulcusNormalizeDepthProfile help file ...
[100%] Generating AimsMeshCoordinatesToDecimated help file ...
[100%] Generating surfStructuralAnalysis help file ...
[100%] Generating AimsConformalMapping help file ...
[100%] Generating AimsExtractGyrus help file ...
[100%] Generating AimsMeshToMeshPoint help file ...
[100%] Generating AimsPlotCoordinatesOnMesh help file ...
[100%] Generating PlotFociForValidation help file ...
[100%] Generating AimsGyriRegularization help file ...
[100%] Generating AimsCoordinatesToIndex help file ...
[100%] Generating AimsGroupGyri help file ...
[100%] Generating AimsGeodesicPath help file ...
[100%] Generating AimsInterpolateVolumeToSurface help file ...
[100%] Generating AimsSulcalLines help file ...
[100%] Generating AimsTextureCompare help file ...
[100%] Generating AimsExactDepthArea help file ...
[100%] Generating documentation commands help index ...
[100%] Built target bv_commands_doc
[100%] Create "share/doc/2.6"
[100%] Built target capsul-devdoc
[100%] Built target capsul-doc
[100%] Built target devdoc
Generating BrainVISA processes documentation
[100%] Built target bv_ontology_doc
[100%] Built target bv_doc_index
[100%] Built target axon-doc
[100%] Built target doc

bv_maker summary:
OK          step doc: /casa/host/build, started: 2025/08/01 05:17, stopped: 2025/08/01 05:20
All went good.

Finished: SUCCESS