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Fix CI #284: eigen export, test fixes, remove MnaStep
WinStatic: - Replace local 'eigen' INTERFACE target with Eigen3::Eigen globally - Export Qt shader resource targets for static builds (disp) Test fixes: - test_bids_coordinate_system: serialize transform matrix in writeJson() - test_crossval_covariance: update deprecated mne.pick_types() API - test_dsp_infomax: fix super-Gaussian nonlinearity (-2 -> -1) - test_inv_cmne: use matDspmData in no-model fallback - test_mna_graph_execution: add connectivity and type mismatch validation - test_mne_browse_data: fix off-by-one in annotation duration - test_sts_cov_estimators: use Toeplitz-structured test data Refactoring: - Remove MnaStep (redundant with MnaNode) - MnaProject::pipeline now stores QList<MnaNode> directly - Update .mna example file to MnaNode JSON format - mne_inverse_pipeline uses MnaGraph + MnaGraphExecutor - Disable auto-fix workflow (workflow_dispatch only)
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‎.github/workflows/auto-fix-build.yml‎

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name: Auto-Fix Build Failures
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# NOTE: Disabled until CI is stable. Uncomment the 'on:' trigger to re-enable.
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# on:
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# workflow_run:
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# workflows: ["Staging"]
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# types: [completed]
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on:
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workflow_run:
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workflows: ["Staging"]
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types: [completed]
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workflow_dispatch: # manual-only for now
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permissions:
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contents: read

‎resources/examples/mna_inverse_dspm.mna‎

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"pipeline": [
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{
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"id": "load_raw",
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"tool": "load_fiff_raw",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "load_fiff_raw",
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"tool_version": "2.2.0",
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"attributes": {
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"raw_path": "${TEST_DATA}/MEG/sample/sample_audvis_trunc_raw.fif"
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},
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"inputs": [],
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"outputs": ["raw_data", "info"]
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"outputs": [
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{"name": "raw_data", "data_kind": "matrix", "direction": "output"},
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{"name": "info", "data_kind": "matrix", "direction": "output"}
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]
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},
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{
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"id": "load_evoked",
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"tool": "load_fiff_evoked",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "load_fiff_evoked",
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"tool_version": "2.2.0",
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"attributes": {
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"evoked_path": "${TEST_DATA}/MEG/sample/sample_audvis-ave.fif",
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"setno": 0
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},
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"inputs": [],
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"outputs": ["evoked"]
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"outputs": [
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{"name": "evoked", "data_kind": "matrix", "direction": "output"}
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]
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},
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{
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"id": "load_cov",
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"tool": "load_fiff_cov",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "load_fiff_cov",
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"tool_version": "2.2.0",
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"attributes": {
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"cov_path": "${TEST_DATA}/MEG/sample/sample_audvis-cov.fif"
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},
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"inputs": [],
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"outputs": ["noise_cov"]
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"outputs": [
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{"name": "noise_cov", "data_kind": "matrix", "direction": "output"}
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]
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},
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{
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"id": "load_fwd",
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"tool": "load_forward",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "load_forward",
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"tool_version": "2.2.0",
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"attributes": {
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"fwd_path": "${TEST_DATA}/Result/ref-sample_audvis-meg-eeg-oct-6-fwd.fif"
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},
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"inputs": [],
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"outputs": ["forward"]
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"outputs": [
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{"name": "forward", "data_kind": "matrix", "direction": "output"}
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]
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},
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{
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"id": "make_inv",
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"tool": "make_inverse_operator",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "make_inverse_operator",
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"tool_version": "2.2.0",
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"attributes": {
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"loose": 0.2,
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"depth": 0.8
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},
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"inputs": ["load_raw::info", "load_fwd::forward", "load_cov::noise_cov"],
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"outputs": ["inverse_operator"]
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"inputs": [
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{"name": "info", "data_kind": "matrix", "direction": "input", "source_node": "load_raw", "source_port": "info"},
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{"name": "forward", "data_kind": "matrix", "direction": "input", "source_node": "load_fwd", "source_port": "forward"},
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{"name": "noise_cov", "data_kind": "matrix", "direction": "input", "source_node": "load_cov", "source_port": "noise_cov"}
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],
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"outputs": [
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{"name": "inverse_operator", "data_kind": "matrix", "direction": "output"}
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]
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},
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{
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"id": "apply_dspm",
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"tool": "apply_inverse",
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"toolVersion": "2.2.0",
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"parameters": {
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"op_type": "apply_inverse",
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"tool_version": "2.2.0",
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"attributes": {
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"method": "dSPM",
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"snr": 3.0,
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"pick_normal": false
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},
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"inputs": ["make_inv::inverse_operator", "load_evoked::evoked"],
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"outputs": ["source_estimate"]
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"inputs": [
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{"name": "inverse_operator", "data_kind": "matrix", "direction": "input", "source_node": "make_inv", "source_port": "inverse_operator"},
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{"name": "evoked", "data_kind": "matrix", "direction": "input", "source_node": "load_evoked", "source_port": "evoked"}
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],
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"outputs": [
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{"name": "source_estimate", "data_kind": "matrix", "direction": "output"}
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]
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}
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]
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}

‎src/CMakeLists.txt‎

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@@ -36,7 +36,7 @@ option(NO_IPC "Build project with no interprocess communication features (shared
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option(WASM "Setup build for wasm" OFF)
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option(USE_FFTW "Use fftw backend for eigen" OFF)
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option(USE_FFTW "Use fftw backend for Eigen3::Eigen" OFF)
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option(USE_ONNXRUNTIME "Enable ONNX Runtime backend for the ml library" ON)
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## Eigen dependency
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set(MNE_CPP_EIGEN_VERSION "5.0.1" CACHE STRING "Preferred Eigen package version for MNE-CPP.")
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set(MNE_CPP_PREBUILT_EIGEN_DIR "${PROJECT_SOURCE_DIR}/external/eigen"
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set(MNE_CPP_PREBUILT_EIGEN_DIR "${PROJECT_SOURCE_DIR}/external/Eigen3::Eigen"
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CACHE PATH "Location of a prebuilt Eigen package prepared by the init scripts or CI helpers.")
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find_package(Eigen3 ${MNE_CPP_EIGEN_VERSION} QUIET NO_MODULE
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HINTS
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"${MNE_CPP_PREBUILT_EIGEN_DIR}"
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"${PROJECT_SOURCE_DIR}/external/eigen-${MNE_CPP_EIGEN_VERSION}-install")
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"${PROJECT_SOURCE_DIR}/external/Eigen3::Eigen-${MNE_CPP_EIGEN_VERSION}-install")
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if(TARGET Eigen3::Eigen)
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if(NOT TARGET eigen)
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add_library(eigen INTERFACE)
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target_link_libraries(eigen INTERFACE Eigen3::Eigen)
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endif()
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if(DEFINED Eigen3_DIR AND NOT Eigen3_DIR STREQUAL "")
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get_filename_component(MNE_CPP_EIGEN_PACKAGE_ROOT "${Eigen3_DIR}/../../.." ABSOLUTE)
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message(STATUS "[MNE-CPP] Using Eigen package from ${MNE_CPP_EIGEN_PACKAGE_ROOT}")

‎src/applications/mne_analyze/libs/anShared/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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${FFTW_LIBS})
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target_compile_definitions(${PROJECT_NAME}

‎src/applications/mne_analyze/libs/events/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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)
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target_compile_definitions(${PROJECT_NAME} PRIVATE MNE_EVENTS_LIBRARY MNE_GIT_HASH_SHORT="${MNE_GIT_HASH_SHORT}" MNE_GIT_HASH_LONG="${MNE_GIT_HASH_LONG}")

‎src/applications/mne_analyze/mne_analyze/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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anShared
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)
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‎src/applications/mne_analyze/plugins/averaging/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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anShared
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${FFTW_LIBS})
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‎src/applications/mne_analyze/plugins/channelselection/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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anShared
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${FFTW_LIBS})
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‎src/applications/mne_analyze/plugins/controlmanager/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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anShared
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${FFTW_LIBS})
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‎src/applications/mne_analyze/plugins/coregistration/CMakeLists.txt‎

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target_link_libraries(${PROJECT_NAME} PRIVATE
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${QT_REQUIRED_COMPONENT_LIBS}
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${MNE_LIBS_REQUIRED}
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eigen
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Eigen3::Eigen
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anShared
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${FFTW_LIBS})
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