Started Running as brainvisa ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=cea-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "1800" "vip_test_well_composed_configurations"' ---------------------------------------- ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=cea-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "1800" "vip_test_well_composed_topology"' ---------------------------------------- ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=cea-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "5400" "python3" "-m" "brainvisa.tests.test_morphologist" "--no-ann" "--test_mode=run"' ---------------------------------------- ['/casa/install/python/brainvisa/tests/test_morphologist.py', '--no-ann', '--test_mode=run'] Starting tests under /tmp/axon_test_sk0g1vpd Loading toolbox baby Loading toolbox bioprocessing Loading toolbox brainrat Loading toolbox constellation Loading toolbox cortical_surface Loading toolbox data management Loading toolbox disco Loading toolbox freesurfer Loading toolbox highres_cortex Loading toolbox morphologist Loading toolbox primatologist Loading toolbox spm Loading toolbox structural_analysis Loading toolbox tools Loading toolbox viewers Loading toolbox My processes The log file for this session is '/tmp/axon_test_sk0g1vpd/bv_home/brainvisa.log' exec: /casa/install/brainvisa/toolboxes/constellation/startup.py exec: /casa/install/brainvisa/toolboxes/morphologist/startup.py SPM dir: /usr/local/spm12-standalone spmtemplates: /usr/local/spm12-standalone/spm12_mcr/spm12/spm12 /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: parse directories and insert items /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: 8 files are stored as 8 DiskItems in 0 seconds test_pipeline_results (__main__.TestMorphologistPipeline) ... Database /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist must be updated because the database file is too old. Generating database tables for /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist: 187 files are stored as 181 DiskItems in 0 seconds * Create test database /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds Generating database tables for /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds * Download https://brainvisa.info/download/data/demo_data.zip to /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline * Import test data _Process **Import T1 MRI** started on 2025/07/29 05:39_ filein : /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima fileout : /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii encoding: Binary normal : 0 rescale : 0 format : type : S16 objtype : xdim : 0 ydim : 0 zdim : 0 imin : default imax : default omin : default omax : default reading /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima as Volume / S16... reading done convert to Volume / S16 converting data... convert done writing /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii... done _Process **Import T1 MRI** finished on 2025/07/29 05:39 (1 seconds)_ (not doing ANN sulci recognition tests today) * Check SPAM models installation _Process **Check SPAM models installation** started on 2025/07/29 05:39_ models: 6 SPAM models are present. _Process **Check SPAM models installation** finished on 2025/07/29 05:39 (0 seconds)_ * Run Morphologist _Process **Morphologist 2021** started on 2025/07/29 05:39_ progress: 0.0 % ... progress: 0.0 % ... WARNING: Left hemisphere point not specified - X axis flip will not be checked --- OK, the image seems to be in the correct orientation. progress: 10.0 % ... progress: 10.0 % ... progress: 20.0 % ... progress: 30.0 % ... progress: 40.0 % ... Skip unselected node: Skull-stripped brain normalization progress: 50.0 % ... progress: 60.0 % ... progress: 70.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... Computing left hemisphere grey-white classification... progress: 80.71428571428572 % ... Detecting left hemisphere spherical inner cortical interface... progress: 81.42857142857143 % ... Reconstructing left hemisphere white mesh... progress: 82.14285714285714 % ... Computing left sulci skeleton and buried gyrus watershed... progress: 82.85714285714286 % ... Detecting left hemisphere spherical outer cortical surface... Reconstructing left hemisphere pial mesh... progress: 83.57142857142857 % ... Building left hemisphere attributed relational sulci graph... _Process **Hemisphere Sulci Voronoi** started on 2025/07/29 05:40_ _Process **Hemisphere Sulci Voronoi** finished on 2025/07/29 05:41 (18 seconds)_ _Process **Hemisphere Sulci Thickness and Volumes** started on 2025/07/29 05:41_ _Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/07/29 05:41 (12 seconds)_ Talairach-AC/PC-Anatomist appended progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... progress: 84.64285714285712 % ... progress: 84.64285714285712 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... Computing right hemisphere grey-white classification... progress: 85.71428571428571 % ... Detecting right hemisphere spherical inner cortical interface... progress: 86.42857142857142 % ... Reconstructing right hemisphere white mesh... progress: 87.14285714285714 % ... Computing right sulci skeleton and buried gyrus watershed... progress: 87.85714285714286 % ... Detecting right hemisphere spherical outer cortical surface... Reconstructing right hemisphere pial mesh... progress: 88.57142857142858 % ... Building right hemisphere attributed relational sulci graph... _Process **Hemisphere Sulci Voronoi** started on 2025/07/29 05:44_ _Process **Hemisphere Sulci Voronoi** finished on 2025/07/29 05:45 (18 seconds)_ _Process **Hemisphere Sulci Thickness and Volumes** started on 2025/07/29 05:45_ _Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/07/29 05:45 (11 seconds)_ Talairach-AC/PC-Anatomist appended progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... progress: 89.64285714285714 % ... progress: 89.64285714285714 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... Reading FGraph version 3.1 Reading FGraph version 3.1 progress: 100.0 % ... _Process **Morphologist 2021** finished on 2025/07/29 05:47 (8 minutes 49 seconds)_ * Run CNN recognition _Process **Morphologist 2021** started on 2025/07/29 05:47_ progress: 0.0 % ... Skip unselected node: Image orientation handling progress: 10.0 % ... Skip unselected node: T1 Bias Correction progress: 20.0 % ... Skip unselected node: Histogram analysis progress: 30.0 % ... Skip unselected node: Compute Brain Mask progress: 40.0 % ... Skip unselected node: Skull-stripped brain normalization progress: 50.0 % ... Skip unselected node: Split Brain Mask progress: 60.0 % ... Skip unselected node: Talairach transformation from manual AC/PC progress: 70.0 % ... Skip unselected node: Head Mesh progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... Skip unselected node: Grey White Classification progress: 80.71428571428572 % ... Skip unselected node: Grey White Topology Correction progress: 81.42857142857143 % ... Skip unselected node: Grey White Mesh progress: 82.14285714285714 % ... Skip unselected node: Sulci Skeleton and Roots progress: 82.85714285714286 % ... Skip unselected node: Pial Mesh progress: 83.57142857142857 % ... Skip unselected node: Cortical Folds Graph progress: 84.28571428571429 % ... progress: 84.28571428571429 % ... CONFIG: {'capsul_engine': {'uses': {'capsul.engine.module.freesurfer': 'ALL', 'capsul.engine.module.fom': 'ALL', 'capsul.engine.module.attributes': 'any', 'capsul.engine.module.axon': 'any', 'capsul.engine.module.spm': 'ALL', 'capsul.engine.module.matlab': 'any', 'capsul.engine.module.fsl': 'ALL', 'capsul.engine.module.ants': 'ALL', 'capsul.engine.module.afni': 'ALL'}}, 'capsul.engine.module.fom': {'config_id': 'fom', 'config_environment': 'global', 'input_fom': 'morpho-deepsulci-1.0', 'output_fom': 'morpho-deepsulci-1.0', 'shared_fom': 'raw-bids-1.0', 'volumes_format': 'gz compressed NIFTI-1 image', 'meshes_format': 'GIFTI file', 'auto_fom': True, 'fom_path': [], 'input_directory': '/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist'}, 'capsul.engine.module.attributes': {'config_id': 'attributes', 'config_environment': 'global', 'attributes_schema_paths': ['capsul.attributes.completion_engine_factory'], 'attributes_schemas': {}, 'process_completion': 'builtin'}, 'capsul.engine.module.axon': {'config_id': 'axon', 'config_environment': 'global', 'shared_directory': '/casa/install/share/brainvisa-share-5.1', 'user_level': 0}, 'capsul.engine.module.spm': {'config_id': 'spm12-standalone', 'config_environment': 'global', 'directory': '/usr/local/spm12-standalone', 'version': '12', 'standalone': True}, 'capsul.engine.module.matlab': {'config_id': 'matlab', 'config_environment': 'global', 'mcr_directory': '/usr/local/spm12-standalone/mcr/v97'}} soma-workflow starting in light mode Workflow controller initialised Soma-workflow temp directory: /tmp/axon_test_sk0g1vpd/tmp/soma_workflow_nqtmmqmc del WorkflowController progress: 85.0 % ... UUID conflict in database, uuid: 84e2bee9-3b9d-662c-ae27-b804381bca17 while inserting: test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg file(s) with the same UUID: ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Lsujet01.arg',) ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Lsujet01.data',) error: UNIQUE constraint failed: _DISKITEMS_._uuid ERROR: ** brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert"/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. ** * * * `**DatabaseError**` Traceback (most recent call last): File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1266, in insertDiskItems cursor.execute( sqlite3.IntegrityError: UNIQUE constraint failed: _DISKITEMS_._uuid During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/casa/install/python/brainvisa/processes.py", line 3500, in _processExecution neuroHierarchy.databases.insertDiskItem( File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 256, in insertDiskItem self.insertDiskItems((item, ), **kwargs) File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 2249, in insertDiskItems database.insertDiskItems((diskItem,), update=update, File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1307, in insertDiskItems raise DatabaseError( brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert "/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Lsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... Skip unselected node: Grey White Classification progress: 85.71428571428571 % ... Skip unselected node: Grey White Topology Correction progress: 86.42857142857142 % ... Skip unselected node: Grey White Mesh progress: 87.14285714285714 % ... Skip unselected node: Sulci Skeleton and Roots progress: 87.85714285714286 % ... Skip unselected node: Pial Mesh progress: 88.57142857142858 % ... Skip unselected node: Cortical Folds Graph progress: 89.28571428571429 % ... progress: 89.28571428571429 % ... CONFIG: {'capsul_engine': {'uses': {'capsul.engine.module.freesurfer': 'ALL', 'capsul.engine.module.fom': 'ALL', 'capsul.engine.module.attributes': 'any', 'capsul.engine.module.axon': 'any', 'capsul.engine.module.spm': 'ALL', 'capsul.engine.module.matlab': 'any', 'capsul.engine.module.fsl': 'ALL', 'capsul.engine.module.ants': 'ALL', 'capsul.engine.module.afni': 'ALL'}}, 'capsul.engine.module.fom': {'config_id': 'fom', 'config_environment': 'global', 'input_fom': 'morpho-deepsulci-1.0', 'output_fom': 'morpho-deepsulci-1.0', 'shared_fom': 'raw-bids-1.0', 'volumes_format': 'gz compressed NIFTI-1 image', 'meshes_format': 'GIFTI file', 'auto_fom': True, 'fom_path': [], 'input_directory': '/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist'}, 'capsul.engine.module.attributes': {'config_id': 'attributes', 'config_environment': 'global', 'attributes_schema_paths': ['capsul.attributes.completion_engine_factory'], 'attributes_schemas': {}, 'process_completion': 'builtin'}, 'capsul.engine.module.axon': {'config_id': 'axon', 'config_environment': 'global', 'shared_directory': '/casa/install/share/brainvisa-share-5.1', 'user_level': 0}, 'capsul.engine.module.spm': {'config_id': 'spm12-standalone', 'config_environment': 'global', 'directory': '/usr/local/spm12-standalone', 'version': '12', 'standalone': True}, 'capsul.engine.module.matlab': {'config_id': 'matlab', 'config_environment': 'global', 'mcr_directory': '/usr/local/spm12-standalone/mcr/v97'}} soma-workflow starting in light mode Workflow controller initialised Soma-workflow temp directory: /tmp/axon_test_sk0g1vpd/tmp/soma_workflow_zhldjuvz del WorkflowController progress: 90.0 % ... UUID conflict in database, uuid: 6b7a22b3-14fc-216d-b97a-264ef1b1a7fe while inserting: test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg file(s) with the same UUID: ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Rsujet01.arg',) ('test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/Rsujet01.data',) error: UNIQUE constraint failed: _DISKITEMS_._uuid ERROR: ** brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert"/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. ** * * * `**DatabaseError**` Traceback (most recent call last): File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1266, in insertDiskItems cursor.execute( sqlite3.IntegrityError: UNIQUE constraint failed: _DISKITEMS_._uuid During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/casa/install/python/brainvisa/processes.py", line 3500, in _processExecution neuroHierarchy.databases.insertDiskItem( File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 256, in insertDiskItem self.insertDiskItems((item, ), **kwargs) File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 2249, in insertDiskItems database.insertDiskItems((diskItem,), update=update, File "/casa/install/python/brainvisa/data/sqlFSODatabase.py", line 1307, in insertDiskItems raise DatabaseError( brainvisa.data.sqlFSODatabase.DatabaseError: Cannot insert "/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/folds/3.1/cnn_auto/Rsujet01_cnn_auto.arg" because its uuid is in conflict with the uuid of another file in the database. progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it progress: 100.0 % ... _Process **Morphologist 2021** finished on 2025/07/29 05:49 (1 minutes 4 seconds)_ Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 ok ---------------------------------------------------------------------- Ran 1 test in 744.132s OK RETURNCODE: True Exception ignored in: Traceback (most recent call last): File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2699, in __del__ TypeError: 'NoneType' object is not callable ================================================================================ SUCCESS (exit code 0) ================================================================================ ---------------------------------------- $ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=cea-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/ref -- sh -c '/casa/install/bin/bv_env_test "timeout" "-k" "10" "5400" "python3" "-m" "morphologist.tests.test_morphologist_capsul"' ---------------------------------------- ['/casa/install/python/morphologist/tests/test_morphologist_capsul.py'] Starting tests under /tmp/axon_test_h9i4e6p5 Loading toolbox baby Loading toolbox bioprocessing Loading toolbox brainrat Loading toolbox constellation Loading toolbox cortical_surface Loading toolbox data management Loading toolbox disco Loading toolbox freesurfer Loading toolbox highres_cortex Loading toolbox morphologist Loading toolbox primatologist Loading toolbox spm Loading toolbox structural_analysis Loading toolbox tools Loading toolbox viewers Loading toolbox My processes The log file for this session is '/tmp/axon_test_h9i4e6p5/bv_home/brainvisa.log' exec: /casa/install/brainvisa/toolboxes/constellation/startup.py exec: /casa/install/brainvisa/toolboxes/morphologist/startup.py SPM dir: /usr/local/spm12-standalone spmtemplates: /usr/local/spm12-standalone/spm12_mcr/spm12/spm12 /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: parse directories and insert items /usr/local/spm12-standalone/spm12_mcr/spm12/spm12: 8 files are stored as 8 DiskItems in 0 seconds test_pipeline_results (__main__.TestMorphologistCapsul) ... * Check SPAM models installation _Process **Check SPAM models installation** started on 2025/07/29 05:50_ models: 6 SPAM models are present. _Process **Check SPAM models installation** finished on 2025/07/29 05:50 (0 seconds)_ * Create test database /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds Generating database tables for /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist: 2 files are stored as 2 DiskItems in 0 seconds * Download https://brainvisa.info/download/data/demo_data.zip to /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul * Import test data _Process **Import T1 MRI** started on 2025/07/29 05:51_ filein : /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima fileout : /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii encoding: Binary normal : 0 rescale : 0 format : type : S16 objtype : xdim : 0 ydim : 0 zdim : 0 imin : default imax : default omin : default omax : default reading /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima as Volume / S16... reading done convert to Volume / S16 converting data... convert done writing /volatile/a-sac-ns-brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii... done _Process **Import T1 MRI** finished on 2025/07/29 05:51 (2 seconds)_ * create process Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' * Run Morphologist_Capsul to get test results _Process **Morphologist CAPSUL iteration** started on 2025/07/29 05:51_ Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' progress: 0.0 % ... Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' Exception: 'StudyConfig' object has no attribute 'use_freesurfer' progress: 100.0 % ... jobs: 26 real, 26 total including barriers _Process **Morphologist CAPSUL iteration** finished on 2025/07/29 05:51 (1 seconds)_ workflow: /tmp/axon_test_h9i4e6p5/tmp/bv_hb20kafu.workflow soma-workflow starting in light mode ** Workflow status OK Workflow controller initialised * running Morphologist... * finished. * Run Morphologist_Capsul CNN sulci recognition _Process **Morphologist CAPSUL iteration** started on 2025/07/29 05:58_ progress: 0.0 % ... progress: 100.0 % ... jobs: 4 real, 4 total including barriers _Process **Morphologist CAPSUL iteration** finished on 2025/07/29 05:58 (0 seconds)_ ** Workflow status OK Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.3 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Warning: wrong filename_base in graph, trying to fix it Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 Reading FGraph version 3.1 ok workflow: /tmp/axon_test_h9i4e6p5/tmp/bv_hb20kafu.workflow * running CNN... * finished. ** No failed jobs. del WorkflowController ** all OK. ---------------------------------------------------------------------- Ran 1 test in 603.642s OK RETURNCODE: True Exception ignored in: Traceback (most recent call last): File "/casa/install/python/brainvisa/data/neuroDiskItems.py", line 2699, in __del__ TypeError: 'NoneType' object is not callable ================================================================================ SUCCESS (exit code 0) Finished: SUCCESS