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" "python3" "-m" "disco.tests.test_processes" "--verbose"' ---------------------------------------- Starting tests under /tmp/axon_test_8as6e3v7 /casa/install/python/soma/qt_gui/qt_backend.py:45: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses import imp /casa/install/python/soma/qt_gui/qt_backend.py:419: ImportWarning: __package__ != __spec__.parent from . import QtCore :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :915: ResourceWarning: unclosed file <_io.BufferedReader name='/usr/local/lib/python3.10/dist-packages/PyQt5/QtCore.so'> ResourceWarning: Enable tracemalloc to get the object allocation traceback :671: ImportWarning: QtImporter.exec_module() not found; falling back to load_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() /casa/install/python/brainvisa/configuration/brainvisa_configuration.py:50: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.spawn import find_executable /casa/install/python/brainvisa/processing/neuroException.py:52: DeprecationWarning: the formatter module is deprecated from . import formatter /casa/install/python/soma/qt_gui/qt_backend.py:404: ImportWarning: __package__ != __spec__.parent from . import QtCore /casa/install/python/soma/qt_gui/qt_backend.py:419: ImportWarning: __package__ != __spec__.parent from . import QtCore :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :915: ResourceWarning: unclosed file <_io.BufferedReader name='/usr/local/lib/python3.10/dist-packages/PyQt5/QtGui.so'> ResourceWarning: Enable tracemalloc to get the object allocation traceback :671: ImportWarning: QtImporter.exec_module() not found; falling back to load_module() /casa/install/python/soma/qt_gui/qt_backend.py:185: ImportWarning: __package__ != __spec__.parent from . import QtCore :915: ResourceWarning: unclosed file <_io.BufferedReader name='/usr/local/lib/python3.10/dist-packages/PyQt5/QtWidgets.so'> ResourceWarning: Enable tracemalloc to get the object allocation traceback :915: ResourceWarning: unclosed file <_io.BufferedReader name='/usr/local/lib/python3.10/dist-packages/PyQt5/Qt.so'> ResourceWarning: Enable tracemalloc to get the object allocation traceback :915: ResourceWarning: unclosed file <_io.BufferedReader name='/usr/local/lib/python3.10/dist-packages/PyQt5/QtWebKit.so'> ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/soma/minf/xml_writer.py:101: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/bv_home/current_runs.minf' mode='w' encoding='UTF-8'> self.__file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback 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_8as6e3v7/bv_home/brainvisa.log' /casa/install/python/soma/sqlite_tools.py:119: DeprecationWarning: getName() is deprecated, get the name attribute instead currentThread = threading.current_thread().getName() /casa/install/python/soma/qt_gui/qt_backend.py:404: ImportWarning: __package__ != __spec__.parent from . import QtCore /casa/install/python/soma/qt_gui/qt_backend.py:419: ImportWarning: __package__ != __spec__.parent from . import QtCore :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :671: ImportWarning: QtImporter.exec_module() not found; falling back to load_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() :914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module() /casa/install/python/soma/sqlite_tools.py:119: DeprecationWarning: getName() is deprecated, get the name attribute instead currentThread = threading.current_thread().getName() 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 Database /neurospin/lnao/Panabase/yleprince/disco_test_data/subjects_db must be updated because some types tables are missing. /casa/install/python/soma/sqlite_tools.py:148: DeprecationWarning: getName() is deprecated, get the name attribute instead currentThread = threading.current_thread().getName() /casa/install/python/soma/sqlite_tools.py:180: DeprecationWarning: getName() is deprecated, get the name attribute instead currentThread = threading.current_thread().getName() Generating database tables for /neurospin/lnao/Panabase/yleprince/disco_test_data/subjects_db /neurospin/lnao/Panabase/yleprince/disco_test_data/subjects_db: parse directories and insert items /neurospin/lnao/Panabase/yleprince/disco_test_data/subjects_db: 394 files are stored as 382 DiskItems in 10 seconds /tmp/axon_test_8as6e3v7/tmp/disco_testu7dz8eti: parse directories and insert items /tmp/axon_test_8as6e3v7/tmp/disco_testu7dz8eti: 2 files are stored as 2 DiskItems in 0 seconds Generating database tables for /tmp/axon_test_8as6e3v7/tmp/disco_testu7dz8eti /tmp/axon_test_8as6e3v7/tmp/disco_testu7dz8eti: parse directories and insert items /tmp/axon_test_8as6e3v7/tmp/disco_testu7dz8eti: 2 files are stored as 2 DiskItems in 0 seconds test_parameter_completion_DISCO_DARTEL_Complete_pipeline (__main__.TestParameterCompletion) ... _Process **01\. Sulci Label Translation** started on 2025/07/30 05:17_ _Process **01\. Sulci Label Translation** finished on 2025/07/30 05:17 (0 seconds)_ /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_n6y0qsa2' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_p76vfr4f' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback _Process **02b. Sulci To Be Added** started on 2025/07/30 05:17_ These sulci **will not be considered** for the DISCO registration: ~~' F.C.L.a.'~~ ~~'F.C.L.p.'~~ ~~'F.C.L.r.ant.'~~ ~~'F.C.L.r.asc.'~~ ~~'F.C.L.r.diag.'~~ ~~'F.C.L.r.retroC.tr.'~~ ~~'F.C.L.r.sc.ant.'~~ ~~'F.C.L.r.sc.post.'~~ ~~'F.C.M.r.AMS.ant.'~~ ~~'F.Cal.ant.-Sc.Cal.'~~ ~~'F.I.P.Po.C.inf.'~~ ~~'F.I.P.r.int.1'~~ ~~'F.I.P.r.int.2'~~ ~~'INSULA'~~ ~~'OCCIPITAL'~~ ~~'S.C.LPC.'~~ ~~'S.C.sylvian.'~~ ~~'S.Call.'~~ ~~'S.Cu.'~~ ~~'S.F.inf.ant.'~~ ~~'S.F.int.'~~ ~~'S.F.inter.'~~ ~~'S.F.marginal.'~~ ~~'S.F.median.'~~ ~~'S.F.orbitaire.'~~ ~~'S.F.polaire.tr.'~~ ~~'S.GSM.'~~ ~~'S.Li.ant.'~~ ~~'S.O.T.lat.ant.'~~ ~~'S.O.T.lat.int.'~~ ~~'S.O.T.lat.med.'~~ ~~'S.O.T.lat.post.'~~ ~~'S.O.p.'~~ ~~'S.Or.'~~ ~~'S.Or.l.'~~ ~~'S.Pa.int.'~~ ~~'S.Pa.sup.'~~ ~~'S.Pa.t.'~~ ~~'S.Pe.C.'~~ ~~'S.Pe.C.inter.'~~ ~~'S.Pe.C.marginal.'~~ ~~'S.Pe.C.median.'~~ ~~'S.Po.C.sup.'~~ ~~'S.R.inf.'~~ ~~'S.R.sup.'~~ ~~'S.Rh.'~~ ~~'S.T.i.ant.'~~ ~~'S.T.i.post.'~~ ~~'S.T.pol.'~~ ~~'S.T.s.ter.asc.ant.'~~ ~~'S.T.s.ter.asc.post.'~~ ~~'S.intraCing.'~~ ~~'S.p.C.'~~ ~~'S.s.P.'~~ ~~'ventricle '~~. These sulci **will be considered** for the DISCO registration: ' F.C.M.ant.' 'F.C.M.post.' 'F.Coll.' 'F.I.P.' 'F.P.O.' 'S.C.' 'S.F.inf.' 'S.F.sup.' 'S.Li.post.' 'S.Olf.' 'S.Pe.C.inf.' 'S.Pe.C.sup.' 'S.T.s. '. _Process **View Sulci to be studied** started on 2025/07/30 05:17_ Sulcus| Left label| Right label| Considered| Unsimplified| Normalized| Full name ---|---|---|---|---|---|--- **C.CALCARIN** F.Cal.ant.-Sc.Cal.| 23| 24| | | | calcarine fissure S.O.p.| 83| 84| | | | occipito-polar sulcus **CENTRAL** S.C.| 43| 44| yes| | | central sulcus S.C.sylvian.| 45| 46| | | | central sylvian sulcus **F.C.L.** F.C.L.a.| 1| 2| | | | anterior lateral fissure F.C.L.p.| 3| 4| | | | posterior lateral fissure F.C.L.r.ant.| 5| 6| | | | anterior ramus of the lateral fissure F.C.L.r.asc.| 7| 8| | | | ascending ramus of the lateral fissure F.C.L.r.diag.| 9| 10| | | | diagonal ramus of the lateral fissure F.C.L.r.retroC.tr.| 11| 12| | | | retro central transverse ramus of the lateral fissure F.C.L.r.sc.ant.| 13| 14| | | | anterior sub-central ramus of the lateral fissure F.C.L.r.sc.post.| 15| 16| | | | posterior sub-central ramus of the lateral fissure **FACEINTERNE.F** F.C.M.ant.| 17| 18| yes| | | calloso-marginal anterior fissure F.C.M.post.| 19| 20| yes| | | calloso-marginal posterior fissure F.C.M.r.AMS.ant.| 21| 22| | | | supplementary motor area ramus of the calloso- marginal anterior fissure S.C.LPC.| 41| 42| | | | paracentral lobule central sulcus S.Call.| 47| 48| | | | subcallosal sulcus S.F.int.| 55| 56| | | | internal frontal sulcus S.R.inf.| 111| 112| | | | inferior rostral sulcus S.R.sup.| 113| 114| | | | superior rostral sulcus S.intraCing.| 129| 130| | | | intracingular sulcus S.p.C.| 131| 132| | | | paracentral sulcus **FACEINTERNE.PO** F.P.O.| 35| 36| yes| | | parieto-occipital fissure S.Cu.| 49| 50| | | | cuneal sulcus S.Li.ant.| 71| 72| | | | anterior intralingual sulcus S.Li.post.| 73| 74| yes| | | posterior intra-lingual sulcus S.Pa.int.| 91| 92| | | | internal parietal sulcus S.s.P.| 133| 134| | | | sub-parietal sulcus **INSULA** INSULA| 37| 38| | | | insula **OCCIPITAL** OCCIPITAL| 39| 40| | | | occipital lobe **PARIETAL** F.I.P.| 29| 30| yes| | | intraparietal sulcus F.I.P.Po.C.inf.| 27| 28| | | | superior postcentral intraparietal superior sulcus F.I.P.r.int.1| 31| 32| | | | primary intermediate ramus of the intraparietal sulcus F.I.P.r.int.2| 33| 34| | | | secondary intermediate ramus of the intraparietal sulcus S.GSM.| 69| 70| | | | sulcus of the supra-marginal gyrus S.Pa.sup.| 93| 94| | | | superior parietal sulcus S.Pa.t.| 95| 96| | | | transverse parietal sulcus S.Po.C.sup.| 109| 110| | | | superior postcentral sulcus **PRECENTRAL** S.Pe.C.| 97| 98| | | | precentral sulcus S.Pe.C.inf.| 99| 100| yes| | | inferior precentral sulcus S.Pe.C.inter.| 101| 102| | | | intermediate precentral sulcus S.Pe.C.marginal.| 103| 104| | | | marginal precentral sulcus S.Pe.C.median.| 105| 106| | | | median precentral sulcus S.Pe.C.sup.| 107| 108| yes| | | superior precentral sulcus **PREFRONTAL** S.F.inf.| 51| 52| yes| | | inferior frontal sulcus S.F.inf.ant.| 53| 54| | | | anterior inferior frontal sulcus S.F.inter.| 57| 58| | | | intermediate frontal sulcus S.F.marginal.| 59| 60| | | | marginal frontal sulcus S.F.median.| 61| 62| | | | median frontal sulcus S.F.orbitaire.| 63| 64| | | | orbital frontal sulcus S.F.polaire.tr.| 65| 66| | | | polar frontal sulcus S.F.sup.| 67| 68| yes| | | superior frontal sulcus S.Olf.| 85| 86| yes| | | olfactory sulcus S.Or.| 87| 88| | | | orbital sulcus S.Or.l.| 89| 90| | | | lateral orbital sulcus **TEMPORAL-BASAL** F.Coll.| 25| 26| yes| | | collateral fissure S.O.T.lat.ant.| 75| 76| | | | anterior occipito-temporal lateral sulcus S.O.T.lat.int.| 77| 78| | | | internal occipito-temporal lateral sulcus S.O.T.lat.med.| 79| 80| | | | median occipito-temporal lateral sulcus S.O.T.lat.post.| 81| 82| | | | posterior occipito-temporal lateral sulcus S.Rh.| 115| 116| | | | rhinal sulcus **TEMPORAL-EXT** S.T.i.ant.| 117| 118| | | | anterior inferior temporal sulcus S.T.i.post.| 119| 120| | | | posterior inferior temporal sulcus S.T.pol.| 121| 122| | | | polar temporal sulcus S.T.s.| 123| 124| yes| | | superior temporal sulcus S.T.s.ter.asc.ant.| 125| 126| | | | anterior terminal ascending branch of the superior temporal sulcus S.T.s.ter.asc.post.| 127| 128| | | | posterior terminal ascending branch of the superior temporal sulcus **ventricle** ventricle| 135| 136| | | | ventricle _Process **View Sulci to be studied** finished on 2025/07/30 05:17 (0 seconds)_ /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_m7lwmd3n' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_g0hwhosk' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback _Process **02b. Sulci To Be Added** finished on 2025/07/30 05:17 (0 seconds)_ /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_o4iscbwy' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_nf4gy6gd' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback _Process **B01. Bundles Label Translation** started on 2025/07/30 05:17_ _Process **B01. Bundles Label Translation** finished on 2025/07/30 05:17 (0 seconds)_ /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_c90lbe3r' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_ntnzs6j4' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback _Process **B02. Bundles To Be Removed** started on 2025/07/30 05:17_ _Process **B02. Bundles To Be Removed** finished on 2025/07/30 05:17 (0 seconds)_ /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_ynp6tf2d' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_2ix3c7gv' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback ok test_instantiate_DISCO_DARTEL_Complete_pipeline (__main__.TestProcessInstantiation) ... ok test_instantiate_DiscoDartelInverseWarping (__main__.TestProcessInstantiation) ... ok test_instantiate_IntensityNormalization (__main__.TestProcessInstantiation) ... ok test_instantiate_average_cortical_ribbon (__main__.TestProcessInstantiation) ... ok test_instantiate_copy_DISCO_study_params (__main__.TestProcessInstantiation) ... ok test_instantiate_copy_analysis (__main__.TestProcessInstantiation) ... ok test_instantiate_create_disco_deffield_betweensubjects (__main__.TestProcessInstantiation) ... ok test_instantiate_create_discodartel_deffield_betweensubjects (__main__.TestProcessInstantiation) ... ok test_instantiate_create_discodartel_deffield_commonspace (__main__.TestProcessInstantiation) ... ok test_instantiate_dartel_pipeline (__main__.TestProcessInstantiation) ... ok test_instantiate_dartel_template_qc_table (__main__.TestProcessInstantiation) ... ok test_instantiate_dartel_templates_qc_table (__main__.TestProcessInstantiation) ... ok test_instantiate_deformation_disco_dartel_pipeline (__main__.TestProcessInstantiation) ... ok test_instantiate_deformation_disco_pipeline (__main__.TestProcessInstantiation) ... ok test_instantiate_disco_and_dartel_inputs_qc_table (__main__.TestProcessInstantiation) ... ok test_instantiate_disco_pipeline (__main__.TestProcessInstantiation) ... ok test_instantiate_disco_studies_qc_table (__main__.TestProcessInstantiation) ... ok test_instantiate_disco_study_qc_table (__main__.TestProcessInstantiation) ... ok test_instantiate_final_deformation_graph (__main__.TestProcessInstantiation) ... ok test_instantiate_final_deformation_mesh (__main__.TestProcessInstantiation) ... ok test_instantiate_final_deformation_volume (__main__.TestProcessInstantiation) ... ok test_instantiate_flip_hemi (__main__.TestProcessInstantiation) ... ok test_instantiate_preprocessing_bundles_processes (__main__.TestProcessInstantiation) ... ok test_instantiate_preprocessing_sulci_processes (__main__.TestProcessInstantiation) ... ok test_instantiate_sulci_viewer (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_bundles_between_subjects (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_bundles_into_common_space (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_graph_between_subjects (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_graph_into_common_space (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_mesh_between_subjects (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_mesh_into_common_space (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_volume_between_subjects (__main__.TestProcessInstantiation) ... ok test_instantiate_transform_volume_into_common_space (__main__.TestProcessInstantiation) ... ok test_instantiate_verify_inverse_deformations (__main__.TestProcessInstantiation) ... ok test_instantiate_view_displacement_grid (__main__.TestProcessInstantiation) ... ok test_instantiate_view_displacement_on_surface (__main__.TestProcessInstantiation) ... ok test_instantiate_view_jacobian_determinant (__main__.TestProcessInstantiation) ... ok test_instantiate_view_sulcal_imprint_mesh (__main__.TestProcessInstantiation) ... ok test_instantiate_view_sulcal_imprint_mesh_list (__main__.TestProcessInstantiation) ... ok /casa/install/python/soma/minf/xml_writer.py:101: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/bv_home/current_runs.minf' mode='w' encoding='UTF-8'> self.__file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_roppgv_y' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/tmp/bv_jpt3rsv4' mode='w' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback /casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_8as6e3v7/bv_home/brainvisa.log' mode='a+' encoding='utf-8'> self._file = None ResourceWarning: Enable tracemalloc to get the object allocation traceback ---------------------------------------------------------------------- Ran 40 tests in 27.156s OK /usr/lib/python3.10/subprocess.py:1072: ResourceWarning: subprocess 164092 is still running ================================================================================ 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" "3000" "python3" "-m" "disco.tests.test_complete_pipeline" "--test_mode=run"' ---------------------------------------- Starting tests under /tmp/axon_test_c0kmgrhz Using SPM12 standalone: /drf/local/spm12-standalone 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_c0kmgrhz/bv_home/brainvisa.log' exec: /casa/install/brainvisa/toolboxes/constellation/startup.py exec: /casa/install/brainvisa/toolboxes/morphologist/startup.py SPM dir: /drf/local/spm12-standalone/spm12_mcr/spm12 spmtemplates: None /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel: 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/disco_dartel /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel: parse directories and insert items /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel: 393 files are stored as 381 DiskItems in 0 seconds test_run_DISCO_DARTEL_Complete_pipeline (__main__.TestDiscoDartelReproducibleRun) ... _Process **01\. Sulci Label Translation** started on 2025/07/30 05:17_ _Process **01\. Sulci Label Translation** finished on 2025/07/30 05:17 (0 seconds)_ _Process **02b. Sulci To Be Added** started on 2025/07/30 05:17_ These sulci **will not be considered** for the DISCO registration: ~~' F.C.L.a.'~~ ~~'F.C.L.p.'~~ ~~'F.C.L.r.ant.'~~ ~~'F.C.L.r.asc.'~~ ~~'F.C.L.r.diag.'~~ ~~'F.C.L.r.retroC.tr.'~~ ~~'F.C.L.r.sc.ant.'~~ ~~'F.C.L.r.sc.post.'~~ ~~'F.C.M.r.AMS.ant.'~~ ~~'F.Cal.ant.-Sc.Cal.'~~ ~~'F.I.P.Po.C.inf.'~~ ~~'F.I.P.r.int.1'~~ ~~'F.I.P.r.int.2'~~ ~~'INSULA'~~ ~~'OCCIPITAL'~~ ~~'S.C.LPC.'~~ ~~'S.C.sylvian.'~~ ~~'S.Call.'~~ ~~'S.Cu.'~~ ~~'S.F.inf.ant.'~~ ~~'S.F.int.'~~ ~~'S.F.inter.'~~ ~~'S.F.marginal.'~~ ~~'S.F.median.'~~ ~~'S.F.orbitaire.'~~ ~~'S.F.polaire.tr.'~~ ~~'S.GSM.'~~ ~~'S.Li.ant.'~~ ~~'S.O.T.lat.ant.'~~ ~~'S.O.T.lat.int.'~~ ~~'S.O.T.lat.med.'~~ ~~'S.O.T.lat.post.'~~ ~~'S.O.p.'~~ ~~'S.Or.'~~ ~~'S.Or.l.'~~ ~~'S.Pa.int.'~~ ~~'S.Pa.sup.'~~ ~~'S.Pa.t.'~~ ~~'S.Pe.C.'~~ ~~'S.Pe.C.inter.'~~ ~~'S.Pe.C.marginal.'~~ ~~'S.Pe.C.median.'~~ ~~'S.Po.C.sup.'~~ ~~'S.R.inf.'~~ ~~'S.R.sup.'~~ ~~'S.Rh.'~~ ~~'S.T.i.ant.'~~ ~~'S.T.i.post.'~~ ~~'S.T.pol.'~~ ~~'S.T.s.ter.asc.ant.'~~ ~~'S.T.s.ter.asc.post.'~~ ~~'S.intraCing.'~~ ~~'S.p.C.'~~ ~~'S.s.P.'~~ ~~'ventricle '~~. These sulci **will be considered** for the DISCO registration: ' F.C.M.ant.' 'F.C.M.post.' 'F.Coll.' 'F.I.P.' 'F.P.O.' 'S.C.' 'S.F.inf.' 'S.F.sup.' 'S.Li.post.' 'S.Olf.' 'S.Pe.C.inf.' 'S.Pe.C.sup.' 'S.T.s. '. _Process **View Sulci to be studied** started on 2025/07/30 05:17_ Sulcus| Left label| Right label| Considered| Unsimplified| Normalized| Full name ---|---|---|---|---|---|--- **C.CALCARIN** F.Cal.ant.-Sc.Cal.| 23| 24| | | | calcarine fissure S.O.p.| 83| 84| | | | occipito-polar sulcus **CENTRAL** S.C.| 43| 44| yes| | | central sulcus S.C.sylvian.| 45| 46| | | | central sylvian sulcus **F.C.L.** F.C.L.a.| 1| 2| | | | anterior lateral fissure F.C.L.p.| 3| 4| | | | posterior lateral fissure F.C.L.r.ant.| 5| 6| | | | anterior ramus of the lateral fissure F.C.L.r.asc.| 7| 8| | | | ascending ramus of the lateral fissure F.C.L.r.diag.| 9| 10| | | | diagonal ramus of the lateral fissure F.C.L.r.retroC.tr.| 11| 12| | | | retro central transverse ramus of the lateral fissure F.C.L.r.sc.ant.| 13| 14| | | | anterior sub-central ramus of the lateral fissure F.C.L.r.sc.post.| 15| 16| | | | posterior sub-central ramus of the lateral fissure **FACEINTERNE.F** F.C.M.ant.| 17| 18| yes| | | calloso-marginal anterior fissure F.C.M.post.| 19| 20| yes| | | calloso-marginal posterior fissure F.C.M.r.AMS.ant.| 21| 22| | | | supplementary motor area ramus of the calloso- marginal anterior fissure S.C.LPC.| 41| 42| | | | paracentral lobule central sulcus S.Call.| 47| 48| | | | subcallosal sulcus S.F.int.| 55| 56| | | | internal frontal sulcus S.R.inf.| 111| 112| | | | inferior rostral sulcus S.R.sup.| 113| 114| | | | superior rostral sulcus S.intraCing.| 129| 130| | | | intracingular sulcus S.p.C.| 131| 132| | | | paracentral sulcus **FACEINTERNE.PO** F.P.O.| 35| 36| yes| | | parieto-occipital fissure S.Cu.| 49| 50| | | | cuneal sulcus S.Li.ant.| 71| 72| | | | anterior intralingual sulcus S.Li.post.| 73| 74| yes| | | posterior intra-lingual sulcus S.Pa.int.| 91| 92| | | | internal parietal sulcus S.s.P.| 133| 134| | | | sub-parietal sulcus **INSULA** INSULA| 37| 38| | | | insula **OCCIPITAL** OCCIPITAL| 39| 40| | | | occipital lobe **PARIETAL** F.I.P.| 29| 30| yes| | | intraparietal sulcus F.I.P.Po.C.inf.| 27| 28| | | | superior postcentral intraparietal superior sulcus F.I.P.r.int.1| 31| 32| | | | primary intermediate ramus of the intraparietal sulcus F.I.P.r.int.2| 33| 34| | | | secondary intermediate ramus of the intraparietal sulcus S.GSM.| 69| 70| | | | sulcus of the supra-marginal gyrus S.Pa.sup.| 93| 94| | | | superior parietal sulcus S.Pa.t.| 95| 96| | | | transverse parietal sulcus S.Po.C.sup.| 109| 110| | | | superior postcentral sulcus **PRECENTRAL** S.Pe.C.| 97| 98| | | | precentral sulcus S.Pe.C.inf.| 99| 100| yes| | | inferior precentral sulcus S.Pe.C.inter.| 101| 102| | | | intermediate precentral sulcus S.Pe.C.marginal.| 103| 104| | | | marginal precentral sulcus S.Pe.C.median.| 105| 106| | | | median precentral sulcus S.Pe.C.sup.| 107| 108| yes| | | superior precentral sulcus **PREFRONTAL** S.F.inf.| 51| 52| yes| | | inferior frontal sulcus S.F.inf.ant.| 53| 54| | | | anterior inferior frontal sulcus S.F.inter.| 57| 58| | | | intermediate frontal sulcus S.F.marginal.| 59| 60| | | | marginal frontal sulcus S.F.median.| 61| 62| | | | median frontal sulcus S.F.orbitaire.| 63| 64| | | | orbital frontal sulcus S.F.polaire.tr.| 65| 66| | | | polar frontal sulcus S.F.sup.| 67| 68| yes| | | superior frontal sulcus S.Olf.| 85| 86| yes| | | olfactory sulcus S.Or.| 87| 88| | | | orbital sulcus S.Or.l.| 89| 90| | | | lateral orbital sulcus **TEMPORAL-BASAL** F.Coll.| 25| 26| yes| | | collateral fissure S.O.T.lat.ant.| 75| 76| | | | anterior occipito-temporal lateral sulcus S.O.T.lat.int.| 77| 78| | | | internal occipito-temporal lateral sulcus S.O.T.lat.med.| 79| 80| | | | median occipito-temporal lateral sulcus S.O.T.lat.post.| 81| 82| | | | posterior occipito-temporal lateral sulcus S.Rh.| 115| 116| | | | rhinal sulcus **TEMPORAL-EXT** S.T.i.ant.| 117| 118| | | | anterior inferior temporal sulcus S.T.i.post.| 119| 120| | | | posterior inferior temporal sulcus S.T.pol.| 121| 122| | | | polar temporal sulcus S.T.s.| 123| 124| yes| | | superior temporal sulcus S.T.s.ter.asc.ant.| 125| 126| | | | anterior terminal ascending branch of the superior temporal sulcus S.T.s.ter.asc.post.| 127| 128| | | | posterior terminal ascending branch of the superior temporal sulcus **ventricle** ventricle| 135| 136| | | | ventricle _Process **View Sulci to be studied** finished on 2025/07/30 05:17 (0 seconds)_ _Process **02b. Sulci To Be Added** finished on 2025/07/30 05:17 (0 seconds)_ _Process **Disco and Dartel complete pipeline** started on 2025/07/30 05:17_ progress: 0.0 % ... progress: 0.0 % ... Skip GUI-only node: View Sulci to be studied progress: 2.5 % ... Skip unselected node: View Bundles to be studied progress: 5.0 % ... progress: 5.0 % ... progress: 6.25 % ... progress: 7.5 % ... progress: 7.5 % ... progress: 7.5 % ... Extracting hull_junction and bottom from graph for sujet01 progress: 8.125 % ... Extracting hull_junction and bottom from graph for sujet02 progress: 8.75 % ... Execution of the DISCO sulcal imprint core method (Standalone/Matlab)... progress: 10.0 % ... progress: 10.0 % ... Execution of the DISCO build template core method (Standalone/Matlab)... progress: 12.5 % ... progress: 12.5 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet01-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet01_grid_init.mesh in process progress: 12.75 % ... Deformation of initial grid in process _Process **Mesh deformation component** started on 2025/07/30 05:22_ Execution of the DISCO mesh deform core (Standalone/Matlab)... /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet01-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet01_grid_init.mesh _Process **Mesh deformation component** finished on 2025/07/30 05:23 (12 seconds)_ progress: 13.0 % ... Inverse deformation of initial grid in process _Process **Mesh deformation component** started on 2025/07/30 05:23_ Execution of the DISCO mesh deform core (Standalone/Matlab)... /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet01-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet01_grid_init.mesh _Process **Mesh deformation component** finished on 2025/07/30 05:23 (11 seconds)_ progress: 13.25 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet01-default_acquisition- disco_analysis- folds-3.1/default_session_auto/mesh/sujet01_default_acquisition_disco_analysis_displ_field.ima in process progress: 13.5 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet01-default_acquisition- disco_analysis- folds-3.1/default_session_auto/mesh/sujet01_default_acquisition_disco_analysis_inv_displ_field.ima in process progress: 13.750000000000002 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet02-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet02_grid_init.mesh in process progress: 13.999999999999998 % ... Deformation of initial grid in process _Process **Mesh deformation component** started on 2025/07/30 05:23_ Execution of the DISCO mesh deform core (Standalone/Matlab)... /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet02-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet02_grid_init.mesh _Process **Mesh deformation component** finished on 2025/07/30 05:23 (11 seconds)_ progress: 14.250000000000002 % ... Inverse deformation of initial grid in process _Process **Mesh deformation component** started on 2025/07/30 05:23_ Execution of the DISCO mesh deform core (Standalone/Matlab)... /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet02-default_acquisition- disco_analysis-folds-3.1/default_session_auto/mesh/sujet02_grid_init.mesh _Process **Mesh deformation component** finished on 2025/07/30 05:23 (11 seconds)_ progress: 14.499999999999998 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet02-default_acquisition- disco_analysis- folds-3.1/default_session_auto/mesh/sujet02_default_acquisition_disco_analysis_displ_field.ima in process progress: 14.750000000000002 % ... Creation of /volatile/a-sac-ns- brainvisa/bbi_nightly/cea-5.1-5.3-userimage/tests/test/disco_dartel/analyzes/DISCO_analyzes/DISCO_TestStudy/deformed_output/sujet02-default_acquisition- disco_analysis- folds-3.1/default_session_auto/mesh/sujet02_default_acquisition_disco_analysis_inv_displ_field.ima in process progress: 15.0 % ... progress: 15.0 % ... progress: 15.0 % ... somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. progress: 16.25 % ... somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. progress: 17.5 % ... progress: 17.5 % ... progress: 17.5 % ... somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. progress: 18.75 % ... somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. progress: 20.0 % ... progress: 20.0 % ... progress: 20.0 % ... Skip unselected node: Deformation DISCO Pipeline progress: 40.0 % ... progress: 40.0 % ... somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. _Process **Resample images into a Talairach-aligned grid** started on 2025/07/30 05:24_ _Process **Resample images into a Talairach-aligned grid** finished on 2025/07/30 05:24 (2 seconds)_ _Process **Resample images into a Talairach-aligned grid** started on 2025/07/30 05:24_ _Process **Resample images into a Talairach-aligned grid** finished on 2025/07/30 05:24 (2 seconds)_ somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. _Process **Resample images into a Talairach-aligned grid** started on 2025/07/30 05:24_ _Process **Resample images into a Talairach-aligned grid** finished on 2025/07/30 05:24 (2 seconds)_ _Process **Resample images into a Talairach-aligned grid** started on 2025/07/30 05:24_ _Process **Resample images into a Talairach-aligned grid** finished on 2025/07/30 05:24 (2 seconds)_ WARNING:Failed to store the sform while preserving the qform somanifti: inserting a dummy scanner-based qform to fix data orientation WARNING:Failed to store the sform while preserving the qform somanifti: inserting a dummy scanner-based qform to fix data orientation WARNING:Failed to store the sform while preserving the qform somanifti: inserting a dummy scanner-based qform to fix data orientation WARNING:Failed to store the sform while preserving the qform somanifti: inserting a dummy scanner-based qform to fix data orientation progress: 46.666666666666664 % ... _Process **spm12 - Run DARTEL (create Templates) - generic** started on 2025/07/30 05:24_ running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_c0kmgrhz/tmp/bv_wpaelmm6/batch_DartelTemplate.m'] ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/drf/local/matlab/MATLAB_Runtime/v97/runtime/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/bin/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/os/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 SPM12, version 7771 (standalone) MATLAB, version 9.7.0.1737446 (R2019b) Update 9 ___ ____ __ __ / __)( _ \( \/ ) \__ \ )___/ ) ( Statistical Parametric Mapping (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ ------------------------------------------------------------------------ 30-Jul-2025 05:25:00 - Running job #1 ------------------------------------------------------------------------ 30-Jul-2025 05:25:01 - Running 'Run Dartel (create Templates)' 0.828483, 0.0338502, 0.00658715, 0.00139318, 0.000343858, 0.000101508, 3.49817e-05, 1.38649e-05, 1 1 1.31768e+06 0 1.31768e+06 239.869 1 2 1.36696e+06 0 1.36696e+06 242.48 0.814868, 0.0291934, 0.00540184, 0.00111219, 0.000269985, 7.92981e-05, 2.75678e-05, 1.11688e-05, 30-Jul-2025 05:28:00 - Done 'Run Dartel (create Templates)' 30-Jul-2025 05:28:00 - Done Bye for now... _Process **spm12 - Run DARTEL (create Templates) - generic** finished on 2025/07/30 05:28 (3 minutes 43 seconds)_ progress: 53.333333333333336 % ... progress: 53.333333333333336 % ... sujet01 in process Creation of coordinates volumes for Inverse Final displacement field Creation of coordinates volumes for Final displacement field progress: 53.333333333333336 % ... DISCO deformation somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. DARTEL deformation _Process **03\. DARTEL Images Warping** started on 2025/07/30 05:28_ somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. _Process **spm12 - create warped - generic** started on 2025/07/30 05:28_ running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_c0kmgrhz/tmp/bv_58g1ulcg/batch_DartelWarping.m'] ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/drf/local/matlab/MATLAB_Runtime/v97/runtime/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/bin/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/os/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 SPM12, version 7771 (standalone) MATLAB, version 9.7.0.1737446 (R2019b) Update 9 ___ ____ __ __ / __)( _ \( \/ ) \__ \ )___/ ) ( Statistical Parametric Mapping (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ ------------------------------------------------------------------------ 30-Jul-2025 05:28:38 - Running job #1 ------------------------------------------------------------------------ 30-Jul-2025 05:28:38 - Running 'Create Warped' u_rc1_Grey_sujet01_default_acquisition_disco_analysis_DISCO_TestTemplate: bv__rz33of7 1,1,1 2,1,1 3,1,1 30-Jul-2025 05:28:45 - Done 'Create Warped' 30-Jul-2025 05:28:45 - Done Bye for now... _Process **spm12 - create warped - generic** finished on 2025/07/30 05:28 (27 seconds)_ _Process **03\. DARTEL Images Warping** finished on 2025/07/30 05:28 (32 seconds)_ progress: 55.00000000000001 % ... DARTEL inverse deformation _Process **04\. DARTEL Images Inverse Warping** started on 2025/07/30 05:28_ _Process **spm12 - create inverse warped - generic** started on 2025/07/30 05:28_ running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_c0kmgrhz/tmp/bv_roxnfni3/batch_inverseDARTEL.m'] ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/drf/local/matlab/MATLAB_Runtime/v97/runtime/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/bin/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/os/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 SPM12, version 7771 (standalone) MATLAB, version 9.7.0.1737446 (R2019b) Update 9 ___ ____ __ __ / __)( _ \( \/ ) \__ \ )___/ ) ( Statistical Parametric Mapping (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ ------------------------------------------------------------------------ 30-Jul-2025 05:29:05 - Running job #1 ------------------------------------------------------------------------ 30-Jul-2025 05:29:05 - Running 'Create Inverse Warped' u_rc1_Grey_sujet01_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_1st5g1jn 1,1,1 2,1,1 3,1,1 30-Jul-2025 05:29:13 - Done 'Create Inverse Warped' 30-Jul-2025 05:29:13 - Done Bye for now... _Process **spm12 - create inverse warped - generic** finished on 2025/07/30 05:29 (28 seconds)_ somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. _Process **04\. DARTEL Images Inverse Warping** finished on 2025/07/30 05:29 (33 seconds)_ DISCO Inverse deformation somanifti warning: cannot determine the orientation of the Nifti file reliably, assuming that the target coordinates of sform have RAS+ orientation (sform_code = 2 a.k.a. Coordinates aligned to another file or to anatomical truth). somanifti warning: cannot determine the orientation of the Nifti file reliably, assuming that the target coordinates of sform have RAS+ orientation (sform_code = 2 a.k.a. Coordinates aligned to another file or to anatomical truth). somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. Creation of the inverse final displacement field Creation of the final displacement field somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. progress: 56.666666666666664 % ... sujet02 in process Creation of coordinates volumes for Inverse Final displacement field Creation of coordinates volumes for Final displacement field progress: 56.666666666666664 % ... DISCO deformation somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. DARTEL deformation _Process **03\. DARTEL Images Warping** started on 2025/07/30 05:29_ somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. _Process **spm12 - create warped - generic** started on 2025/07/30 05:29_ running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_c0kmgrhz/tmp/bv_ks_5x538/batch_DartelWarping.m'] ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/drf/local/matlab/MATLAB_Runtime/v97/runtime/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/bin/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/os/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 SPM12, version 7771 (standalone) MATLAB, version 9.7.0.1737446 (R2019b) Update 9 ___ ____ __ __ / __)( _ \( \/ ) \__ \ )___/ ) ( Statistical Parametric Mapping (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ ------------------------------------------------------------------------ 30-Jul-2025 05:30:09 - Running job #1 ------------------------------------------------------------------------ 30-Jul-2025 05:30:09 - Running 'Create Warped' u_rc1_Grey_sujet02_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_k48pd_t5 1,1,1 2,1,1 3,1,1 30-Jul-2025 05:30:16 - Done 'Create Warped' 30-Jul-2025 05:30:16 - Done Bye for now... _Process **spm12 - create warped - generic** finished on 2025/07/30 05:30 (28 seconds)_ _Process **03\. DARTEL Images Warping** finished on 2025/07/30 05:30 (33 seconds)_ progress: 58.33333333333333 % ... DARTEL inverse deformation _Process **04\. DARTEL Images Inverse Warping** started on 2025/07/30 05:30_ _Process **spm12 - create inverse warped - generic** started on 2025/07/30 05:30_ running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_c0kmgrhz/tmp/bv_8r8a_peq/batch_inverseDARTEL.m'] ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/drf/local/matlab/MATLAB_Runtime/v97/runtime/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/bin/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/os/glnxa64:/drf/local/matlab/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 SPM12, version 7771 (standalone) MATLAB, version 9.7.0.1737446 (R2019b) Update 9 ___ ____ __ __ / __)( _ \( \/ ) \__ \ )___/ ) ( Statistical Parametric Mapping (___/(__) (_/\/\_) SPM12 - https://www.fil.ion.ucl.ac.uk/spm/ ------------------------------------------------------------------------ 30-Jul-2025 05:30:39 - Running job #1 ------------------------------------------------------------------------ 30-Jul-2025 05:30:39 - Running 'Create Inverse Warped' u_rc1_Grey_sujet02_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_bjo6uoe_ 1,1,1 2,1,1 3,1,1 30-Jul-2025 05:30:46 - Done 'Create Inverse Warped' 30-Jul-2025 05:30:46 - Done Bye for now... _Process **spm12 - create inverse warped - generic** finished on 2025/07/30 05:30 (31 seconds)_ somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. _Process **04\. DARTEL Images Inverse Warping** finished on 2025/07/30 05:30 (35 seconds)_ DISCO Inverse deformation somanifti warning: cannot determine the orientation of the Nifti file reliably, assuming that the target coordinates of sform have RAS+ orientation (sform_code = 2 a.k.a. Coordinates aligned to another file or to anatomical truth). somanifti warning: cannot determine the orientation of the Nifti file reliably, assuming that the target coordinates of sform have RAS+ orientation (sform_code = 2 a.k.a. Coordinates aligned to another file or to anatomical truth). somanifti warning: the data of the saved Nifti file will be loaded in a different in-memory order when opened by somanifti. Creation of the inverse final displacement field Creation of the final displacement field somanifti warning: this Nifti file has neither a qform nor a sform, assuming that the on-disk data order is RAS+. progress: 60.0 % ... progress: 60.0 % ... progress: 60.0 % ... progress: 60.0 % ... progress: 60.0 % ... progress: 60.83333333333333 % ... progress: 61.66666666666667 % ... progress: 62.5 % ... progress: 63.33333333333333 % ... progress: 63.33333333333333 % ... progress: 63.33333333333333 % ... progress: 65.0 % ... progress: 66.66666666666667 % ... progress: 66.66666666666667 % ... progress: 66.66666666666667 % ... progress: 68.33333333333333 % ... progress: 70.0 % ... progress: 70.0 % ... progress: 70.0 % ... progress: 71.66666666666667 % ... progress: 73.33333333333333 % ... progress: 73.33333333333333 % ... progress: 73.33333333333333 % ... progress: 75.0 % ... progress: 76.66666666666667 % ... progress: 76.66666666666667 % ... progress: 76.66666666666667 % ... progress: 78.33333333333333 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 80.0 % ... progress: 82.5 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 85.0 % ... progress: 87.5 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 90.0 % ... progress: 93.33333333333333 % ... progress: 96.66666666666666 % ... progress: 100.0 % ... progress: 100.0 % ... progress: 100.0 % ... progress: 100.0 % ... _Process **Disco and Dartel complete pipeline** finished on 2025/07/30 05:32 (14 minutes 14 seconds)_ ok Comparison report ================= 842 equivalent files 0 different files 0 files without reference 521 skipped files ---------------------------------------------------------------------- Ran 1 test in 1165.476s OK 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