Console Output
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_8jiovx_f
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_8jiovx_f/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 2025/06/30 05:43_
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 2025/06/30 05:43 (1 seconds)_
(not doing ANN sulci recognition tests today)
* Check SPAM models installation
_Process **Check SPAM models installation** started on 2025/06/30 05:43_
models: 6
SPAM models are present.
_Process **Check SPAM models installation** finished on 2025/06/30 05:43 (0
seconds)_
* Run Morphologist
_Process **Morphologist 2021** started on 2025/06/30 05:43_
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 2025/06/30 05:45_
_Process **Hemisphere Sulci Voronoi** finished on 2025/06/30 05:45 (18
seconds)_
_Process **Hemisphere Sulci Thickness and Volumes** started on 2025/06/30
05:45_
_Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/06/30
05:45 (11 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 2025/06/30 05:49_
_Process **Hemisphere Sulci Voronoi** finished on 2025/06/30 05:49 (18
seconds)_
_Process **Hemisphere Sulci Thickness and Volumes** started on 2025/06/30
05:49_
_Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/06/30
05:49 (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 2025/06/30 05:52 (8 minutes 50
seconds)_
* Run CNN recognition
_Process **Morphologist 2021** started on 2025/06/30 05:52_
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_8jiovx_f/tmp/soma_workflow_860ffctb
del WorkflowController
progress: 85.0 % ...
UUID conflict in database, uuid: 8975c730-8520-9166-072f-5eb34d00a6ab
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_8jiovx_f/tmp/soma_workflow_kqf0aodi
del WorkflowController
progress: 90.0 % ...
UUID conflict in database, uuid: e44cf0d7-7174-18e5-b48a-03b4bdf597d5
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 2025/06/30 05:53 (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 742.713s
OK
RETURNCODE: True
Exception ignored in: <function TemporaryDirectory.__del__ at 0x722bdbe3ca60>
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_wlfq3gfj
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_wlfq3gfj/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 2025/06/30 05:55_
models: 6
SPAM models are present.
_Process **Check SPAM models installation** finished on 2025/06/30 05:55 (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 2025/06/30 05:55_
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 2025/06/30 05:55 (1 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 2025/06/30 05:55_
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 2025/06/30 05:55 (1
seconds)_
workflow: /tmp/axon_test_wlfq3gfj/tmp/bv_ubsror0z.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 2025/06/30 06:02_
progress: 0.0 % ...
progress: 100.0 % ...
jobs: 4 real, 4 total including barriers
_Process **Morphologist CAPSUL iteration** finished on 2025/06/30 06:02 (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_wlfq3gfj/tmp/bv_ubsror0z.workflow
* running CNN...
* finished.
** No failed jobs.
del WorkflowController
** all OK.
----------------------------------------------------------------------
Ran 1 test in 598.357s
OK
RETURNCODE: True
Exception ignored in: <function TemporaryDirectory.__del__ at 0x7a8b3ee24430>
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
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