Console Output
Started
Running as brainvisa
================================================================================
----------------------------------------
$ /usr/bin/python3 /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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_p_llfva9
Loading toolbox brainrat
Loading toolbox cortical_surface
Loading toolbox data management
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_p_llfva9/bv_home/brainvisa.log'
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/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist:
parse directories and insert items
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/ref/test_morphologist_pipeline/db_morphologist:
188 files are stored as 182 DiskItems in 0 seconds
* Create test database
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist:
parse directories and insert items
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist:
parse directories and insert items
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline
* Import test data
_Process **Import T1 MRI** started on 2025/06/30 04:19_
filein : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima
fileout : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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/brainvisa-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/brainvisa-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 04:19 (1 seconds)_
(not doing ANN sulci recognition tests today)
* Check SPAM models installation
_Process **Check SPAM models installation** started on 2025/06/30 04:19_
models: 6
SPAM models are present.
_Process **Check SPAM models installation** finished on 2025/06/30 04:19 (0
seconds)_
* Run Morphologist
_Process **Morphologist 2021** started on 2025/06/30 04:19_
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 04:22_
_Process **Hemisphere Sulci Voronoi** finished on 2025/06/30 04:22 (24
seconds)_
_Process **Hemisphere Sulci Thickness and Volumes** started on 2025/06/30
04:22_
_Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/06/30
04:22 (19 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 04:28_
_Process **Hemisphere Sulci Voronoi** finished on 2025/06/30 04:28 (25
seconds)_
_Process **Hemisphere Sulci Thickness and Volumes** started on 2025/06/30
04:28_
_Process **Hemisphere Sulci Thickness and Volumes** finished on 2025/06/30
04:29 (18 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 04:33 (13 minutes 50
seconds)_
* Run CNN recognition
_Process **Morphologist 2021** started on 2025/06/30 04:33_
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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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_p_llfva9/tmp/soma_workflow_jrpdo9nu
del WorkflowController
progress: 85.0 % ...
UUID conflict in database, uuid: 77b3f5e2-deb7-a9b2-e890-2f94b87417cf
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/brainvisa-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/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_pipeline/db_morphologist', 'output_directory': '/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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_p_llfva9/tmp/soma_workflow_1gjk9j1y
del WorkflowController
progress: 90.0 % ...
UUID conflict in database, uuid: e8ba4850-c71f-b4af-c026-7f4614e873c4
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/brainvisa-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/brainvisa-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 04:35 (1 minutes 50
seconds)_
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
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 3.3
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
ok
----------------------------------------------------------------------
Ran 1 test in 1201.621s
OK
RETURNCODE: True
Exception ignored in: <function TemporaryDirectory.__del__ at 0x7be36279c700>
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/brainvisa-master-5.3/src/development/casa-distro/master/bin/casa_distro run name=brainvisa-5.1-5.3-userimage env=BRAINVISA_TEST_RUN_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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_u_q952lz
Loading toolbox brainrat
Loading toolbox cortical_surface
Loading toolbox data management
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_u_q952lz/bv_home/brainvisa.log'
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 04:38_
models: 6
SPAM models are present.
_Process **Check SPAM models installation** finished on 2025/06/30 04:38 (0
seconds)_
* Create test database
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist:
parse directories and insert items
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/db_morphologist:
parse directories and insert items
/volatile/a-sac-ns-brainvisa/bbi-
nightly/brainvisa-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/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul
* Import test data
_Process **Import T1 MRI** started on 2025/06/30 04:39_
filein : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-5.1-5.3-userimage/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima
fileout : /volatile/a-sac-ns-brainvisa/bbi-nightly/brainvisa-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/brainvisa-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/brainvisa-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 04:39 (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 04:39_
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 04:39 (2
seconds)_
workflow: /tmp/axon_test_u_q952lz/tmp/bv_n4hu0kjl.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 04:48_
progress: 0.0 % ...
progress: 100.0 % ...
jobs: 4 real, 4 total including barriers
_Process **Morphologist CAPSUL iteration** finished on 2025/06/30 04:48 (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 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
Reading FGraph version 3.1
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 3.3
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
ok
workflow: /tmp/axon_test_u_q952lz/tmp/bv_n4hu0kjl.workflow
* running CNN...
* finished.
** No failed jobs.
del WorkflowController
** all OK.
----------------------------------------------------------------------
Ran 1 test in 913.850s
OK
RETURNCODE: True
Exception ignored in: <function TemporaryDirectory.__del__ at 0x72b766f3c0d0>
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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