Console Output
Skipping 40 KB..
Full Logdownload done
installing demo_data.zip ...
* Import test data
Process Import T1 MRI started on 2025/09/17 04:28filein : /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_pipeline/data_unprocessed/sujet01/anatomy/sujet01.ima
fileout : /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/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 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/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 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii...
done
Process Import T1 MRI finished on 2025/09/17 04:28 (0 seconds)(not doing ANN sulci recognition tests today)
* Check SPAM models installation
Process Check SPAM models installation started on 2025/09/17 04:28models: 6SPAM models are present.Process Check SPAM models installation finished on 2025/09/17 04:28 (0 seconds)* Run Morphologist
Process Morphologist 2023 started on 2025/09/17 04:28progress: 0.0 % ...progress: 0.0 % ...Left hemisphere point not specified - X axis flip will not be checkedOK, the image seems to be in the correct orientation.progress: 8.333333333333332 % ...progress: 8.333333333333332 % ...progress: 16.666666666666664 % ...progress: 25.0 % ...progress: 33.33333333333333 % ...Skip unselected node: Skull-stripped brain normalizationprogress: 41.66666666666667 % ...progress: 50.0 % ...progress: 58.333333333333336 % ...progress: 66.66666666666666 % ...progress: 66.66666666666666 % ...progress: 66.66666666666666 % ...Computing left hemisphere grey-white classification...progress: 67.26190476190476 % ...Detecting left hemisphere spherical inner cortical interface...progress: 67.85714285714285 % ...Reconstructing left hemisphere white mesh...progress: 68.45238095238095 % ...Computing left sulci skeleton and buried gyrus watershed...progress: 69.04761904761905 % ...Detecting left hemisphere spherical outer cortical surface...Reconstructing left hemisphere pial mesh...progress: 69.64285714285715 % ...Building left hemisphere attributed relational sulci graph...Process Hemisphere Sulci Voronoi started on 2025/09/17 04:30Process Hemisphere Sulci Voronoi finished on 2025/09/17 04:31 (17 seconds)Process Hemisphere Sulci Thickness and Volumes started on 2025/09/17 04:31Process Hemisphere Sulci Thickness and Volumes finished on 2025/09/17 04:31 (13
seconds)Talairach-AC/PC-Anatomist appended
progress: 70.23809523809524 % ...progress: 70.23809523809524 % ...progress: 70.23809523809524 % ...progress: 70.53571428571428 % ...progress: 70.53571428571428 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...Computing right hemisphere grey-white classification...progress: 71.42857142857143 % ...Detecting right hemisphere spherical inner cortical interface...progress: 72.02380952380952 % ...Reconstructing right hemisphere white mesh...progress: 72.61904761904762 % ...Computing right sulci skeleton and buried gyrus watershed...progress: 73.21428571428572 % ...Detecting right hemisphere spherical outer cortical surface...Reconstructing right hemisphere pial mesh...progress: 73.80952380952381 % ...Building right hemisphere attributed relational sulci graph...Process Hemisphere Sulci Voronoi started on 2025/09/17 04:36Process Hemisphere Sulci Voronoi finished on 2025/09/17 04:36 (17 seconds)Process Hemisphere Sulci Thickness and Volumes started on 2025/09/17 04:36Process Hemisphere Sulci Thickness and Volumes finished on 2025/09/17 04:36 (13
seconds)Talairach-AC/PC-Anatomist appended
progress: 74.40476190476191 % ...progress: 74.40476190476191 % ...progress: 74.40476190476191 % ...progress: 74.70238095238095 % ...progress: 74.70238095238095 % ...progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...Reading FGraph version 3.1
Reading FGraph version 3.1
progress: 83.33333333333334 % ...Extracting left and right CSF inside sulci.Process CSF Classif started on 2025/09/17 04:40Process CSF Classif finished on 2025/09/17 04:40 (11 seconds)Computing volumes.Reading FGraph version 3.1
Reading FGraph version 3.1
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2 components
component 1 : 6602396 points
subjectleft.WMright.WMboth.WMleft.GMright.GMboth.GMleft.CSFright.CSFboth.CSFleft.hemi_volumeright.hemi_volumeboth.brain_volumeboth.hemi_closed_volumeboth.eTIVboth.cerebellum_stem_volumeleft.brain_volumeright.brain_volumeleft.hull_arearight.hull_arealeft.skel_pointsright.skel_pointsleft.skel_labelled_pointsright.skel_labelled_pointslog_ratio.skel_pointslog_ratio.skel_labelled_pointsleft.gi_native_spaceleft.gi_talairach_spaceboth.gi_native_spaceboth.gi_talairach_spaceleft.fold_lengthright.fold_lengthboth.fold_lengthleft.mean_depthright.mean_depthboth.mean_depthleft.mean_thicknessright.mean_thicknessboth.mean_thicknessleft.mean_openingright.mean_openingboth.mean_openingboth.skel_pointsboth.skel_labelled_pointsleft.GM_arearight.GM_areaboth.GM_arealeft.WM_arearight.WM_areaboth.WM_areasujet01274622.706278323.605552946.311326422.63326002.865604746.23576861.39874417.703151279.102601045.336604326.4691347397.0851403757.4781607415.533142014.732641998.602645435.29749038.60249076.30147597478914266042872-0.006-0.0052.1252.1252.132.133932.44040.87973.212.56612.49612.5314.2224.1944.2080.650.6510.6519548885532124376.789123553.281247930.07102920.727102707.25205627.977progress: 91.66666666666666 % ...Morphologist reportfiltering...
after filtering: 1 components
Starting Anatomist.....
config file : /home/a-sac-ns-brainvisa/.anatomist/config/settings.cfg
This plugin does not support propagateSizeHints()
PyAnatomist Module present
PythonLauncher::runModules()
nifti transfo: 1
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Multitexturing present
function glActiveTexture found.
function glClientActiveTexture found.
function glBlendEquation found.
function glTexImage3D found.
function glMultiTexCoord3f found.
function glBindFramebuffer found.
function glBindRenderbuffer found.
function glFramebufferTexture2D found.
function glGenFramebuffers found.
function glGenRenderbuffers found.
function glFramebufferRenderbuffer found.
function glRenderbufferStorage found.
function glCheckFramebufferStatus found.
function glDeleteRenderbuffers found.
function glDeleteFramebuffers found.
Number of texture units: 8
function glUniform1f found.
function glUniform1i found.
function glUniform4fv found.
function glGetUniformLocation found.
function glMultTransposeMatrixf found.
function glAttachShader found.
function glDetachShader found.
function glCompileShader found.
function glCreateProgram found.
function glCreateShader found.
function glDeleteProgram found.
function glDeleteShader found.
function glGetProgramiv found.
function glGetShaderiv found.
function glLinkProgram found.
function glShaderSource found.
function glUseProgram found.
GL_ARB_shadow present
GL_SGIX_shadow extension not available
GL_SGIX_depth_texture extension not available
GL_ARB_depth_texture extension present
GL_ARB_texture_cube_map extension present
GL_EXT_texture_cube_map extension present
Number of texture units: 8
This plugin does not support raise()
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
memory limit: 384658138726
Reading FGraph version 3.1
bounding box found : 116, 53, 15
203, 237, 114
memory limit: 384657319526
Reading FGraph version 3.1
bounding box found : 46, 52, 10
132, 238, 108
snap 1 : OpenGL error: invalid operation
global modules: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/anatomist-5.2/python_plugins
home modules: /home/a-sac-ns-brainvisa/.anatomist/python_plugins
loading module statsplotwindow
loading module gltf_io
Anatomist started.
loading module valuesplotwindow
loading module anacontrolmenu
loading module ana_image_math
loading module histogram
loading module modelGraphs
loading module infowindow
loading module volumepalettes
loading module profilewindow
loading module simple_controls
loading module gradientpalette
loading module bundles_small_brains
loading module bsa_proba
loading module paletteViewer
loading module selection
loading module foldsplit
loading module bundles_split_by_cortical_regions
loading module meshsplit
loading module measure
loading module save_resampled
loading module palettecontrols
all python modules loaded
Anatomist started.
Status: OKobservable 0x649068bdc6b0(N9anatomist7AVolumeIsEE) could not be removed from observer 0x649068bdb498 (N9anatomist8Fusion2DE)
progress: 100.0 % ...Process Morphologist 2023 finished on 2025/09/17 04:40 (11 minutes 35 seconds)* Run CNN recognition
Process Morphologist 2023 started on 2025/09/17 04:40progress: 0.0 % ...Skip unselected node: Image orientation handlingprogress: 8.333333333333332 % ...Skip unselected node: T1 Bias Correctionprogress: 16.666666666666664 % ...Skip unselected node: Histogram analysisprogress: 25.0 % ...Skip unselected node: Compute Brain Maskprogress: 33.33333333333333 % ...Skip unselected node: Skull-stripped brain normalizationprogress: 41.66666666666667 % ...Skip unselected node: Split Brain Maskprogress: 50.0 % ...Skip unselected node: Talairach transformation from manual AC/PCprogress: 58.333333333333336 % ...Skip unselected node: Head Meshprogress: 66.66666666666666 % ...progress: 66.66666666666666 % ...progress: 66.66666666666666 % ...Skip unselected node: Grey White Classificationprogress: 67.26190476190476 % ...Skip unselected node: Grey White Topology Correctionprogress: 67.85714285714285 % ...Skip unselected node: Grey White Meshprogress: 68.45238095238095 % ...Skip unselected node: Sulci Skeleton and Rootsprogress: 69.04761904761905 % ...Skip unselected node: Pial Meshprogress: 69.64285714285715 % ...Skip unselected node: Cortical Folds Graphprogress: 70.23809523809524 % ...progress: 70.23809523809524 % ...soma-workflow starting in light mode
Workflow controller initialised
Soma-workflow temp directory: /home_local/a-sac-ns-brainvisa/tmp/axon_test_9ljxr2qg/tmp/soma_workflow_o3kwfaqt
del WorkflowController
progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...progress: 70.83333333333334 % ...Skip unselected node: Grey White Classificationprogress: 71.42857142857143 % ...Skip unselected node: Grey White Topology Correctionprogress: 72.02380952380952 % ...Skip unselected node: Grey White Meshprogress: 72.61904761904762 % ...Skip unselected node: Sulci Skeleton and Rootsprogress: 73.21428571428572 % ...Skip unselected node: Pial Meshprogress: 73.80952380952381 % ...Skip unselected node: Cortical Folds Graphprogress: 74.40476190476191 % ...progress: 74.40476190476191 % ...soma-workflow starting in light mode
Workflow controller initialised
Soma-workflow temp directory: /home_local/a-sac-ns-brainvisa/tmp/axon_test_9ljxr2qg/tmp/soma_workflow_7_mlkr3e
del WorkflowController
progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...progress: 75.0 % ...Reading FGraph version 3.3
Reading FGraph version 3.1
Warning: wrong filename_base in graph, trying to fix it
progress: 83.33333333333334 % ...Extracting left and right CSF inside sulci.Process CSF Classif started on 2025/09/17 04:42Process CSF Classif finished on 2025/09/17 04:42 (16 seconds)Computing volumes.Reading FGraph version 3.3
Reading FGraph version 3.1
Warning: wrong filename_base in graph, trying to fix it
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2 components
component 1 : 6602396 points
subjectleft.WMright.WMboth.WMleft.GMright.GMboth.GMleft.CSFright.CSFboth.CSFleft.hemi_volumeright.hemi_volumeboth.brain_volumeboth.hemi_closed_volumeboth.eTIVboth.cerebellum_stem_volumeleft.brain_volumeright.brain_volumeleft.hull_arearight.hull_arealeft.skel_pointsright.skel_pointsleft.skel_labelled_pointsright.skel_labelled_pointslog_ratio.skel_pointslog_ratio.skel_labelled_pointsleft.gi_native_spaceleft.gi_talairach_spaceboth.gi_native_spaceboth.gi_talairach_spaceleft.fold_lengthright.fold_lengthboth.fold_lengthleft.mean_depthright.mean_depthboth.mean_depthleft.mean_thicknessright.mean_thicknessboth.mean_thicknessleft.mean_openingright.mean_openingboth.mean_openingboth.skel_pointsboth.skel_labelled_pointsleft.GM_arearight.GM_areaboth.GM_arealeft.WM_arearight.WM_areaboth.WM_areasujet01274622.706278323.605552946.311326422.63326002.865604746.23589999.60274417.703164417.305601045.336604326.4691347397.0851403757.4781607415.533142014.732628860.398645435.29749038.60249076.30147597478914268942777-0.006-0.0022.1252.1252.1312.133931.44040.87972.212.57612.50712.5423.8374.1884.0120.7820.6510.7179548885466124376.789123553.281247930.07102920.727102707.25205627.977progress: 91.66666666666666 % ...Morphologist reportThis plugin does not support propagateSizeHints()
This plugin does not support raise()
This plugin does not support propagateSizeHints()
filtering...
after filtering: 1 components
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
This plugin does not support propagateSizeHints()
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
memory limit: 383920213196
Reading FGraph version 3.3
bounding box found : 116, 52, 14
203, 238, 114
Load transformation : overriding existing one
Load transformation : overriding existing one
memory limit: 383971354214
Reading FGraph version 3.1
Warning: wrong filename_base in graph, trying to fix it
bounding box found : 46, 52, 10
132, 238, 108
Load transformation : overriding existing one
Load transformation : overriding existing one
snap 1 : OpenGL error: invalid operation
Status: OKobservable 0x6490704ff450(N9anatomist7AVolumeIsEE) could not be removed from observer 0x649064bc9d08 (N9anatomist8Fusion2DE)
progress: 100.0 % ...Process Morphologist 2023 finished on 2025/09/17 04:42 (2 minutes 19 seconds)FAIL
======================================================================
FAIL: test_pipeline_results (__main__.TestMorphologistPipeline.test_pipeline_results)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/tests/test_morphologist.py", line 478, in test_pipeline_results
self.assertTrue(
AssertionError: False is not true : The content of /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/segmentation/brain_volumes_sujet01.csv in test is different from the reference results /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/ref/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/segmentation/brain_volumes_sujet01.csv.
----------------------------------------------------------------------
Ran 1 test in 883.316s
FAILED (failures=1)
RETURNCODE: False
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86RefreshRateToggle
> Warning: Could not resolve keysym XF86Accessibility
> Warning: Could not resolve keysym XF86DoNotDisturb
Errors from xkbcomp are not fatal to the X server
Exception ignored in: <function TemporaryDirectory.__del__ at 0x7152a0348cc0>
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/data/neuroDiskItems.py", line 2669, in __del__
TypeError: 'NoneType' object is not callable
Exiting Anatomist --- Goodbye.
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0/src/brainvisa-cmake/bin/bv_run_pixi_env.py", line 75, in <module>
subprocess.check_call(cmd, cwd=wd, env=env)
File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['pixi', 'run', '--frozen', 'sh', '-c', 'timeout -k 10 5400 python3.11 -m brainvisa.tests.test_morphologist --no-ann --test_mode=run']' returned non-zero exit status 1.
================================================================================
FAILED with exit code 1
================================================================================
----------------------------------------
$ /usr/bin/python3 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0/src/brainvisa-cmake/bin/bv_run_pixi_env.py run name=brainvisa-sf-6.0_user env=BRAINVISA_TEST_RUN_DATA_DIR=/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test,BRAINVISA_TEST_REF_DATA_DIR=/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/ref -- sh -c 'timeout -k 10 5400 python3.11 -m morphologist.tests.test_morphologist_capsul'
----------------------------------------
['/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/morphologist/tests/test_morphologist_capsul.py']
Starting tests under /home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40
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 nuclearimaging
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
'/home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/bv_home/brainvisa.log'QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/tmp/runtime-a-sac-ns-brainvisa'
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86RefreshRateToggle
> Warning: Could not resolve keysym XF86Accessibility
> Warning: Could not resolve keysym XF86DoNotDisturb
Errors from xkbcomp are not fatal to the X server
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86RefreshRateToggle
> Warning: Could not resolve keysym XF86Accessibility
> Warning: Could not resolve keysym XF86DoNotDisturb
Errors from xkbcomp are not fatal to the X server
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/tmp/runtime-a-sac-ns-brainvisa'
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86RefreshRateToggle
> Warning: Could not resolve keysym XF86Accessibility
> Warning: Could not resolve keysym XF86DoNotDisturb
Errors from xkbcomp are not fatal to the X server
Qt WebEngine seems to be initialized from a plugin. Please set Qt::AA_ShareOpenGLContexts using QCoreApplication::setAttribute before constructing QGuiApplication.
Attribute Qt::AA_ShareOpenGLContexts must be set before QCoreApplication is created.
QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/tmp/runtime-a-sac-ns-brainvisa'
error: XDG_RUNTIME_DIR is invalid or not set in the environment.
Qt offscreen does not work.
Cannot allocate an OpenGL context. Using Xvfb if possible.
using DISPLAY=:3
VirtualGL found.
exec: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/toolboxes/constellation/startup.py
Database
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/constellation-5.2/constellation_atlas_hcp_200s/constellation_matrix
must be updated because the database file is too old.Database
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/constellation-5.2/constellation_atlas_hcp_200s/freesurfer_gyri
must be updated because the database file is too old.exec: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/toolboxes/disco/startup.py
Database
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/disco-5.2/disco_templates_hbp_morpho
must be updated because the database file is too old.exec: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/toolboxes/morphologist/startup.py
SPM dir: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/spm12/spm12_mcr/spm/spm12
spmtemplates: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/spm12/spm12_mcr/spm/spm12
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/spm12/spm12_mcr/spm/spm12:
parse directories and insert items/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/spm12/spm12_mcr/spm/spm12:
8 files are stored as 8 DiskItems in 0 secondsGenerating database tables for
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/brainvisa-share-5.2/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/brainvisa-share-5.2:
parse directories and insert items/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/brainvisa-share-5.2:
196 files are stored as 183 DiskItems in 0 secondstest_pipeline_results (__main__.TestMorphologistCapsul.test_pipeline_results) ... * Check SPAM models installation
Process Check SPAM models installation started on 2025/09/17 04:43models: 6SPAM models are present.Process Check SPAM models installation finished on 2025/09/17 04:43 (0 seconds)* Create test database
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist:
parse directories and insert items/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist:
2 files are stored as 2 DiskItems in 0 secondsGenerating database tables for
/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist:
parse directories and insert items/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist:
2 files are stored as 2 DiskItems in 0 secondsdownload dir: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/share/brainvisa_demo
install dir: /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul
already downloaded, skipping download.
installing demo_data.zip ...
* Import test data
Process Import T1 MRI started on 2025/09/17 04:43filein : /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/data_unprocessed/sujet01/anatomy/sujet01.ima
fileout : /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/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 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/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 /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/sujet01.nii...
done
Process Import T1 MRI finished on 2025/09/17 04:43 (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'
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 2025/09/17 04:43Exception: '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'
Exception: 'StudyConfig' object has no attribute 'use_freesurfer'
progress: 100.0 % ...jobs: 28 real, 28 total including barriersProcess Morphologist CAPSUL iteration finished on 2025/09/17 04:43 (2 seconds)workflow: /home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/tmp/bv_l08j8hyu.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 2025/09/17 04:52progress: 0.0 % ...progress: 100.0 % ...jobs: 6 real, 6 total including barriersProcess Morphologist CAPSUL iteration finished on 2025/09/17 04:52 (0 seconds)** Workflow status OK
FAIL
workflow: /home_local/a-sac-ns-brainvisa/tmp/axon_test_371wax40/tmp/bv_l08j8hyu.workflow
* running CNN...
* finished.
** No failed jobs.
del WorkflowController
======================================================================
FAIL: test_pipeline_results (__main__.TestMorphologistCapsul.test_pipeline_results)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/morphologist/tests/test_morphologist_capsul.py", line 358, in test_pipeline_results
self.assertTrue(
AssertionError: False is not true : The content of /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/test/test_morphologist_capsul/db_morphologist/test/sujet01/t1mri/default_acquisition/capsul/segmentation/brain_volumes_sujet01.csv in test is different from the reference results /home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/tests/ref/test_morphologist_pipeline/db_morphologist/test/sujet01/t1mri/default_acquisition/default_analysis/segmentation/brain_volumes_sujet01.csv.
----------------------------------------------------------------------
Ran 1 test in 683.150s
FAILED (failures=1)
RETURNCODE: False
The XKEYBOARD keymap compiler (xkbcomp) reports:
> Warning: Could not resolve keysym XF86RefreshRateToggle
> Warning: Could not resolve keysym XF86Accessibility
> Warning: Could not resolve keysym XF86DoNotDisturb
Errors from xkbcomp are not fatal to the X server
Exception ignored in: <function TemporaryDirectory.__del__ at 0x76b4d639a480>
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0_user/.pixi/envs/default/lib/python3.11/site-packages/brainvisa/data/neuroDiskItems.py", line 2669, in __del__
TypeError: 'NoneType' object is not callable
Traceback (most recent call last):
File "/home_local/a-sac-ns-brainvisa/bbi-daily/brainvisa-sf-6.0/src/brainvisa-cmake/bin/bv_run_pixi_env.py", line 75, in <module>
subprocess.check_call(cmd, cwd=wd, env=env)
File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['pixi', 'run', '--frozen', 'sh', '-c', 'timeout -k 10 5400 python3.11 -m morphologist.tests.test_morphologist_capsul']' returned non-zero exit status 1.
================================================================================
FAILED with exit code 1
Finished: FAILURE
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