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" "python3" "-m" "disco.tests.test_processes" "--verbose"'
----------------------------------------
Starting tests under /tmp/axon_test_hypns6wn
/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
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>:671: ImportWarning: QtImporter.exec_module() not found; falling back to load_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>: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
<frozen importlib._bootstrap>: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_hypns6wn/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_hypns6wn/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
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:671: ImportWarning: QtImporter.exec_module() not found; falling back to load_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>:914: ImportWarning: QtImporter.find_spec() not found; falling back to find_module()
<frozen importlib._bootstrap>: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 29 seconds
/tmp/axon_test_hypns6wn/tmp/disco_test1ug9ztns: parse directories and insert
items
/tmp/axon_test_hypns6wn/tmp/disco_test1ug9ztns: 2 files are stored as 2
DiskItems in 0 seconds
Generating database tables for /tmp/axon_test_hypns6wn/tmp/disco_test1ug9ztns
/tmp/axon_test_hypns6wn/tmp/disco_test1ug9ztns: parse directories and insert
items
/tmp/axon_test_hypns6wn/tmp/disco_test1ug9ztns: 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 2025/06/30 05:17_
_Process **01\. Sulci Label Translation** finished on 2025/06/30 05:17 (0
seconds)_
/casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_hypns6wn/tmp/bv_cgrtxsqr' 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_hypns6wn/tmp/bv_ojtymryn' 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 2025/06/30 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 2025/06/30 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 2025/06/30 05:17 (0
seconds)_
/casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_hypns6wn/tmp/bv_k15nyy6t' 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_hypns6wn/tmp/bv_j_wrpjgu' 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 2025/06/30 05:17 (0 seconds)_
/casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_hypns6wn/tmp/bv_jliua_vx' 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_hypns6wn/tmp/bv_gjgozorm' mode='w' encoding='utf-8'>
self._file = None
ResourceWarning: Enable tracemalloc to get the object allocation traceback
_Process **B01. Bundles Label Translation** started on 2025/06/30 05:17_
_Process **B01. Bundles Label Translation** finished on 2025/06/30 05:17 (0
seconds)_
/casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_hypns6wn/tmp/bv_3jov9qpc' 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_hypns6wn/tmp/bv_l9a0ufq5' 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 2025/06/30 05:17_
_Process **B02. Bundles To Be Removed** finished on 2025/06/30 05:17 (0
seconds)_
/casa/install/python/brainvisa/processing/neuroLog.py:349: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/axon_test_hypns6wn/tmp/bv_ecrhbck1' 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_hypns6wn/tmp/bv_xkzkgkpy' 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_hypns6wn/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_hypns6wn/tmp/bv_nmbs6y9k' 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_hypns6wn/tmp/bv_t8i5sgi7' 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_hypns6wn/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 45.601s
OK
/usr/lib/python3.10/subprocess.py:1072: ResourceWarning: subprocess 1431471 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_7xh5300s
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_7xh5300s/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 2025/06/30 05:19_
_Process **01\. Sulci Label Translation** finished on 2025/06/30 05:19 (0
seconds)_
_Process **02b. Sulci To Be Added** started on 2025/06/30 05:19_
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 2025/06/30 05:19_
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 2025/06/30 05:19 (0
seconds)_
_Process **02b. Sulci To Be Added** finished on 2025/06/30 05:19 (0 seconds)_
_Process **Disco and Dartel complete pipeline** started on 2025/06/30 05:19_
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 2025/06/30 05:26_
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 2025/06/30 05:27 (13
seconds)_
progress: 13.0 % ...
Inverse deformation of initial grid in process
_Process **Mesh deformation component** started on 2025/06/30 05:27_
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 2025/06/30 05:27 (12
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 2025/06/30 05:27_
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 2025/06/30 05:27 (12
seconds)_
progress: 14.250000000000002 % ...
Inverse deformation of initial grid in process
_Process **Mesh deformation component** started on 2025/06/30 05:27_
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 2025/06/30 05:27 (12
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
2025/06/30 05:27_
_Process **Resample images into a Talairach-aligned grid** finished on
2025/06/30 05:27 (2 seconds)_
_Process **Resample images into a Talairach-aligned grid** started on
2025/06/30 05:27_
_Process **Resample images into a Talairach-aligned grid** finished on
2025/06/30 05:28 (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
2025/06/30 05:28_
_Process **Resample images into a Talairach-aligned grid** finished on
2025/06/30 05:28 (2 seconds)_
_Process **Resample images into a Talairach-aligned grid** started on
2025/06/30 05:28_
_Process **Resample images into a Talairach-aligned grid** finished on
2025/06/30 05:28 (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
2025/06/30 05:28_
running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_7xh5300s/tmp/bv_bbxkd84m/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-Jun-2025 05:29:16 - Running job #1
------------------------------------------------------------------------
30-Jun-2025 05:29:17 - 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-Jun-2025 05:32:16 - Done 'Run Dartel (create Templates)'
30-Jun-2025 05:32:16 - Done
Bye for now...
_Process **spm12 - Run DARTEL (create Templates) - generic** finished on
2025/06/30 05:32 (4 minutes 5 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 2025/06/30 05:32_
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 2025/06/30 05:32_
running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_7xh5300s/tmp/bv__2ncnl8x/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-Jun-2025 05:32:55 - Running job #1
------------------------------------------------------------------------
30-Jun-2025 05:32:56 - Running 'Create Warped'
u_rc1_Grey_sujet01_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_1ri71jvv 1,1,1 2,1,1 3,1,1
30-Jun-2025 05:33:03 - Done 'Create Warped'
30-Jun-2025 05:33:03 - Done
Bye for now...
_Process **spm12 - create warped - generic** finished on 2025/06/30 05:33 (29
seconds)_
_Process **03\. DARTEL Images Warping** finished on 2025/06/30 05:33 (34
seconds)_
progress: 55.00000000000001 % ...
DARTEL inverse deformation
_Process **04\. DARTEL Images Inverse Warping** started on 2025/06/30 05:33_
_Process **spm12 - create inverse warped - generic** started on 2025/06/30
05:33_
running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_7xh5300s/tmp/bv__psecwex/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-Jun-2025 05:33:25 - Running job #1
------------------------------------------------------------------------
30-Jun-2025 05:33:25 - Running 'Create Inverse Warped'
u_rc1_Grey_sujet01_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_5ba4qjmg 1,1,1 2,1,1 3,1,1
30-Jun-2025 05:33:33 - Done 'Create Inverse Warped'
30-Jun-2025 05:33:33 - Done
Bye for now...
_Process **spm12 - create inverse warped - generic** finished on 2025/06/30
05:33 (30 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 2025/06/30 05:33
(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: 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 2025/06/30 05:34_
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 2025/06/30 05:34_
running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_7xh5300s/tmp/bv_eindumnd/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-Jun-2025 05:34:30 - Running job #1
------------------------------------------------------------------------
30-Jun-2025 05:34:30 - Running 'Create Warped'
u_rc1_Grey_sujet02_default_acquisition_disco_analysis_DISCO_TestTemplate: bv__vroluuu 1,1,1 2,1,1 3,1,1
30-Jun-2025 05:34:37 - Done 'Create Warped'
30-Jun-2025 05:34:37 - Done
Bye for now...
_Process **spm12 - create warped - generic** finished on 2025/06/30 05:34 (29
seconds)_
_Process **03\. DARTEL Images Warping** finished on 2025/06/30 05:34 (34
seconds)_
progress: 58.33333333333333 % ...
DARTEL inverse deformation
_Process **04\. DARTEL Images Inverse Warping** started on 2025/06/30 05:34_
_Process **spm12 - create inverse warped - generic** started on 2025/06/30
05:34_
running SPM standalone command: ['/drf/local/spm12-standalone/run_spm12.sh', '/drf/local/matlab/MATLAB_Runtime/v97', 'batch', '/tmp/axon_test_7xh5300s/tmp/bv_fb4u7ro3/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-Jun-2025 05:34:58 - Running job #1
------------------------------------------------------------------------
30-Jun-2025 05:34:58 - Running 'Create Inverse Warped'
u_rc1_Grey_sujet02_default_acquisition_disco_analysis_DISCO_TestTemplate: bv_6zmyd8ua 1,1,1 2,1,1 3,1,1
30-Jun-2025 05:35:06 - Done 'Create Inverse Warped'
30-Jun-2025 05:35:06 - Done
Bye for now...
_Process **spm12 - create inverse warped - generic** finished on 2025/06/30
05:35 (29 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 2025/06/30 05:35
(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: 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 2025/06/30 05:36
(16 minutes 59 seconds)_
ok
Comparison report
=================
842 equivalent files
0 different files
0 files without reference
521 skipped files
----------------------------------------------------------------------
Ran 1 test in 1383.374s
OK
Exception ignored in: <function TemporaryDirectory.__del__ at 0x7555ebff5240>
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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