Commit ac71642a by arnaud.marcoux

Fix installation of pybids + grabbit - minor fix in pet-surface pipeline

parent da61a7a1
Pipeline #906 failed with stages
in 16 seconds
{
"name": "caps",
"root": ".",
"entities": [
{
"name": "subject",
......
......@@ -812,7 +812,7 @@ def get_wf(subject_id,
from nipype.interfaces.fsl import Merge
from nipype.interfaces.petpvc import PETPVC
from nipype.interfaces.spm import Coregister, Normalize12
import clinica_aramis.pipelines.pet_surface.pet_surface_utils as utils
import clinica.pipelines.pet_surface.pet_surface_utils as utils
cprint('***** Beginning processing of ' + subject_id + ' on ' + session_id + ' *****')
......
REGION,SOURCE,DST
Unknown,0,0
Vermis,172,36
Air,130,0
Skull,165,0
CSF-ExtraCerebral,257,13
Pons,174,20
Head-ExtraCerebral,258,0
Left-Cerebral-Exterior,1,0
Left-Cerebral-White-Matter,2,25
Left-Cerebral-Cortex,3,0
Left-Lateral-Ventricle,4,14
Left-Inf-Lat-Vent,5,14
Left-Cerebellum-Exterior,6,23
Left-Cerebellum-White-Matter,7,24
Left-Cerebellum-Cortex,8,36
Left-Thalamus,9,33
Left-Thalamus-Proper,10,33
Left-Caudate,11,22
Left-Putamen,12,31
Left-Pallidum,13,29
3rd-Ventricle,14,14
4th-Ventricle,15,14
Brain-Stem,16,20
Left-Hippocampus,17,27
Left-Amygdala,18,18
Left-Insula,19,4
Left-Operculum,20,2
CSF,24,13
Left-Lesion,25,25
Left-Accumbens-area,26,16
Left-Substancia-Nigra,27,38
Left-VentralDC,28,34
Left-undetermined,29,0
Left-vessel,30,0
Left-choroid-plexus,31,13
Right-Cerebral-Exterior,40,0
Right-Cerebral-White-Matter,41,25
Right-Cerebral-Cortex,42,0
Right-Lateral-Ventricle,43,14
Right-Inf-Lat-Vent,44,14
Right-Cerebellum-Exterior,45,23
Right-Cerebellum-White-Matter,46,24
Right-Cerebellum-Cortex,47,36
Right-Thalamus,48,32
Right-Thalamus-Proper,49,32
Right-Caudate,50,21
Right-Putamen,51,30
Right-Pallidum,52,28
Right-Hippocampus,53,26
Right-Amygdala,54,17
Right-Insula,55,3
Right-Operculum,56,1
Right-Lesion,57,25
Right-Accumbens-area,58,15
Right-Substancia-Nigra,59,37
Right-VentralDC,60,34
Right-undetermined,61,0
Right-vessel,62,0
Right-choroid-plexus,63,13
5th-Ventricle,72,14
WM-hypointensities,77,25
Left-WM-hypointensities,78,25
Right-WM-hypointensities,79,25
non-WM-hypointensities,80,25
Left-non-WM-hypointensities,81,25
Right-non-WM-hypointensities,82,25
Optic-Chiasm,85,35
Corpus_Callosum,192,25
Left-Amygdala-Anterior,96,18
Right-Amygdala-Anterior,97,17
Fornix,250,25
CC_Posterior,251,25
CC_Mid_Posterior,252,25
CC_Central,253,25
CC_Mid_Anterior,254,25
CC_Anterior,255,25
ctx-lh-bankssts,1001,6
ctx-lh-caudalanteriorcingulate,1002,46
ctx-lh-caudalmiddlefrontal,1003,2
ctx-lh-corpuscallosum,1004,25
ctx-lh-cuneus,1005,10
ctx-lh-entorhinal,1006,40
ctx-lh-fusiform,1007,6
ctx-lh-inferiorparietal,1008,8
ctx-lh-inferiortemporal,1009,6
ctx-lh-isthmuscingulate,1010,48
ctx-lh-lateraloccipital,1011,10
ctx-lh-lateralorbitofrontal,1012,2
ctx-lh-lingual,1013,10
ctx-lh-medialorbitofrontal,1014,2
ctx-lh-middletemporal,1015,6
ctx-lh-parahippocampal,1016,12
ctx-lh-paracentral,1017,2
ctx-lh-parsopercularis,1018,2
ctx-lh-parsorbitalis,1019,2
ctx-lh-parstriangularis,1020,2
ctx-lh-pericalcarine,1021,10
ctx-lh-postcentral,1022,8
ctx-lh-posteriorcingulate,1023,47
ctx-lh-precentral,1024,2
ctx-lh-precuneus,1025,8
ctx-lh-rostralanteriorcingulate,1026,45
ctx-lh-rostralmiddlefrontal,1027,2
ctx-lh-superiorfrontal,1028,2
ctx-lh-superiorparietal,1029,8
ctx-lh-superiortemporal,1030,6
ctx-lh-supramarginal,1031,8
ctx-lh-frontalpole,1032,2
ctx-lh-temporalpole,1033,50
ctx-lh-transversetemporal,1034,6
ctx-lh-insula,1035,4
ctx-rh-unknown,2000,0
ctx-rh-bankssts,2001,5
ctx-rh-caudalanteriorcingulate,2002,42
ctx-rh-caudalmiddlefrontal,2003,1
ctx-rh-corpuscallosum,2004,25
ctx-rh-cuneus,2005,9
ctx-rh-entorhinal,2006,39
ctx-rh-fusiform,2007,5
ctx-rh-inferiorparietal,2008,7
ctx-rh-inferiortemporal,2009,5
ctx-rh-isthmuscingulate,2010,44
ctx-rh-lateraloccipital,2011,9
ctx-rh-lateralorbitofrontal,2012,1
ctx-rh-lingual,2013,9
ctx-rh-medialorbitofrontal,2014,1
ctx-rh-middletemporal,2015,5
ctx-rh-parahippocampal,2016,11
ctx-rh-paracentral,2017,1
ctx-rh-parsopercularis,2018,1
ctx-rh-parsorbitalis,2019,1
ctx-rh-parstriangularis,2020,1
ctx-rh-pericalcarine,2021,9
ctx-rh-postcentral,2022,7
ctx-rh-posteriorcingulate,2023,43
ctx-rh-precentral,2024,1
ctx-rh-precuneus,2025,7
ctx-rh-rostralanteriorcingulate,2026,41
ctx-rh-rostralmiddlefrontal,2027,1
ctx-rh-superiorfrontal,2028,1
ctx-rh-superiorparietal,2029,7
ctx-rh-superiortemporal,2030,5
ctx-rh-supramarginal,2031,7
ctx-rh-frontalpole,2032,1
ctx-rh-temporalpole,2033,49
ctx-rh-transversetemporal,2034,5
ctx-rh-insula,2035,3
......@@ -8,7 +8,7 @@ dependencies:
- pip=9.*
- nibabel>=2.0.2
- nipype==0.12.1
- pybids>=0.1
- pybids==0.5.1
- dipy>=0.6.0
- argcomplete>=1.4.1
- configparser>=3.5.0
......@@ -25,7 +25,7 @@ dependencies:
- scikit-image>=0.13.0
- sharedmem>=0.3.5
- xlrd>=0.9.0
- grabbit==0.0.8
- grabbit==0.1.2
- colorama>=0.3.9
- prov==1.5.0
- pytest>=3.4.0
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