Question about the PET scan surface-pipeline
Thandar Aung
{
"Modality": "PT",
"Manufacturer": "GE",
"ManufacturersModelName": "Discovery_STE",
"InstitutionName": "St_Josephs_Outpatient_Imaging",
"StationName": "dstop",
"PatientPosition": "HFS",
"SoftwareVersions": "41.04",
"SeriesDescription": "PET_BRAIN",
"ProtocolName": "PET_BRAIN",
"ImageType": ["ORIGINAL", "PRIMARY"],
"SeriesNumber": 5,
"AcquisitionTime": "12:18:0.000000",
"RadionuclidePositronFraction": 0.97,
"RadionuclideTotalDose": 3.885e+08,
"RadionuclideHalfLife": 6588,
"DoseCalibrationFactor": 214,
"SliceThickness": 3.27,
"ReconMatrixPE": 128,
"SliceTiming": [
0,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001,
-0.001 ],
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
-0 ],
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20190902",
"Psf": [
{
"EffectiveResolutionInPlane": 5.5,
"EffectiveResolutionAxial": 5.5
}
]
}
Alexandre Routier
Thandar Aung
(clinicaEnv) ThandarAung@Scotts-MacBook-Pro ~ % nipypecli crash /Users/ThandarAung/crash-20200829-184333-ThandarAung-tkreg-7ec84343-e933-4746-85f3-c0f7349e0793.pklz
Working directory: /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpod5o123e/sub_001_ses_M00/tkreg
Node inputs:
args = <undefined>
environ = {'SUBJECTS_DIR': '/Applications/freesurfer/subjects'}
fsl_in_matrix = <undefined>
fsl_out = <undefined>
fstal = <undefined>
fstarg = <undefined>
invert_lta_in = <undefined>
invert_lta_out = <undefined>
lta_in = <undefined>
lta_out = <undefined>
moving_image = /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpod5o123e/sub_001_ses_M00/gtmseg/gtmseg.mgz
movscale = <undefined>
noedit = True
reg_file = register.dat
reg_header = True
subject_id = <undefined>
subjects_dir = /Applications/freesurfer/subjects
target_image = /Users/ThandarAung/Desktop/CAPS/subjects/sub-001/ses-M00/t1/freesurfer_cross_sectional/sub-001_ses-M00/mri/orig_nu.mgz
xfm = <undefined>
Traceback:
Traceback (most recent call last):
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
return super(FSCommand, self).run(**inputs)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1033, in _run_interface
self.raise_exception(runtime)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 970, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
tkregister2 --mov /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpod5o123e/sub_001_ses_M00/gtmseg/gtmseg.mgz --noedit --reg register.dat --regheader --targ /Users/ThandarAung/Desktop/CAPS/subjects/sub-001/ses-M00/t1/freesurfer_cross_sectional/sub-001_ses-M00/mri/orig_nu.mgz
Standard output:
Standard error:
/Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable.
Return code: 1
(clinicaEnv) Scotts-MBP:~ ThandarAung$
"Psf": [
{
"EffectiveResolutionInPlane": 1.95,
"EffectiveResolutionAxial": 3.2
}
]
}
"Psf": [
{
"EffectiveResolutionInPlane": 5.5,
"EffectiveResolutionAxial": 5.5
}
]
}
Thandar Aung
200901-16:21:43,61 nipype.workflow INFO:
Workflow pet-surface settings: ['check', 'execution', 'logging', 'monitoring']
200901-16:21:43,69 nipype.workflow INFO:
Running in parallel.
200901-16:21:43,72 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 14.40/14.40, Free processors: 7/7.
200901-16:21:43,240 nipype.workflow INFO:
[Node] Setting-up "pet-surface.full_pipeline_mapnode" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/pet-surface/full_pipeline_mapnode".
200901-16:21:43,251 nipype.workflow INFO:
[Node] Setting-up "_full_pipeline_mapnode0" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/pet-surface/full_pipeline_mapnode/mapflow/_full_pipeline_mapnode0".
200901-16:21:43,317 nipype.workflow INFO:
[Node] Running "_full_pipeline_mapnode0" ("nipype.interfaces.utility.wrappers.Function")
200901-16:21:43,555 nipype.workflow INFO:
Workflow sub_007_ses_M00 settings: ['check', 'execution', 'logging', 'monitoring']
200901-16:21:43,606 nipype.workflow INFO:
Running serially.
200901-16:21:43,607 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.reformat_surface_name" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_rh/reformat_surface_name".
200901-16:21:43,634 nipype.workflow INFO:
[Node] Running "reformat_surface_name" ("nipype.interfaces.utility.wrappers.Function")
200901-16:21:43,650 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.reformat_surface_name".
200901-16:21:43,652 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.mris_expand_white" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_rh/mris_expand_white".
200901-16:21:43,669 nipype.workflow INFO:
[Node] Running "mris_expand_white" ("nipype.interfaces.utility.wrappers.Function")
200901-16:21:45,74 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 14.20/14.40, Free processors: 6/7.
Currently running:
* pet-surface.full_pipeline_mapnode
200901-16:30:33,31 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.mris_expand_white".
200901-16:30:33,33 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.extract_mid_surface" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_rh/extract_mid_surface".
200901-16:30:33,173 nipype.workflow INFO:
[Node] Running "extract_mid_surface" ("nipype.interfaces.utility.wrappers.Function")
200901-16:30:33,189 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.extract_mid_surface".
200901-16:30:33,191 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.reformat_surface_name" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_lh/reformat_surface_name".
200901-16:30:33,224 nipype.workflow INFO:
[Node] Running "reformat_surface_name" ("nipype.interfaces.utility.wrappers.Function")
200901-16:30:33,239 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.reformat_surface_name".
200901-16:30:33,241 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.mris_expand_white" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_lh/mris_expand_white".
200901-16:30:33,262 nipype.workflow INFO:
[Node] Running "mris_expand_white" ("nipype.interfaces.utility.wrappers.Function")
200901-16:39:23,289 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.mris_expand_white".
200901-16:39:23,290 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.extract_mid_surface" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/_hemi_lh/extract_mid_surface".
200901-16:39:23,444 nipype.workflow INFO:
[Node] Running "extract_mid_surface" ("nipype.interfaces.utility.wrappers.Function")
200901-16:39:23,461 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.extract_mid_surface".
200901-16:39:23,463 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.psfreader" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/psfreader".
200901-16:39:23,468 nipype.workflow INFO:
[Node] Running "psfreader" ("nipype.interfaces.utility.wrappers.Function")
200901-16:39:23,484 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.psfreader".
200901-16:39:23,486 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.gtmseg" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg".
200901-16:39:23,490 nipype.workflow INFO:
[Node] Running "gtmseg" ("nipype.interfaces.utility.wrappers.Function")
200901-16:39:23,515 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.gtmseg".
200901-16:39:23,517 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.convert_gtmseg" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_gtmseg".
200901-16:39:23,532 nipype.workflow INFO:
[Node] Running "convert_gtmseg" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --input_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --output_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_gtmseg/gtmseg_out.nii.gz
200901-16:39:23,645 nipype.interface INFO:
stdout 2020-09-01T16:39:23.644665:mri_convert.bin --input_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --output_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_gtmseg/gtmseg_out.nii.gz
200901-16:39:26,133 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
200901-16:39:26,134 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:reading from /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz...
200901-16:39:26,135 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
200901-16:39:26,136 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:i_ras = (-1, -5.12227e-09, -3.72529e-09)
200901-16:39:26,137 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:j_ras = (-3.72529e-09, -2.98023e-08, -1)
200901-16:39:26,137 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:k_ras = (5.58794e-09, 1, 0)
200901-16:39:26,138 nipype.interface INFO:
stdout 2020-09-01T16:39:26.133647:writing to /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_gtmseg/gtmseg_out.nii.gz...
200901-16:39:26,206 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.convert_gtmseg".
200901-16:39:26,207 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.conversion_of_labels" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels".
200901-16:39:26,220 nipype.workflow INFO:
[Node] Running "conversion_of_labels" ("nipype.interfaces.utility.wrappers.Function")
200901-16:40:21,3 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.conversion_of_labels".
200901-16:40:21,4 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.merge_volume" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/merge_volume".
200901-16:40:21,55 nipype.workflow INFO:
[Node] Running "merge_volume" ("nipype.interfaces.fsl.utils.Merge"), a CommandLine Interface with command:
fslmerge -t 0_merged.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/0.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/1.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/2.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/3.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/4.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/5.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/6.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/7.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/8.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/9.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/10.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/11.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/12.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/13.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/14.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/15.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/16.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/17.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/18.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/20.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/21.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/22.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/24.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/25.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/26.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/27.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/28.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/29.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/30.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/31.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/32.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/33.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/34.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/35.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/36.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/39.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/40.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/41.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/42.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/43.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/44.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/45.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/46.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/47.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/48.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/49.nii.gz /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/conversion_of_labels/50.nii.gz
200901-16:40:40,108 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.merge_volume".
200901-16:40:40,109 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.unzip_mask" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/unzip_mask".
200901-16:40:40,113 nipype.workflow INFO:
[Node] Running "unzip_mask" ("nipype.interfaces.utility.wrappers.Function")
200901-16:40:41,32 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.unzip_mask".
200901-16:40:41,34 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.tkreg" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/tkreg".
200901-16:40:41,64 nipype.workflow INFO:
[Node] Running "tkreg" ("nipype.interfaces.freesurfer.utils.Tkregister2"), a CommandLine Interface with command:
tkregister2_cmdl --mov /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --noedit --reg register.dat --regheader --targ /Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz
200901-16:40:41,136 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683:dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
200901-16:40:41,137 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683: Referenced from: /Applications/freesurfer/tktools/../lib/gcc/lib/libgomp.1.dylib
200901-16:40:41,138 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683: Expected in: /usr/lib/libSystem.B.dylib
200901-16:40:41,139 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683:
200901-16:40:41,139 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683:dyld: Symbol not found: ___emutls_get_address
200901-16:40:41,140 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683: Referenced from: /Applications/freesurfer/tktools/../lib/gcc/lib/libgomp.1.dylib
200901-16:40:41,141 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683: Expected in: /usr/lib/libSystem.B.dylib
200901-16:40:41,141 nipype.interface INFO:
stderr 2020-09-01T16:40:41.135683:
200901-16:40:41,195 nipype.workflow WARNING:
[Node] Error on "sub_007_ses_M00.tkreg" (/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/tkreg)
200901-16:40:41,199 nipype.workflow ERROR:
Node tkreg failed to run on host sjhlrsh070.chw.edu.
200901-16:40:41,205 nipype.workflow ERROR:
Saving crash info to /Users/ThandarAung/crash-20200901-164041-ThandarAung-tkreg-7265deb5-d80d-434d-ba51-660c986aa5de.pklz
Traceback (most recent call last):
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
return super(FSCommand, self).run(**inputs)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1033, in _run_interface
self.raise_exception(runtime)
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 970, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
tkregister2_cmdl --mov /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --noedit --reg register.dat --regheader --targ /Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz
Standard output:
Standard error:
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/tktools/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address
Referenced from: /Applications/freesurfer/tktools/../lib/gcc/lib/libgomp.1.dylib
Expected in: /usr/lib/libSystem.B.dylib
Return code: -6
200901-16:40:41,208 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.convert_mgh" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_mgh".
200901-16:40:41,235 nipype.workflow INFO:
[Node] Running "convert_mgh" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --input_volume /Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz --output_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_mgh/orig_nu_out.nii.gz
200901-16:40:41,326 nipype.interface INFO:
stdout 2020-09-01T16:40:41.325889:mri_convert.bin --input_volume /Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz --output_volume /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_mgh/orig_nu_out.nii.gz
200901-16:40:42,643 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
200901-16:40:42,644 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:reading from /Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz...
200901-16:40:42,645 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
200901-16:40:42,645 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:i_ras = (-1, -5.12227e-09, -3.72529e-09)
200901-16:40:42,646 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:j_ras = (-3.72529e-09, -2.98023e-08, -1)
200901-16:40:42,647 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:k_ras = (5.58794e-09, 1, 0)
200901-16:40:42,648 nipype.interface INFO:
stdout 2020-09-01T16:40:42.642867:writing to /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/convert_mgh/orig_nu_out.nii.gz...
200901-16:40:42,702 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.convert_mgh".
200901-16:40:42,703 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.unzip_orig_nu" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/unzip_orig_nu".
200901-16:40:42,729 nipype.workflow INFO:
[Node] Running "unzip_orig_nu" ("nipype.interfaces.utility.wrappers.Function")
200901-16:40:42,832 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.unzip_orig_nu".
200901-16:40:42,833 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.normalize_to_MNI" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/normalize_to_MNI".
200901-16:40:43,69 nipype.workflow INFO:
[Node] Running "normalize_to_MNI" ("nipype.interfaces.spm.preprocess.Normalize12")
200901-16:42:58,152 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.normalize_to_MNI".
200901-16:42:58,154 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.applyInverseDeformation" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/applyInverseDeformation".
200901-16:42:58,301 nipype.workflow INFO:
[Node] Running "applyInverseDeformation" ("nipype.interfaces.utility.wrappers.Function")
200901-16:43:42,847 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.applyInverseDeformation".
200901-16:43:42,848 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.vol2vol_mask" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol_mask".
200901-16:43:42,922 nipype.workflow INFO:
[Node] Running "vol2vol_mask" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --interp nearest --regheader --mov /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol_mask/subject_space_region-pons_eroded-6mm_mask.nii --targ /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --o /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol_mask/subject_space_region-pons_eroded-6mm_mask_warped.nii
200901-16:43:43,617 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:movvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol_mask/subject_space_region-pons_eroded-6mm_mask.nii
200901-16:43:43,618 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:targvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz
200901-16:43:43,618 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:outvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol_mask/subject_space_region-pons_eroded-6mm_mask_warped.nii
200901-16:43:43,619 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:invert 0
200901-16:43:43,620 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:tal 0
200901-16:43:43,621 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:talres 2
200901-16:43:43,621 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:regheader 1
200901-16:43:43,622 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:noresample 0
200901-16:43:43,623 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:interp nearest (0)
200901-16:43:43,624 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:precision float (3)
200901-16:43:43,624 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:Gdiag_no -1
200901-16:43:43,625 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:Synth 0
200901-16:43:43,626 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:SynthSeed 1599018967
200901-16:43:43,626 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:
200901-16:43:43,627 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:Computing registration based on scanner-to-scanner
200901-16:43:43,628 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:
200901-16:43:43,629 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:Final tkRAS-to-tkRAS Matrix is:
200901-16:43:43,630 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 1.00000 0.00000 0.00000 2.25000;
200901-16:43:43,630 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.00000 1.00000 0.00000 -13.75001;
200901-16:43:43,631 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.00000 0.00000 1.00000 -11.75002;
200901-16:43:43,632 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.00000 0.00000 0.00000 1.00000;
200901-16:43:43,632 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:
200901-16:43:43,633 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:
200901-16:43:43,634 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:Vox2Vox Matrix is:
200901-16:43:43,635 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.50000 0.00000 -0.00000 39.75000;
200901-16:43:43,635 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.00000 0.50000 0.00000 51.75002;
200901-16:43:43,636 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876:-0.00000 -0.00000 0.50000 24.74999;
200901-16:43:43,637 nipype.interface INFO:
stdout 2020-09-01T16:43:43.616876: 0.00000 0.00000 0.00000 1.00000;
200901-16:43:46,361 nipype.interface INFO:
stdout 2020-09-01T16:43:46.361560:
200901-16:43:46,362 nipype.interface INFO:
stdout 2020-09-01T16:43:46.361560:Resampling
200901-16:43:46,363 nipype.interface INFO:
stdout 2020-09-01T16:43:46.361560:Output registration matrix is identity
200901-16:43:46,364 nipype.interface INFO:
stdout 2020-09-01T16:43:46.361560:
200901-16:43:46,365 nipype.interface INFO:
stdout 2020-09-01T16:43:46.361560:mri_vol2vol done
200901-16:43:46,422 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.vol2vol_mask".
200901-16:43:46,423 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.unzip_pet" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/unzip_pet".
200901-16:43:46,433 nipype.workflow INFO:
[Node] Running "unzip_pet" ("nipype.interfaces.utility.wrappers.Function")
200901-16:43:46,461 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.unzip_pet".
200901-16:43:46,462 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.coreg" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/coreg".
200901-16:43:46,531 nipype.workflow INFO:
[Node] Running "coreg" ("nipype.interfaces.spm.preprocess.Coregister")
200901-16:44:24,178 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.coreg".
200901-16:44:24,180 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.removenan" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/removenan".
200901-16:44:24,400 nipype.workflow INFO:
[Node] Running "removenan" ("nipype.interfaces.utility.wrappers.Function")
200901-16:44:25,776 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.removenan".
200901-16:44:25,777 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.vol2vol" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol".
200901-16:44:25,886 nipype.workflow INFO:
[Node] Running "vol2vol" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --interp trilin --regheader --mov /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol/no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET.nii.gz --targ /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz --o /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol/no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET_warped.nii.gz
200901-16:44:26,652 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:movvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol/no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET.nii.gz
200901-16:44:26,653 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:targvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/gtmseg/gtmseg.mgz
200901-16:44:26,654 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:outvol /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/vol2vol/no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET_warped.nii.gz
200901-16:44:26,654 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:invert 0
200901-16:44:26,655 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:tal 0
200901-16:44:26,656 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:talres 2
200901-16:44:26,656 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:regheader 1
200901-16:44:26,657 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:noresample 0
200901-16:44:26,658 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:interp trilin (1)
200901-16:44:26,658 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:precision float (3)
200901-16:44:26,659 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:Gdiag_no -1
200901-16:44:26,660 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:Synth 0
200901-16:44:26,660 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:SynthSeed 1599965629
200901-16:44:26,661 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:
200901-16:44:26,662 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:Computing registration based on scanner-to-scanner
200901-16:44:26,662 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:
200901-16:44:26,663 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:Final tkRAS-to-tkRAS Matrix is:
200901-16:44:26,664 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 1.00000 0.00000 0.00000 2.25000;
200901-16:44:26,664 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.00000 1.00000 0.00000 -13.75001;
200901-16:44:26,665 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.00000 0.00000 1.00000 -11.75002;
200901-16:44:26,666 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.00000 0.00000 0.00000 1.00000;
200901-16:44:26,666 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:
200901-16:44:26,667 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:
200901-16:44:26,668 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:Vox2Vox Matrix is:
200901-16:44:26,668 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.50000 0.00000 -0.00000 39.75000;
200901-16:44:26,669 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.00000 0.50000 0.00000 51.75002;
200901-16:44:26,670 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913:-0.00000 -0.00000 0.50000 24.74999;
200901-16:44:26,670 nipype.interface INFO:
stdout 2020-09-01T16:44:26.651913: 0.00000 0.00000 0.00000 1.00000;
200901-16:44:35,619 nipype.interface INFO:
stdout 2020-09-01T16:44:35.618703:
200901-16:44:35,620 nipype.interface INFO:
stdout 2020-09-01T16:44:35.618703:Resampling
200901-16:44:35,621 nipype.interface INFO:
stdout 2020-09-01T16:44:35.618703:Output registration matrix is identity
200901-16:44:35,621 nipype.interface INFO:
stdout 2020-09-01T16:44:35.618703:
200901-16:44:35,622 nipype.interface INFO:
stdout 2020-09-01T16:44:35.618703:mri_vol2vol done
200901-16:44:35,683 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.vol2vol".
200901-16:44:35,684 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.pons_normalization" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/pons_normalization".
200901-16:44:36,584 nipype.workflow INFO:
[Node] Running "pons_normalization" ("nipype.interfaces.utility.wrappers.Function")
200901-16:44:42,598 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.pons_normalization".
200901-16:44:42,599 nipype.workflow INFO:
[Node] Setting-up "sub_007_ses_M00.petpvc" in "/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/petpvc".
200901-16:44:43,8 nipype.workflow INFO:
[Node] Running "petpvc" ("nipype.interfaces.petpvc.PETPVC"), a CommandLine Interface with command:
petpvc -a 1.5000 -x 5.5000 -y 5.5000 -z 5.5000 -i /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/pons_normalization/suvr_no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET_warped.nii.gz -m /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/merge_volume/0_merged.nii.gz -k 10 -n 10 -o /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/sub_007_ses_M00/petpvc/suvr_no_nan_rsub-007_ses-M00_task-rest_acq-fdg_PET_warped_iy_pvc.nii.gz -p IY -a 0.0100
200901-16:45:00,519 nipype.interface INFO:
stdout 2020-09-01T16:45:00.517838:Performing iterative Yang...
200901-16:45:00,951 nipype.interface INFO:
stderr 2020-09-01T16:45:00.951211:sum in region 1 = 3.32654e+07
200901-16:45:45,138 nipype.interface INFO:
stderr 2020-09-01T16:45:45.136999:sum in region 2 = 736710
200901-16:46:26,556 nipype.interface INFO:
stderr 2020-09-01T16:46:26.555150:sum in region 3 = 732880
200901-16:47:07,770 nipype.interface INFO:
stderr 2020-09-01T16:47:07.769070:sum in region 4 = 46038
200901-16:47:48,992 nipype.interface INFO:
stderr 2020-09-01T16:47:48.990864:sum in region 5 = 50621
200901-16:48:30,309 nipype.interface INFO:
stderr 2020-09-01T16:48:30.308360:sum in region 6 = 330105
200901-16:49:11,539 nipype.interface INFO:
stderr 2020-09-01T16:49:11.537376:sum in region 7 = 332763
200901-16:49:52,885 nipype.interface INFO:
stderr 2020-09-01T16:49:52.884575:sum in region 8 = 418065
200901-16:50:34,136 nipype.interface INFO:
stderr 2020-09-01T16:50:34.134852:sum in region 9 = 413986
200901-16:51:15,454 nipype.interface INFO:
stderr 2020-09-01T16:51:15.453503:sum in region 10 = 145559
200901-16:51:56,941 nipype.interface INFO:
stderr 2020-09-01T16:51:56.939766:sum in region 11 = 131444
200901-16:52:38,122 nipype.interface INFO:
stderr 2020-09-01T16:52:38.121201:sum in region 12 = 11217
200901-16:53:19,386 nipype.interface INFO:
stderr 2020-09-01T16:53:19.384525:sum in region 13 = 11932
200901-16:54:00,961 nipype.interface INFO:
stderr 2020-09-01T16:54:00.960590:sum in region 14 = 1.66615e+06
200901-16:54:42,175 nipype.interface INFO:
stderr 2020-09-01T16:54:42.175396:sum in region 15 = 67120
200901-16:55:23,423 nipype.interface INFO:
stderr 2020-09-01T16:55:23.421347:sum in region 16 = 4368
200901-16:56:04,579 nipype.interface INFO:
stderr 2020-09-01T16:56:04.578009:sum in region 17 = 3760
200901-16:56:46,463 nipype.interface INFO:
stderr 2020-09-01T16:56:46.462124:sum in region 18 = 11352
200901-16:57:27,712 nipype.interface INFO:
stderr 2020-09-01T16:57:27.711355:sum in region 19 = 11200
200901-16:58:08,941 nipype.interface INFO:
stderr 2020-09-01T16:58:08.940266:sum in region 20 = 137208
200901-16:58:50,215 nipype.interface INFO:
stderr 2020-09-01T16:58:50.214197:sum in region 21 = 25576
200901-16:59:31,567 nipype.interface INFO:
stderr 2020-09-01T16:59:31.566553:sum in region 22 = 25184
200901-17:00:16,553 nipype.interface INFO:
stderr 2020-09-01T17:00:16.552247:sum in region 23 = 185952
200901-17:01:01,167 nipype.interface INFO:
stderr 2020-09-01T17:01:01.165780:sum in region 24 = 3.45345e+06
200901-17:01:46,499 nipype.interface INFO:
stderr 2020-09-01T17:01:46.499005:sum in region 25 = 29816
200901-17:02:31,134 nipype.interface INFO:
stderr 2020-09-01T17:02:31.133165:sum in region 26 = 26112
200901-17:03:16,282 nipype.interface INFO:
stderr 2020-09-01T17:03:16.280662:sum in region 27 = 15848
200901-17:04:00,918 nipype.interface INFO:
stderr 2020-09-01T17:04:00.916864:sum in region 28 = 15384
200901-17:04:45,778 nipype.interface INFO:
stderr 2020-09-01T17:04:45.778018:sum in region 29 = 32520
200901-17:05:30,603 nipype.interface INFO:
stderr 2020-09-01T17:05:30.602995:sum in region 30 = 35184
200901-17:06:15,389 nipype.interface INFO:
stderr 2020-09-01T17:06:15.387745:sum in region 31 = 67224
200901-17:07:00,33 nipype.interface INFO:
stderr 2020-09-01T17:07:00.031504:sum in region 32 = 68920
200901-17:07:44,535 nipype.interface INFO:
stderr 2020-09-01T17:07:44.533921:sum in region 33 = 63952
200901-17:08:29,199 nipype.interface INFO:
stderr 2020-09-01T17:08:29.198199:sum in region 34 = 2328
200901-17:09:13,582 nipype.interface INFO:
stderr 2020-09-01T17:09:13.580667:sum in region 35 = 589680
200901-17:09:58,148 nipype.interface INFO:
stderr 2020-09-01T17:09:58.147086:sum in region 36 = 8496
200901-17:10:42,738 nipype.interface INFO:
stderr 2020-09-01T17:10:42.736400:sum in region 37 = 12007
200901-17:11:27,372 nipype.interface INFO:
stderr 2020-09-01T17:11:27.370925:sum in region 38 = 13829
200901-17:12:11,897 nipype.interface INFO:
stderr 2020-09-01T17:12:11.894954:sum in region 39 = 18438
200901-17:12:56,476 nipype.interface INFO:
stderr 2020-09-01T17:12:56.474971:sum in region 40 = 18541
200901-17:13:41,249 nipype.interface INFO:
stderr 2020-09-01T17:13:41.248225:sum in region 41 = 8440
200901-17:14:25,696 nipype.interface INFO:
stderr 2020-09-01T17:14:25.696551:sum in region 42 = 19896
200901-17:15:10,209 nipype.interface INFO:
stderr 2020-09-01T17:15:10.207537:sum in region 43 = 14258
200901-17:15:54,758 nipype.interface INFO:
stderr 2020-09-01T17:15:54.757562:sum in region 44 = 23164
200901-17:16:39,326 nipype.interface INFO:
stderr 2020-09-01T17:16:39.324338:sum in region 45 = 10569
200901-17:17:23,807 nipype.interface INFO:
stderr 2020-09-01T17:17:23.806679:sum in region 46 = 20487
200901-17:18:08,344 nipype.interface INFO:
stderr 2020-09-01T17:18:08.342589:sum in region 47 = 16398
200901-17:38:11,27 nipype.workflow INFO:
[Node] Finished "sub_007_ses_M00.petpvc".
200901-17:38:11,30 nipype.workflow INFO:
***********************************
200901-17:38:11,31 nipype.workflow ERROR:
could not run node: sub_007_ses_M00.tkreg
200901-17:38:11,32 nipype.workflow INFO:
crashfile: /Users/ThandarAung/crash-20200901-164041-ThandarAung-tkreg-7265deb5-d80d-434d-ba51-660c986aa5de.pklz
200901-17:38:11,33 nipype.workflow INFO:
***********************************
200901-17:38:11,45 nipype.workflow WARNING:
[Node] Error on "_full_pipeline_mapnode0" (/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/pet-surface/full_pipeline_mapnode/mapflow/_full_pipeline_mapnode0)
200901-17:38:11,51 nipype.workflow WARNING:
[Node] Error on "pet-surface.full_pipeline_mapnode" (/private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/pet-surface/full_pipeline_mapnode)
200901-17:38:12,349 nipype.workflow ERROR:
Node full_pipeline_mapnode failed to run on host sjhlrsh070.chw.edu.
200901-17:38:12,351 nipype.workflow ERROR:
Saving crash info to /Users/ThandarAung/crash-20200901-173812-ThandarAung-full_pipeline_mapnode-c846187e-8792-46be-9570-33e449adec79.pklz
200901-17:38:12,359 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 14.40/14.40, Free processors: 7/7.
200901-17:38:14,350 nipype.workflow INFO:
***********************************
200901-17:38:14,351 nipype.workflow ERROR:
could not run node: pet-surface.full_pipeline_mapnode
200901-17:38:14,351 nipype.workflow INFO:
crashfile: /Users/ThandarAung/crash-20200901-173812-ThandarAung-full_pipeline_mapnode-c846187e-8792-46be-9570-33e449adec79.pklz
200901-17:38:14,351 nipype.workflow INFO:
***********************************
(clinicaEnv) ThandarAung@sjhlrsh070 ~ % nipypecli crash /Users/ThandarAung/crash-20200901-173812-ThandarAung-full_pipeline_mapnode-c846187e-8792-46be-9570-33e449adec79.pklz
File: /Users/ThandarAung/crash-20200901-173812-ThandarAung-full_pipeline_mapnode-c846187e-8792-46be-9570-33e449adec79.pklz
Node: pet-surface.full_pipeline_mapnode
Working directory: /private/var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76/pet-surface/full_pipeline_mapnode
Node inputs:
caps_dir = /Users/ThandarAung/Desktop/CAPS
csv_segmentation = /Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/resources/label_conversion_gtmsegmentation.csv
desikan_left = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/label/lh.aparc.annot']
desikan_right = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/label/rh.aparc.annot']
destrieux_left = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/label/lh.aparc.a2009s.annot']
destrieux_right = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/label/rh.aparc.a2009s.annot']
function_str = def get_wf(subject_id,
session_id,
psf,
caps_dir,
pet,
orig_nu,
white_surface_left,
white_surface_right,
working_directory_subjects,
pet_tracer,
csv_segmentation,
subcortical_eroded_mask,
matscript_folder_inverse_deformation,
destrieux_left,
destrieux_right,
desikan_left,
desikan_right,
use_spm_standalone,
is_longitudinal):
"""get_wf create a full workflow for only one subject, and then executes it
Args:
(string) subject_id : The subject id
(string) session_id : The session id
(string) psf : Path the json file containing information on the point spread function
(string) caps_dir : Path to the CAPS directory
(string) pet : Path to the PET image in the bids directory
(string) orig_nu : Path to the orig_nu file (must be in the CAPS directory, in mri)
(string) white_surface_left : Path to the left white surface in native space of subject
(string) white_surface_right : Path to the right white suface in native space of subject
(string) csv_segmentation : Path to the csv for the segmentation (problems encountered while using __file__)
(string) subcortical_eroded_mask : Path to the mask of the eroded version used for the suvr
(string) matscript_folder_inverse_deformation : Path to the current foler (containing the matlab script
used to call the spm function for the inverse deformation
Returns:
Void
"""
import os
import datetime
import nibabel as nib
from colorama import Fore
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import nipype.interfaces.io as nio
from nipype.interfaces.freesurfer import Tkregister2, ApplyVolTransform, MRIConvert
from nipype.interfaces.fsl import Merge
from nipype.interfaces.petpvc import PETPVC
from nipype.interfaces.spm import Coregister, Normalize12
import clinica.pipelines.pet_surface.pet_surface_utils as utils
from clinica.utils.filemanip import unzip_nii
from clinica.utils.spm import get_tpm
from clinica.utils.stream import cprint
from clinica.utils.ux import print_begin_image
# Check that the PET file is a 3D volume
img = nib.load(pet)
if len(img.shape) == 4:
now = datetime.datetime.now().strftime('%H:%M:%S')
error_msg = '%s[%s] Error: Clinica does not handle 4D volumes for %s | %s%s'\
% (Fore.RED, now, subject_id, session_id, Fore.RESET)
cprint(error_msg)
raise NotImplementedError(error_msg)
print_begin_image(subject_id + '_' + session_id)
# Creation of workflow
# 1 Creation of node
unzip_pet = pe.Node(niu.Function(input_names=['in_file'],
output_names=['out_file'],
function=unzip_nii),
name='unzip_pet')
unzip_orig_nu = unzip_pet.clone(name='unzip_orig_nu')
unzip_mask = unzip_pet.clone(name='unzip_mask')
unzip_mask.inputs.in_file = subcortical_eroded_mask
coreg = pe.Node(Coregister(), name='coreg')
convert_mgh = pe.Node(MRIConvert(), name='convert_mgh')
removenan = pe.Node(niu.Function(input_names=['volname'],
output_names=['vol_wo_nan'],
function=utils.remove_nan),
name='removenan')
gtmsegmentation = pe.Node(niu.Function(input_names=['caps_dir',
'subject_id',
'session_id',
'is_longitudinal'],
output_names=['gtmseg_file'],
function=utils.perform_gtmseg),
name='gtmseg')
gtmsegmentation.inputs.caps_dir = caps_dir
gtmsegmentation.inputs.subject_id = subject_id
gtmsegmentation.inputs.session_id = session_id
gtmsegmentation.inputs.is_longitudinal = is_longitudinal
tkregister = pe.Node(Tkregister2(reg_header=True), name='tkreg')
convert_gtmseg = convert_mgh.clone(name='convert_gtmseg')
labelconversion = pe.Node(niu.Function(input_names=['gtmsegfile',
'csv'],
output_names=['list_of_regions'],
function=utils.make_label_conversion),
name='conversion_of_labels')
labelconversion.inputs.csv = csv_segmentation
if not os.path.exists(labelconversion.inputs.csv):
raise Exception('CSV file : ' + labelconversion.inputs.csv + ' does not exist.')
merge_volume = pe.Node(Merge(output_type='NIFTI_GZ', dimension='t'),
name='merge_volume')
vol2vol = pe.Node(ApplyVolTransform(reg_header=True, interp='trilin'),
name='vol2vol')
vol2vol_mask = pe.Node(ApplyVolTransform(reg_header=True, interp='nearest'),
name='vol2vol_mask')
tpm_nii = get_tpm()
normalize12 = pe.Node(Normalize12(tpm=tpm_nii,
affine_regularization_type='mni',
jobtype='est',
bias_fwhm=60,
bias_regularization=0.0001,
warping_regularization=[0, 0.001, 0.5, 0.05, 0.2]),
name='normalize_to_MNI')
if use_spm_standalone is True:
fun_apply_inverse_deformation = utils.runApplyInverseDeformationField_SPM_standalone
else:
fun_apply_inverse_deformation = utils.runApplyInverseDeformationField
apply_inverse_deformation = pe.Node(niu.Function(input_names=['target',
'deformation_field',
'img',
'matscript_folder'],
output_names=['freesurfer_space_eroded_mask'],
function=fun_apply_inverse_deformation),
name='applyInverseDeformation')
apply_inverse_deformation.inputs.matscript_folder = matscript_folder_inverse_deformation
pons_normalization = pe.Node(niu.Function(input_names=['pet_path',
'mask'],
output_names=['suvr'],
function=utils.suvr_normalization),
name='pons_normalization')
pons_normalization.inputs.pet_tracer = pet_tracer
pvc = pe.Node(PETPVC(pvc='IY'), name='petpvc')
reformat_surface_name = pe.Node(niu.Function(input_names=['hemi',
'left_surface',
'right_surface'],
output_names=['out'],
function=utils.reformat_surfname),
name='reformat_surface_name')
reformat_surface_name.inputs.left_surface = white_surface_left
reformat_surface_name.inputs.right_surface = white_surface_right
reformat_surface_name.iterables = ('hemi', ['lh', 'rh'])
mris_exp = pe.Node(niu.Function(input_names=['in_surface'],
output_names=['out_surface'],
function=utils.mris_expand),
name='mris_expand_white')
surf_conversion = pe.MapNode(niu.Function(input_names=['in_surface',
'reg_file',
'gtmsegfile',
'subject_id',
'session_id',
'caps_dir',
'is_longitudinal'],
output_names=['tval'],
function=utils.surf2surf),
name='surf_conversion',
iterfield=['in_surface'])
surf_conversion.inputs.subject_id = subject_id
surf_conversion.inputs.session_id = session_id
surf_conversion.inputs.caps_dir = caps_dir
surf_conversion.inputs.is_longitudinal = is_longitudinal
vol_on_surf = pe.MapNode(niu.Function(input_names=['volume',
'surface',
'subject_id',
'session_id',
'caps_dir',
'gtmsegfile',
'is_longitudinal'],
output_names=['output'],
function=utils.vol2surf),
name='vol_on_surf',
iterfield=['surface'])
vol_on_surf.inputs.subject_id = subject_id
vol_on_surf.inputs.session_id = session_id
vol_on_surf.inputs.caps_dir = caps_dir
vol_on_surf.inputs.is_longitudinal = is_longitudinal
normal_average = pe.Node(niu.Function(input_names=['in_surfaces'],
output_names=['out_surface'],
function=utils.weighted_mean),
name='normal_average')
project_on_fsaverage = pe.Node(niu.Function(input_names=['projection',
'subject_id',
'caps_dir',
'session_id',
'fwhm',
'is_longitudinal'],
output_names=['out_fsaverage'],
function=utils.fsaverage_projection),
name='project_on_fsaverage')
project_on_fsaverage.iterables = ('fwhm', [0, 5, 10, 15, 20, 25])
project_on_fsaverage.inputs.subject_id = subject_id
project_on_fsaverage.inputs.session_id = session_id
project_on_fsaverage.inputs.caps_dir = caps_dir
project_on_fsaverage.inputs.is_longitudinal = is_longitudinal
extract_mid_surface = pe.Node(niu.Function(input_names=['in_surfaces'],
output_names=['mid_surface'],
function=utils.get_mid_surface),
name='extract_mid_surface')
psfreader = pe.Node(niu.Function(input_names=['json_path'],
output_names=['in_plane', 'axial'],
function=utils.readpsf),
name='psfreader')
surface_atlas = {'destrieux': {'lh': destrieux_left,
'rh': destrieux_right},
'desikan': {'lh': desikan_left,
'rh': desikan_right}}
gather_pet_projection = pe.JoinNode(niu.IdentityInterface(fields=['pet_projection_lh_rh']),
name='gather_pet_projection_hemisphere',
joinsource='reformat_surface_name',
joinfield=['pet_projection_lh_rh'])
atlas_tsv = pe.Node(
niu.Function(input_names=['pet', 'atlas_files'],
output_names=['destrieux_tsv', 'desikan_tsv'],
function=utils.produce_tsv),
name='atlas_tsv')
atlas_tsv.inputs.atlas_files = surface_atlas
# 2 creation of workflow : working dir, inputnode, outputnode and datasink
name_workflow = subject_id.replace('-', '_') + '_' + session_id.replace('-', '_')
if is_longitudinal:
name_workflow += '_long'
wf = pe.Workflow(name=name_workflow)
wf.base_dir = working_directory_subjects
inputnode = pe.Node(niu.IdentityInterface(fields=['orig_nu',
'pet',
'psf',
'white_surface_left',
'white_surface_right']),
name='inputnode',
mandatory_inputs=True)
inputnode.inputs.orig_nu = orig_nu
inputnode.inputs.pet = pet
inputnode.inputs.psf = psf
inputnode.inputs.white_surface_right = white_surface_right
inputnode.inputs.white_surface_left = white_surface_left
outputnode = pe.Node(niu.IdentityInterface(fields=['mid_surf',
'projection_native_subject',
'projection_fsaverage_smoothed',
'destrieux_tsv',
'desikan_tsv']),
name='outputnode',
mandatory_inputs=True)
datasink = pe.Node(nio.DataSink(),
name='sinker')
def get_output_dir(is_longitudinal, caps_dir, subject_id, session_id):
import os
from clinica.utils.exceptions import ClinicaCAPSError
if is_longitudinal:
root = os.path.join(caps_dir, 'subjects', subject_id, session_id, 't1')
long_folds = [f for f in os.listdir(root) if f.startswith('long-')]
if len(long_folds) > 1:
raise ClinicaCAPSError('[Error] Folder ' + root + ' contains ' + str(len(long_folds))
+ ' folders labeled long-*. Only 1 can exist')
elif len(long_folds) == 0:
raise ClinicaCAPSError(
'[Error] Folder ' + root + ' does not contains a folder labeled long-*. Have you run t1-freesurfer-longitudinal ?')
else:
output_dir = os.path.join(caps_dir, 'subjects', subject_id, session_id,
'pet', long_folds[0], 'surface_longitudinal')
else:
output_dir = os.path.join(caps_dir, 'subjects', subject_id, session_id,
'pet', 'surface')
return output_dir
datasink.inputs.base_directory = get_output_dir(is_longitudinal, caps_dir, subject_id, session_id)
datasink.inputs.parameterization = True
cross_sectional_regexp_substitutions = [
# Mid surface
(r'(.*(sub-.*)\/(ses-.*)\/pet\/surface)\/midsurface\/.*_hemi_([a-z]+)(.*)$',
r'\1/\2_\3_hemi-\4_midcorticalsurface'),
# Projection in native space
(r'(.*(sub-.*)\/(ses-.*)\/pet\/surface)\/projection_native\/.*_hemi_([a-z]+).*',
r'\1/\2_\3_task-rest_acq-' + pet_tracer + r'_pet_space-native_suvr-' + utils.normalization_areas(pet_tracer) + r'_pvc-iy_hemi-\4_projection.mgh'),
# Projection in fsaverage
(r'(.*(sub-.*)\/(ses-.*)\/pet\/surface)\/projection_fsaverage\/.*_hemi_([a-z]+).*_fwhm_([0-9]+).*',
r'\1/\2_\3_task-rest_acq-' + pet_tracer + r'_pet_space-fsaverage_suvr-' + utils.normalization_areas(pet_tracer) + r'_pvc-iy_hemi-\4_fwhm-\5_projection.mgh'),
# TSV file for Destrieux atlas
(r'(.*(sub-.*)\/(ses-.*)\/pet\/surface)\/destrieux_tsv\/destrieux.tsv',
r'\1/atlas_statistics/\2_\3_task-rest_acq-' + pet_tracer.lower() + '_pet_space-destrieux_pvc-iy_suvr-' + utils.normalization_areas(pet_tracer) + '_statistics.tsv'),
# TSV file for Desikan atlas
(r'(.*(sub-.*)\/(ses-.*)\/pet\/surface)\/desikan_tsv\/desikan.tsv',
r'\1/atlas_statistics/\2_\3_task-rest_acq-' + pet_tracer.lower() + '_pet_space-desikan_pvc-iy_suvr-' + utils.normalization_areas(pet_tracer) + '_statistics.tsv')
]
longitudinal_regexp_substitutions = [
# Mid surface
(r'(.*(sub-.*)\/(ses-.*)\/pet\/(long-.*)\/surface_longitudinal)\/midsurface\/.*_hemi_([a-z]+)(.*)$',
r'\1/\2_\3_\4_hemi-\5_midcorticalsurface'),
# Projection in native space
(r'(.*(sub-.*)\/(ses-.*)\/pet\/(long-.*)\/surface_longitudinal)\/projection_native\/.*_hemi_([a-z]+).*',
r'\1/\2_\3_\4_task-rest_acq-' + pet_tracer + r'_pet_space-native_suvr-' + utils.normalization_areas(
pet_tracer) + r'_pvc-iy_hemi-\5_projection.mgh'),
# Projection in fsaverage
(r'(.*(sub-.*)\/(ses-.*)\/pet\/(long-.*)\/surface_longitudinal)\/projection_fsaverage\/.*_hemi_([a-z]+).*_fwhm_([0-9]+).*',
r'\1/\2_\3_\4_task-rest_acq-' + pet_tracer + r'_pet_space-fsaverage_suvr-' + utils.normalization_areas(
pet_tracer) + r'_pvc-iy_hemi-\5_fwhm-\6_projection.mgh'),
# TSV file for Destrieux atlas
(r'(.*(sub-.*)\/(ses-.*)\/pet\/(long-.*)\/surface_longitudinal)\/destrieux_tsv\/destrieux.tsv',
r'\1/atlas_statistics/\2_\3_\4_task-rest_acq-' + pet_tracer.lower() + '_pet_space-destrieux_pvc-iy_suvr-' + utils.normalization_areas(
pet_tracer) + '_statistics.tsv'),
# TSV file for Desikan atlas
(r'(.*(sub-.*)\/(ses-.*)\/pet\/(long-.*)\/surface_longitudinal)\/desikan_tsv\/desikan.tsv',
r'\1/atlas_statistics/\2_\3_\4_task-rest_acq-' + pet_tracer.lower() + '_pet_space-desikan_pvc-iy_suvr-' + utils.normalization_areas(
pet_tracer) + '_statistics.tsv')
]
if is_longitudinal:
datasink.inputs.regexp_substitutions = longitudinal_regexp_substitutions
else:
datasink.inputs.regexp_substitutions = cross_sectional_regexp_substitutions
# 3 Connecting the nodes
# TODO(@arnaud.marcoux): Add titles for sections of connections.
# Could be useful to add sections title to group similar connections
# together.
wf.connect([(inputnode, unzip_pet, [('pet', 'in_file')]),
(unzip_pet, coreg, [('out_file', 'source')]),
(inputnode, convert_mgh, [('orig_nu', 'in_file')]),
(convert_mgh, unzip_orig_nu, [('out_file', 'in_file')]),
(unzip_orig_nu, coreg, [('out_file', 'target')]),
(coreg, removenan, [('coregistered_source', 'volname')]),
(removenan, vol2vol, [('vol_wo_nan', 'source_file')]),
(inputnode, tkregister, [('orig_nu', 'target_image')]),
(unzip_orig_nu, normalize12, [('out_file', 'image_to_align')]),
(unzip_mask, apply_inverse_deformation, [('out_file', 'img')]),
(normalize12, apply_inverse_deformation, [('deformation_field', 'deformation_field')]),
(unzip_orig_nu, apply_inverse_deformation, [('out_file', 'target')]),
(apply_inverse_deformation, vol2vol_mask, [('freesurfer_space_eroded_mask', 'source_file')]),
(gtmsegmentation, vol2vol_mask, [('gtmseg_file', 'target_file')]),
(gtmsegmentation, tkregister, [('gtmseg_file', 'moving_image')]),
(gtmsegmentation, convert_gtmseg, [('gtmseg_file', 'in_file')]),
(gtmsegmentation, vol2vol, [('gtmseg_file', 'target_file')]),
(vol2vol, pons_normalization, [('transformed_file', 'pet_path')]),
(vol2vol_mask, pons_normalization, [('transformed_file', 'mask')]),
(convert_gtmseg, labelconversion, [('out_file', 'gtmsegfile')]),
(labelconversion, merge_volume, [('list_of_regions', 'in_files')]),
(inputnode, psfreader, [('psf', 'json_path')]),
(psfreader, pvc, [('in_plane', 'fwhm_x')]),
(psfreader, pvc, [('in_plane', 'fwhm_y')]),
(psfreader, pvc, [('axial', 'fwhm_z')]),
(merge_volume, pvc, [('merged_file', 'mask_file')]),
(pons_normalization, pvc, [('suvr', 'in_file')]),
(reformat_surface_name, mris_exp, [('out', 'in_surface')]),
(mris_exp, extract_mid_surface, [('out_surface', 'in_surfaces')]),
(mris_exp, surf_conversion, [('out_surface', 'in_surface')]),
(tkregister, surf_conversion, [('reg_file', 'reg_file')]),
(gtmsegmentation, surf_conversion, [('gtmseg_file', 'gtmsegfile')]),
(pvc, vol_on_surf, [('out_file', 'volume')]),
(surf_conversion, vol_on_surf, [('tval', 'surface')]),
(gtmsegmentation, vol_on_surf, [('gtmseg_file', 'gtmsegfile')]),
(vol_on_surf, normal_average, [('output', 'in_surfaces')]),
(normal_average, project_on_fsaverage, [('out_surface', 'projection')]),
(normal_average, gather_pet_projection, [('out_surface', 'pet_projection_lh_rh')]),
(gather_pet_projection, atlas_tsv, [('pet_projection_lh_rh', 'pet')]),
(atlas_tsv, outputnode, [('destrieux_tsv', 'destrieux_tsv')]),
(atlas_tsv, outputnode, [('desikan_tsv', 'desikan_tsv')]),
(project_on_fsaverage, outputnode, [('out_fsaverage', 'projection_fsaverage_smoothed')]),
(extract_mid_surface, outputnode, [('mid_surface', 'mid_surf')]),
(normal_average, outputnode, [('out_surface', 'projection_native_subject')]),
(outputnode, datasink, [('projection_fsaverage_smoothed', 'projection_fsaverage')]),
(outputnode, datasink, [('mid_surf', 'midsurface')]),
(outputnode, datasink, [('projection_native_subject', 'projection_native')]),
(outputnode, datasink, [('destrieux_tsv', 'destrieux_tsv')]),
(outputnode, datasink, [('desikan_tsv', 'desikan_tsv')])
])
# wf.write_graph(graph2use='flat')
wf.run()
pass
is_longitudinal = False
matscript_folder_inverse_deformation = /Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/pipelines/pet_surface
orig_nu = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/mri/orig_nu.mgz']
pet = ['/Users/ThandarAung/Desktop/BIDS_centered/sub-007/ses-M00/sub-007_ses-M00/pet/sub-007_ses-M00_task-rest_acq-fdg_PET.nii.gz']
pet_tracer = fdg
psf = ['/Users/ThandarAung/Desktop/BIDS_centered/sub-007/ses-M00/sub-007_ses-M00/pet/sub-007_ses-M00_task-rest_acq-fdg_PET.json']
session_id = ['ses-M00']
subcortical_eroded_mask = /Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/clinica/resources/masks/region-pons_eroded-6mm_mask.nii.gz
subject_id = ['sub-007']
use_spm_standalone = False
white_surface_left = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/surf/lh.white']
white_surface_right = ['/Users/ThandarAung/Desktop/CAPS/subjects/sub-007/ses-M00/t1/freesurfer_cross_sectional/sub-007_ses-M00/surf/rh.white']
working_directory_subjects = /var/folders/4y/hvzhd40x2bl3wq3s4jj02y_40000gq/T/tmpu26idz76
Traceback:
Traceback (most recent call last):
File "/Users/ThandarAung/opt/miniconda3/envs/clinicaEnv/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
(clinicaEnv) ThandarAung@sjhlrsh070 ~ %