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mincreshape with -dimrange error in 3D volumes #18

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guilhermepovala opened this issue Feb 14, 2019 · 9 comments
Open

mincreshape with -dimrange error in 3D volumes #18

guilhermepovala opened this issue Feb 14, 2019 · 9 comments
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@tfunck
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@guilhermepovala
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Hi again,

When I try to run the default Launcher.py, it gives an error in the mincreshape call:

Standard error:
Unknown image dimension "time"
Return code: 1
Interface ReshapeCommand failed to run.
Interface pet3DVolume failed to run.

It probably happens because of the -dimrange 'time=0,1' parameter.

Could it be optional?

APPIAN/Initialization/initialization.py

Line 426 in 800f60d

run_mincreshape.inputs.dimrange = 'time='+str(first)+','+str(count)

@guilhermepovala
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Here's the full error output:

"python2.7 /opt/APPIAN/Launcher.py -s "/adni" -t "/adni/out" --no-results-report --no-dashboard ";/
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
Warning : No subject arguments passed. Will run all subjects found in source directory /adni
('Subjects:', '01')
Warning : No session variables. Will run all sessions found in source directory /adni
('Sessions:', '01')
Warning : No task variables. Will run all sessions found in source directory /adni
('Task:', '')
Warning : No run variables. Will process all runs found in source directory /adni
('Runs:', '')

  • Pipeline started at Thu Feb 14 17:40:24 2019on Linux 0dff14881019 4.4.0-142-generic

  • Command line is :
    ['/opt/APPIAN/Launcher.py', '-s', '/adni', '-t', '/adni/out', '--no-results-report', '--no-dashboard']

  • The source directory is : /adni

  • The target directory is : /adni/out

  • Data-set Subject ID(s) is/are : 01

  • Sessions : ['01']

  • Tasks : []

  • Runs : []

  • Acquisition :

  • Reconstruction :

mincresample -clobber -like /opt/beast-library-1.0/union_mask.mnc /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c.mnc /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl.mnc
190214-17:40:25,205 interface INFO:
stderr 2019-02-14T17:40:25.205438:Transforming slices:.................................................................................................................................................................................................Done
190214-17:40:26,240 interface INFO:
stderr 2019-02-14T17:40:26.240033:Transforming slices:.................................................................................................................................................................................................Done
mincresample -clobber -like /opt/beast-library-1.0/union_mask.mnc /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_mask.mnc /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl_mask.mnc
[initialization.petVolume, initialization.outputnode, initialization.inputnode, initialization.petSettings, initialization.petCenter, preproc.infosource, preproc.preinfosource, masking.resultsLabels, masking.inputnode, masking.brain_mask, preproc.coreg_qc_metrics, preproc.datasourcePET, preproc.datasource, pet_coregistration.outputnode, pet_coregistration.PETMNIXfm_node, pet_coregistration.MNIPETXfm_node, pet_coregistration.inputnode, pet_coregistration.pet2mri, pet_coregistration.pet_brainmask, preproc.output, mri.inputnode, mri.t1_mni_brain_mask, mri.segmentation_ants, mri.transform_brain_mask, mri.mri_normalize, mri.MNIT1, mri.outputnode, mri.t1_nat, preproc.t1_analysis_space, preproc.datasourceAnat, preproc.t1_pet_space]
190214-17:40:27,49 workflow INFO:
['check', 'execution', 'logging']
190214-17:40:27,63 workflow INFO:
Running serially.
190214-17:40:27,64 workflow INFO:
Executing node infosource.a0 in dir: /adni/out/preproc/_args_run.task.ses01.sid01/infosource
190214-17:40:27,65 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,67 workflow INFO:
Executing node datasourceAnat.a0 in dir: /adni/out/preproc/_args_run.task.ses01.sid01/datasourceAnat
190214-17:40:27,73 workflow INFO:
Runtime memory and threads stats unavailable
190214-17:40:27,74 workflow INFO:
Executing node t1_nat.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_nat
190214-17:40:27,75 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,76 workflow INFO:
Executing node mri_normalize.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize
190214-17:40:27,76 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,78 workflow INFO:
Executing node t1_mni_brain_mask.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask
190214-17:40:27,79 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,84 workflow INFO:
Executing node datasourcePET.a0 in dir: /adni/out/preproc/_args_run.task.ses01.sid01/datasourcePET
190214-17:40:27,92 workflow INFO:
Runtime memory and threads stats unavailable
190214-17:40:27,93 workflow INFO:
Executing node petCenter.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petCenter
190214-17:40:27,93 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,95 workflow INFO:
Executing node petSettings.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petSettings
190214-17:40:27,95 workflow INFO:
Collecting precomputed outputs
190214-17:40:27,98 workflow INFO:
Executing node petVolume.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petVolume
190214-17:40:27,127 interface INFO:
stderr 2019-02-14T17:40:27.127023:Unknown image dimension "time"
190214-17:40:28,133 workflow ERROR:
['Node petVolume.a0 failed to run on host 0dff14881019.']
190214-17:40:28,134 workflow INFO:
Saving crash info to /opt/crash-20190214-174028-root-petVolume.a0-57950973-3925-4eb3-bf9e-218bd5cef0ef.pklz
190214-17:40:28,134 workflow INFO:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 39, in run
node.run(updatehash=updatehash)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 394, in run
self._run_interface()
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
self._result = self._run_command(execute)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
result = self._interface.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1043, in run
runtime = self._run_wrapper(runtime)
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper
runtime = self._run_interface(runtime)
File "/opt/APPIAN/Initialization/initialization.py", line 428, in _run_interface
run_mincreshape.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1043, in run
runtime = self._run_wrapper(runtime)
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
runtime = self._run_interface(runtime)
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1694, in _run_interface
self.raise_exception(runtime)
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1618, in raise_exception
raise RuntimeError(message)
RuntimeError: Command:
mincreshape /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petCenter/sub-01_ses-01_pet_center.mnc /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petVolume/sub-01_ses-01_pet_center_reshape.mnc -dimrange 'time=0,1' -clobber -verbose
Standard output:

Standard error:
Unknown image dimension "time"
Return code: 1
Interface ReshapeCommand failed to run.
Interface pet3DVolume failed to run.

190214-17:40:28,138 workflow INFO:
Executing node segmentation_ants.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants
190214-17:40:28,138 workflow INFO:
Collecting precomputed outputs
190214-17:40:28,140 workflow INFO:
Executing node MNIT1.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/MNIT1
190214-17:40:28,140 workflow INFO:
Collecting precomputed outputs
190214-17:40:28,143 workflow INFO:
Executing node transform_brain_mask.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/transform_brain_mask
190214-17:40:28,143 workflow INFO:
Collecting precomputed outputs
190214-17:40:28,144 workflow INFO:
***********************************
190214-17:40:28,144 workflow ERROR:
could not run node: preproc.initialization.petVolume.a0
190214-17:40:28,144 workflow INFO:
crashfile: /opt/crash-20190214-174028-root-petVolume.a0-57950973-3925-4eb3-bf9e-218bd5cef0ef.pklz
190214-17:40:28,144 workflow INFO:
***********************************
Traceback (most recent call last):
File "/opt/APPIAN/Launcher.py", line 43, in
run_scan_level(opts,args)
File "/opt/APPIAN/scanLevel.py", line 31, in run_scan_level
scan_level_workflow.workflow.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 57, in run
report_nodes_not_run(notrun)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details
bash: /: Is a directory

@tfunck
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tfunck commented Feb 14, 2019

I think I know what's causing the problem. Is the PET image you are trying to process a 3D volume? I think it's crashing because the mincreshape command was expecting a 4D image with a time dimension.

I can change it so that this step is skipped if a 3D image is provided.

@tfunck tfunck added the bug label Feb 14, 2019
@tfunck tfunck self-assigned this Feb 14, 2019
@guilhermepovala
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Hi,

That's exactly what I'm doing.
Well, I'll wait for a new version and than I try again.

@tfunck
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tfunck commented Feb 14, 2019

Ok great. I've made the fix and am testing it right now. I'll push the change shortly and let you know.

@tfunck
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tfunck commented Feb 14, 2019

Okay, I pushed a new version to tffunck/appian:latest-dev. Let me know if this solves the problem for you and I'll close the issue.

Essentially, the stage where it was crashing was redundant for your data. The petVolume node is used to average over later frames of the 4D PET image to create a 3D volume that can be used for co-registration.

@guilhermepovala
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So, I tried to run with the last version and it gives the same error =/

 stdout 2019-02-19T16:41:55.669315:Making byte volume...

190219-16:41:55,669 interface INFO:
stdout 2019-02-19T16:41:55.669315:mincblur -clobber -no_apodize -fwhm 8 /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_8
190219-16:41:57,702 interface INFO:
stdout 2019-02-19T16:41:57.701955:Making byte volume...
190219-16:41:57,702 interface INFO:
stdout 2019-02-19T16:41:57.701955:minctracc -clobber -lsq9 -step 4 4 4 -simplex 16 -tol 0.004 -transformation /tmp/bestlinreg_s-WUscFyEx/s_normal2_0.xfm -source_mask /tmp/tmp.eVulnzH2Ol/mask.mnc -model_mask /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl_mask.mnc -xcorr /tmp/bestlinreg_s-WUscFyEx/s_normal2_8_blur.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_8_blur.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_1.xfm
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447:Initial objective function val = 0.01484956
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447:Final objective function value = 0.01394908
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447:-+-------------------------[2]-------------------------
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447: | steps: 4 4 4
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447: | blur_fwhm: 4
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447: | simplex: 8
190219-16:41:58,713 interface INFO:
stdout 2019-02-19T16:41:58.713447: | source: /tmp/bestlinreg_s-WUscFyEx/s_normal2_4_blur.mnc
190219-16:41:58,714 interface INFO:
stdout 2019-02-19T16:41:58.713447: | target: /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4_blur.mnc
190219-16:41:58,714 interface INFO:
stdout 2019-02-19T16:41:58.713447: | xfm: /tmp/bestlinreg_s-WUscFyEx/s_normal2_2.xfm
190219-16:41:58,714 interface INFO:
stdout 2019-02-19T16:41:58.713447:-+-----------------------------------------------------
190219-16:41:58,714 interface INFO:
stdout 2019-02-19T16:41:58.713447:
190219-16:41:58,714 interface INFO:
stdout 2019-02-19T16:41:58.713447:mincblur -clobber -no_apodize -fwhm 4 /tmp/tmp.eVulnzH2Ol/normal2.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_4
190219-16:42:01,768 interface INFO:
stdout 2019-02-19T16:42:01.767960:Making byte volume...
190219-16:42:01,768 interface INFO:
stdout 2019-02-19T16:42:01.767960:mincblur -clobber -no_apodize -fwhm 4 /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4
190219-16:42:02,779 interface INFO:
stdout 2019-02-19T16:42:02.779422:Making byte volume...
190219-16:42:02,779 interface INFO:
stdout 2019-02-19T16:42:02.779422:minctracc -clobber -lsq9 -step 4 4 4 -simplex 8 -tol 0.004 -transformation /tmp/bestlinreg_s-WUscFyEx/s_normal2_1.xfm -source_mask /tmp/tmp.eVulnzH2Ol/mask.mnc -model_mask /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl_mask.mnc -xcorr /tmp/bestlinreg_s-WUscFyEx/s_normal2_4_blur.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4_blur.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_2.xfm
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:Initial objective function val = 0.02864027
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:Final objective function value = 0.02092978
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:-+-------------------------[3]-------------------------
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | steps: 4 4 4
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | blur_fwhm: 8
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | simplex: 4
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | source: /tmp/bestlinreg_s-WUscFyEx/s_normal2_8_dxyz.mnc
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | target: /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_8_dxyz.mnc
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092: | xfm: /tmp/bestlinreg_s-WUscFyEx/s_normal2_3.xfm
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:-+-----------------------------------------------------
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:
190219-16:42:06,344 interface INFO:
stdout 2019-02-19T16:42:06.344092:mincblur -clobber -no_apodize -fwhm 8 -gradient /tmp/tmp.eVulnzH2Ol/normal2.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_8
190219-16:42:10,920 interface INFO:
stdout 2019-02-19T16:42:10.920273:Making byte volume...
190219-16:42:10,920 interface INFO:
stdout 2019-02-19T16:42:10.920273:Making byte volume dx...Making byte volume dy...Making byte volume dz...mincblur -clobber -no_apodize -fwhm 8 -gradient /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_8
190219-16:42:10,920 interface INFO:
stderr 2019-02-19T16:42:10.920515:Transforming slices:................................................................................................................................................................................................................................................................Done
190219-16:42:13,974 interface INFO:
stdout 2019-02-19T16:42:13.973961:Making byte volume...
190219-16:42:13,974 interface INFO:
stdout 2019-02-19T16:42:13.973961:Making byte volume dx...Making byte volume dy...Making byte volume dz...minctracc -clobber -lsq9 -step 4 4 4 -simplex 4 -tol 0.004 -transformation /tmp/bestlinreg_s-WUscFyEx/s_normal2_2.xfm -source_mask /tmp/tmp.eVulnzH2Ol/mask.mnc -model_mask /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl_mask.mnc -xcorr /tmp/bestlinreg_s-WUscFyEx/s_normal2_8_dxyz.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_8_dxyz.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_3.xfm
190219-16:42:13,974 interface INFO:
stderr 2019-02-19T16:42:13.974203:Transforming slices:.................................................................................................................................................................................................Done
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155:Initial objective function val = 0.15070185
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155:Final objective function value = 0.12474231
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155:-+-------------------------[4]-------------------------
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | steps: 4 4 4
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | blur_fwhm: 4
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | simplex: 2
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | source: /tmp/bestlinreg_s-WUscFyEx/s_normal2_4_dxyz.mnc
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | target: /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4_dxyz.mnc
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155: | xfm: /tmp/bestlinreg_s-WUscFyEx/s_normal2_4.xfm
190219-16:42:17,28 interface INFO:
stdout 2019-02-19T16:42:17.028155:-+-----------------------------------------------------
190219-16:42:17,29 interface INFO:
stdout 2019-02-19T16:42:17.028155:
190219-16:42:17,29 interface INFO:
stdout 2019-02-19T16:42:17.028155:mincblur -clobber -no_apodize -fwhm 4 -gradient /tmp/tmp.eVulnzH2Ol/normal2.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_4
190219-16:42:21,604 interface INFO:
stdout 2019-02-19T16:42:21.604690:Making byte volume...
190219-16:42:21,604 interface INFO:
stdout 2019-02-19T16:42:21.604690:Making byte volume dx...Making byte volume dy...Making byte volume dz...mincblur -clobber -no_apodize -fwhm 4 -gradient /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4
190219-16:42:21,604 interface INFO:
stderr 2019-02-19T16:42:21.604957:Transforming slices:................................................................................................................................................................................................................................................................Done
190219-16:42:24,648 interface INFO:
stdout 2019-02-19T16:42:24.648641:Making byte volume...
190219-16:42:24,648 interface INFO:
stdout 2019-02-19T16:42:24.648641:Making byte volume dx...Making byte volume dy...Making byte volume dz...minctracc -clobber -lsq9 -step 4 4 4 -simplex 2 -tol 0.004 -transformation /tmp/bestlinreg_s-WUscFyEx/s_normal2_3.xfm -source_mask /tmp/tmp.eVulnzH2Ol/mask.mnc -model_mask /opt/APPIAN//Atlas/MNI152/mni_icbm152_t1_tal_nlin_asym_09c_rsl_mask.mnc -xcorr /tmp/bestlinreg_s-WUscFyEx/s_normal2_4_dxyz.mnc /tmp/bestlinreg_s-WUscFyEx/t_mni_icbm152_t1_tal_nlin_asym_09c_rsl_4_dxyz.mnc /tmp/bestlinreg_s-WUscFyEx/s_normal2_4.xfm
190219-16:42:24,648 interface INFO:
stderr 2019-02-19T16:42:24.648935:Transforming slices:.................................................................................................................................................................................................Done
190219-16:42:25,660 interface INFO:
stdout 2019-02-19T16:42:25.660355:Initial objective function val = 0.19629560
190219-16:42:25,660 interface INFO:
stdout 2019-02-19T16:42:25.660355:Final objective function value = 0.19229193
190219-16:42:25,661 interface INFO:
stdout 2019-02-19T16:42:25.660355:mv -f /tmp/bestlinreg_s-WUscFyEx/s_normal2_4.xfm /tmp/tmp.eVulnzH2Ol/lin2.xfm
190219-16:42:54,194 interface INFO:
stderr 2019-02-19T16:42:54.194137:Transforming slices:.................................................................................................................................................................................................Done
mincconvert -clobber -2 /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/tmp/mri_norm.mnc /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/sub-01_ses-01_T1w_normalized.mnc
190219-16:42:55,731 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:42:55,732 workflow INFO:
Executing node t1_mni_brain_mask.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask
190219-16:42:55,750 interface INFO:
stderr 2019-02-19T16:42:55.750800:
190219-16:42:55,751 interface INFO:
stderr 2019-02-19T16:42:55.750800:mincbeast -- an implementation of BEaST (Brain Extraction
190219-16:42:55,751 interface INFO:
stderr 2019-02-19T16:42:55.750800: using non-local Segmentation Technique) version 1.16.00
190219-16:42:55,751 interface INFO:
stderr 2019-02-19T16:42:55.750800:
190219-16:42:56,252 interface INFO:
stderr 2019-02-19T16:42:56.252160:3 scale steps:
190219-16:42:56,252 interface INFO:
stderr 2019-02-19T16:42:56.252160:4 1 2 0.20 0.25 0.95 20
190219-16:42:56,252 interface INFO:
stderr 2019-02-19T16:42:56.252160:2 1 4 0.50 0.25 0.95 20
190219-16:42:56,252 interface INFO:
stderr 2019-02-19T16:42:56.252160:1 2 6 0.50 0.25 0.95 20
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Performing pre-selection (0 MB/subject)....................done
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Patch size: 1
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Search area: 2
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Beta: 0.250000
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Threshold: 0.950000
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Selection: 20
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Dimensions: 48 57 48
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Computing first moment image...done (0 sec)
190219-16:42:56,753 interface INFO:
stderr 2019-02-19T16:42:56.753060:Computing second moment image...done (0 sec)
190219-16:43:00,758 interface INFO:
stderr 2019-02-19T16:43:00.758234:Segment 48 / 48 (redoing 2326 voxels) t=0.902500, min=95 (4 sec)
190219-16:43:00,758 interface INFO:
stderr 2019-02-19T16:43:00.758234:Segment 48 / 48 (redoing 64 voxels) t=0.857375, min=90 (0 sec)
190219-16:43:01,259 interface INFO:
stderr 2019-02-19T16:43:01.259058:Segment 48 / 48 (redoing 10 voxels) t=0.814506, min=85 (0 sec)
190219-16:43:01,259 interface INFO:
stderr 2019-02-19T16:43:01.259058:Segment 48 / 48 (redoing 1 voxels) t=0.773781, min=80 (0 sec)
190219-16:43:01,259 interface INFO:
stderr 2019-02-19T16:43:01.259058:Segment 48 / 48 done (0 sec, t=0.773781, min=80)
190219-16:43:01,259 interface INFO:
stderr 2019-02-19T16:43:01.259058:Performing pre-selection (4 MB/subject)....................done
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Patch size: 1
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Search area: 4
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Beta: 0.250000
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Threshold: 0.950000
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Selection: 20
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Dimensions: 96 114 96
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Computing first moment image...done (0 sec)
190219-16:43:03,802 interface INFO:
stderr 2019-02-19T16:43:03.802573:Computing second moment image...done (0 sec)
190219-16:43:22,825 interface INFO:
stderr 2019-02-19T16:43:22.825077:Segment 96 / 96 (redoing 2001 voxels) t=0.902500, min=95 (19 sec)
190219-16:43:23,325 interface INFO:
stderr 2019-02-19T16:43:23.325864:Segment 96 / 96 (redoing 375 voxels) t=0.857375, min=90 (1 sec)
190219-16:43:23,826 interface INFO:
stderr 2019-02-19T16:43:23.826636:Segment 96 / 96 (redoing 114 voxels) t=0.814506, min=85 (0 sec)
190219-16:43:23,826 interface INFO:
stderr 2019-02-19T16:43:23.826636:Segment 96 / 96 (redoing 54 voxels) t=0.773781, min=80 (0 sec)
190219-16:43:24,327 interface INFO:
stderr 2019-02-19T16:43:24.327447:Segment 96 / 96 (redoing 19 voxels) t=0.735092, min=76 (0 sec)
190219-16:43:24,327 interface INFO:
stderr 2019-02-19T16:43:24.327447:Segment 96 / 96 (redoing 6 voxels) t=0.698337, min=72 (0 sec)
190219-16:43:24,327 interface INFO:
stderr 2019-02-19T16:43:24.327447:Segment 96 / 96 (redoing 1 voxels) t=0.663420, min=68 (0 sec)
190219-16:43:24,828 interface INFO:
stderr 2019-02-19T16:43:24.828371:Segment 96 / 96 done (0 sec, t=0.663420, min=68)
190219-16:43:26,330 interface INFO:
stderr 2019-02-19T16:43:26.330329:Performing pre-selection (32 MB/subject)....................done
190219-16:44:31,683 interface INFO:
stderr 2019-02-19T16:44:31.683913:Patch size: 2
190219-16:44:31,684 interface INFO:
stderr 2019-02-19T16:44:31.683913:Search area: 6
190219-16:44:31,684 interface INFO:
stderr 2019-02-19T16:44:31.683913:Beta: 0.250000
190219-16:44:31,684 interface INFO:
stderr 2019-02-19T16:44:31.683913:Threshold: 0.950000
190219-16:44:31,684 interface INFO:
stderr 2019-02-19T16:44:31.683913:Selection: 20
190219-16:44:31,684 interface INFO:
stderr 2019-02-19T16:44:31.683913:Dimensions: 193 229 193
190219-16:44:32,695 interface INFO:
stderr 2019-02-19T16:44:32.695498:Computing first moment image...done (1 sec)
190219-16:44:34,218 interface INFO:
stderr 2019-02-19T16:44:34.218355:Computing second moment image...done (2 sec)
190219-16:44:34,719 interface INFO:
stderr 2019-02-19T16:44:34.719133:Segment193 / 193 done (0 sec, t=0.950000, min=100)
190219-16:44:37,265 interface INFO:
stdout 2019-02-19T16:44:37.265827:Writing a binary volume...
mincresample -2 /tmp/6701026_sub-01_ses-01_T1w_normalized_brain_mask.mnc /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask/sub-01_ses-01_T1w_normalized_brain_mask.mnc
190219-16:44:38,789 interface INFO:
stderr 2019-02-19T16:44:38.789291:Transforming slices:.................................................................................................................................................................................................Done
190219-16:44:39,292 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:44:39,293 workflow INFO:
Executing node MNIT1.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/MNIT1
190219-16:44:39,296 workflow INFO:
Running: xfminvert -clobber /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/sub-01_ses-01_T1w_normalized.xfm /adni/out/preproc/mri/_args_run.task.ses01.sid01/MNIT1/sub-01_ses-01_T1w_normalized_xfminvert_output.mnc.xfm
190219-16:44:40,322 workflow INFO:
Executing node transform_brain_mask.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/transform_brain_mask
190219-16:44:40,327 workflow INFO:
Running: mincresample -clobber -invert_transformation -like /adni/sub-01/ses-01/anat/sub-01_ses-01_T1w.mnc -nearest_neighbour -transformation /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/sub-01_ses-01_T1w_normalized.xfm /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask/sub-01_ses-01_T1w_normalized_brain_mask.mnc sub-01_ses-01_T1w_normalized_brain_mask_resample.mnc
190219-16:44:40,847 interface INFO:
stderr 2019-02-19T16:44:40.847463:Transforming slices:................................................................................................................................................................................................................................................................Done
190219-16:44:41,353 workflow INFO:
Executing node segmentation_ants.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068:
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068:+++ infiles +++
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068: | [00]: /adni/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/sub-01_ses-01_T1w_normalized.mnc
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068: | [01]: /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask/sub-01_ses-01_T1w_normalized_brain_mask.mnc
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068:
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068:+++ outfiles +++
190219-16:44:41,373 interface INFO:
stderr 2019-02-19T16:44:41.373068: | [00]: /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain.mnc
190219-16:44:41,874 interface INFO:
stdout 2019-02-19T16:44:41.874249:Processing:.................................................................................................................................................................................................Done
('File Name:', '/adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain.mnc')
190219-16:44:42,911 interface INFO:
stdout 2019-02-19T16:44:42.911577:found zspace at 0 0
190219-16:44:42,912 interface INFO:
stdout 2019-02-19T16:44:42.911577:found yspace at 1 1
190219-16:44:42,912 interface INFO:
stdout 2019-02-19T16:44:42.911577:found xspace at 2 2
190219-16:44:42,912 interface INFO:
stdout 2019-02-19T16:44:42.911577:0 2 0 1 193 1.000000
190219-16:44:42,912 interface INFO:
stdout 2019-02-19T16:44:42.911577:1 1 1 1 229 1.000000
190219-16:44:42,912 interface INFO:
stdout 2019-02-19T16:44:42.911577:2 0 2 1 193 1.000000
('File Name:', 'sub-01_ses-01_T1w_normalized_brain_mask.mnc')
190219-16:44:43,939 interface INFO:
stdout 2019-02-19T16:44:43.939740:found zspace at 0 0
190219-16:44:43,940 interface INFO:
stdout 2019-02-19T16:44:43.939740:found yspace at 1 1
190219-16:44:43,940 interface INFO:
stdout 2019-02-19T16:44:43.939740:found xspace at 2 2
190219-16:44:43,940 interface INFO:
stdout 2019-02-19T16:44:43.939740:0 2 0 1 193 1.000000
190219-16:44:43,940 interface INFO:
stdout 2019-02-19T16:44:43.939740:1 1 1 1 229 1.000000
190219-16:44:43,940 interface INFO:
stdout 2019-02-19T16:44:43.939740:2 0 2 1 193 1.000000
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:431: UserWarning: Input initialization requires inputs: number_of_tissue_classes
warn(msg)
Atropos --image-dimensionality 3 --initialization Otsu[3] --intensity-image /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain.nii --mask-image /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_mask.nii --output [sub-01_ses-01_T1w_normalized_brain_labeled.nii] --use-random-seed 1
nii2mnc /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/tmp_mnc_201902191645231725940134.mnc
190219-16:45:24,310 interface INFO:
stdout 2019-02-19T16:45:24.310657:Using q-form transform:
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657: 1.0000, 0.0000, 0.0000, -96.0000,
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657: 0.0000, 1.0000, 0.0000, -132.0000,
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657: 0.0000, 0.0000, 1.0000, -78.0000,
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657: 0.0000, 0.0000, 0.0000, 1.0000,
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657:
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657:name | start | step | cosines
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657:zspace | -78.0000 | 1.0000 | 0.0000 0.0000 1.0000
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657:yspace | -132.0000 | 1.0000 | 0.0000 1.0000 0.0000
190219-16:45:24,311 interface INFO:
stdout 2019-02-19T16:45:24.310657:xspace | -96.0000 | 1.0000 | 1.0000 0.0000 0.0000
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585:<nifti_image
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: nifti_type = 'NIFTI-1+'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: header_filename = '/adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: image_filename = '/adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: image_offset = '352'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: ndim = '3'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: nx = '193'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: ny = '229'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: nz = '193'
190219-16:45:24,311 interface INFO:
stderr 2019-02-19T16:45:24.311585: dx = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: dy = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: dz = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: datatype = '768'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: datatype_name = 'UINT32'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: nvox = '8530021'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: nbyper = '4'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: byteorder = 'LSB_FIRST'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: scl_slope = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: scl_inter = '0'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: xyz_units = '2'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: xyz_units_name = 'mm'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qform_code = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qform_code_name = 'Scanner Anat'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qto_xyz_matrix = '1 0 0 -96 0 1 0 -132 0 0 1 -78 0 0 0 1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qto_ijk_matrix = '1 0 0 96 0 1 0 132 0 0 1 78 0 0 0 1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: quatern_b = '0'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: quatern_c = '0'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: quatern_d = '0'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qoffset_x = '-96'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qoffset_y = '-132'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qoffset_z = '-78'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qfac = '1'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qform_i_orientation = 'Left-to-Right'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qform_j_orientation = 'Posterior-to-Anterior'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: qform_k_orientation = 'Inferior-to-Superior'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585: num_ext = '0'
190219-16:45:24,312 interface INFO:
stderr 2019-02-19T16:45:24.311585:/>
mincconvert -clobber -2 /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/tmp_mnc_201902191645231725940134.mnc /adni/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.mnc
190219-16:45:25,856 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:45:25,857 workflow INFO:
Executing node t1_nat.a0 in dir: /adni/out/preproc/mri/_args_run.task.ses01.sid01/t1_nat
190219-16:45:25,874 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:45:25,876 workflow INFO:
Executing node petCenter.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petCenter
190219-16:45:28,995 interface INFO:
stderr 2019-02-19T16:45:28.995805:micreate_group_variable: MINC package entry point
190219-16:45:29,496 interface INFO:
stderr 2019-02-19T16:45:29.496707:micreate_group_variable: MINC package entry point
190219-16:45:30,53 interface INFO:
stderr 2019-02-19T16:45:30.052847:HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
190219-16:45:30,54 interface INFO:
stderr 2019-02-19T16:45:30.052847: #000: /opt/minc/build/HDF5/src/H5Adeprec.c line 243 in H5Aopen_name(): can't open attribute: 'length'
190219-16:45:30,54 interface INFO:
stderr 2019-02-19T16:45:30.052847: major: Attribute
190219-16:45:30,55 interface INFO:
stderr 2019-02-19T16:45:30.052847: minor: Can't open object
190219-16:45:30,55 interface INFO:
stderr 2019-02-19T16:45:30.052847: #1: /opt/minc/build/HDF5/src/H5Aint.c line 456 in H5A_open_by_name(): unable to load attribute info from object header
190219-16:45:30,55 interface INFO:
stderr 2019-02-19T16:45:30.052847: major: Attribute
190219-16:45:30,56 interface INFO:
stderr 2019-02-19T16:45:30.052847: minor: Unable to initialize object
190219-16:45:30,56 interface INFO:
stderr 2019-02-19T16:45:30.052847: #2: /opt/minc/build/HDF5/src/H5Oattribute.c line 537 in H5O_attr_open_by_name(): can't locate attribute: 'length'
190219-16:45:30,56 interface INFO:
stderr 2019-02-19T16:45:30.052847: major: Attribute
190219-16:45:30,56 interface INFO:
stderr 2019-02-19T16:45:30.052847: minor: Object not found
190219-16:45:30,57 interface INFO:
stderr 2019-02-19T16:45:30.052847:/opt/minc/minc-toolkit-v2/libminc/libsrc/hdf_convenience.c:2191 (from miopen): Should not happen!
190219-16:45:30,558 interface INFO:
stderr 2019-02-19T16:45:30.558093:Transforming slices:................................................................................................Done
190219-16:45:31,98 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:45:31,100 workflow INFO:
Executing node petVolume.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petVolume
190219-16:45:31,109 workflow ERROR:
['Node petVolume.a0 failed to run on host 56eda210aa05.']
190219-16:45:31,110 workflow INFO:
Saving crash info to /opt/crash-20190219-164531-root-petVolume.a0-ba375fc1-172e-4bfc-8d51-9cc961be39e6.pklz
190219-16:45:31,110 workflow INFO:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 39, in run
node.run(updatehash=updatehash)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 394, in run
self._run_interface()
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
self._result = self._run_command(execute)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
result = self._interface.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1043, in run
runtime = self._run_wrapper(runtime)
File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1000, in _run_wrapper
runtime = self._run_interface(runtime)
File "/opt/APPIAN/Initialization/initialization.py", line 410, in _run_interface
o=infile.dimnames.index("time")
ValueError: 'time' is not in list
Interface pet3DVolume failed to run.

190219-16:45:31,117 workflow INFO:
Executing node petSettings.a0 in dir: /adni/out/preproc/initialization/_args_run.task.ses01.sid01/petSettings
HDF5-DIAG: Error detected in HDF5 (1.8.18) thread 0:
#000: /opt/minc/build/HDF5/src/H5Adeprec.c line 243 in H5Aopen_name(): can't open attribute: 'length'
major: Attribute
minor: Can't open object
#1: /opt/minc/build/HDF5/src/H5Aint.c line 456 in H5A_open_by_name(): unable to load attribute info from object header
major: Attribute
minor: Unable to initialize object
#2: /opt/minc/build/HDF5/src/H5Oattribute.c line 519 in H5O_attr_open_by_name(): can't open attribute
major: Attribute
minor: Can't open object
#3: /opt/minc/build/HDF5/src/H5Adense.c line 405 in H5A_dense_open(): can't locate attribute in name index
major: Attribute
minor: Object not found
/opt/minc/minc-toolkit-v2/libminc/libsrc/hdf_convenience.c:2191 (from miopen): Should not happen!
('Target:', 'halflife')
190219-16:45:31,153 workflow INFO:
Runtime memory and threads stats unavailable
190219-16:45:31,153 workflow INFO:
***********************************
190219-16:45:31,153 workflow ERROR:
could not run node: preproc.initialization.petVolume.a0
190219-16:45:31,154 workflow INFO:
crashfile: /opt/crash-20190219-164531-root-petVolume.a0-ba375fc1-172e-4bfc-8d51-9cc961be39e6.pklz
190219-16:45:31,154 workflow INFO:
***********************************
Traceback (most recent call last):
File "/opt/APPIAN/Launcher.py", line 43, in
run_scan_level(opts,args)
File "/opt/APPIAN/scanLevel.py", line 31, in run_scan_level
scan_level_workflow.workflow.run()
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 57, in run
report_nodes_not_run(notrun)
File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details
bash: /: Is a directory

@tfunck
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tfunck commented Feb 19, 2019

Sorry I made a silly mistake in my bug fix. I'm going to add a 3D image to my test data so that I can catch these mistakes myself. I'll have a new version on docker probably by the end of they, but tomorrow at the latest.

@tfunck
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tfunck commented Feb 20, 2019

Ok I pushed new changes to tffunck/appian:latest-dev (and tested it on some 3D PET images this time), so it should work.

Please let me know how it goes!

Thomas

@jcazeredo
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Hi Thomas,

I am a colleague of Guilherme Povala (creator of this thread). Following your latest reply and update, we have been trying to implement a APPIAN pipeline using 3D PET images but still found some issues. The command I am running is: sudo docker run -v /home/julio/codes/appian_test/in/:/data/in -v /home/julio/codes/appian_test/out/:"/data/out" tffunck/appian:latest bash -c "python2.7 /opt/APPIAN/Launcher.py -s "/data/in" -t "/data/out" ";

See bellow the detailed report printed by APPIAN:

('File Name:', '/data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain.mnc')
190603-21:52:50,991 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:found zspace at 0 0
190603-21:52:50,992 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:found yspace at 1 1
190603-21:52:50,992 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:found xspace at 2 2
190603-21:52:50,992 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:0 2 0 1 193 1.000000
190603-21:52:50,992 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:1 1 1 1 229 1.000000
190603-21:52:50,993 interface INFO:
	 stdout 2019-06-03T21:52:50.990918:2 0 2 1 193 1.000000
('File Name:', 'sub-01_ses-01_T1w_normalized_brain_mask.mnc')
190603-21:52:52,25 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:found zspace at 0 0
190603-21:52:52,25 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:found yspace at 1 1
190603-21:52:52,26 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:found xspace at 2 2
190603-21:52:52,26 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:0 2 0 1 193 1.000000
190603-21:52:52,26 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:1 1 1 1 229 1.000000
190603-21:52:52,26 interface INFO:
	 stdout 2019-06-03T21:52:52.024726:2 0 2 1 193 1.000000
/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py:431: UserWarning: Input initialization requires inputs: number_of_tissue_classes
  warn(msg)
Atropos --image-dimensionality 3 --initialization Otsu[3] --intensity-image /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain.nii --mask-image /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_mask.nii --output [sub-01_ses-01_T1w_normalized_brain_labeled.nii] --use-random-seed 1
nii2mnc /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/tmp_mnc_201906032153353881302959.mnc
190603-21:53:36,493 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:Using q-form transform:
190603-21:53:36,494 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:  1.0000,   0.0000,   0.0000, -96.0000, 
190603-21:53:36,495 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:  0.0000,   1.0000,   0.0000, -132.0000, 
190603-21:53:36,495 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:  0.0000,   0.0000,   1.0000, -78.0000, 
190603-21:53:36,495 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:  0.0000,   0.0000,   0.0000,   1.0000, 
190603-21:53:36,495 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:
190603-21:53:36,496 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:name   | start      | step    | cosines
190603-21:53:36,496 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:zspace |   -78.0000 |  1.0000 |  0.0000  0.0000  1.0000
190603-21:53:36,496 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:yspace |  -132.0000 |  1.0000 |  0.0000  1.0000  0.0000
190603-21:53:36,496 interface INFO:
	 stdout 2019-06-03T21:53:36.493194:xspace |   -96.0000 |  1.0000 |  1.0000  0.0000  0.0000
190603-21:53:36,497 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:<nifti_image
190603-21:53:36,497 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  nifti_type = 'NIFTI-1+'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  header_filename = '/data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  image_filename = '/data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.nii'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  image_offset = '352'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  ndim = '3'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  nx = '193'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  ny = '229'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  nz = '193'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  dx = '1'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  dy = '1'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  dz = '1'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  datatype = '768'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  datatype_name = 'UINT32'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  nvox = '8530021'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  nbyper = '4'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  byteorder = 'LSB_FIRST'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  scl_slope = '1'
190603-21:53:36,498 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  scl_inter = '0'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  xyz_units = '2'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  xyz_units_name = 'mm'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qform_code = '1'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qform_code_name = 'Scanner Anat'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qto_xyz_matrix = '1 0 0 -96 0 1 0 -132 0 0 1 -78 0 0 0 1'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qto_ijk_matrix = '1 0 0 96 0 1 0 132 0 0 1 78 0 0 0 1'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  quatern_b = '0'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  quatern_c = '0'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  quatern_d = '0'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qoffset_x = '-96'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qoffset_y = '-132'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qoffset_z = '-78'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qfac = '1'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qform_i_orientation = 'Left-to-Right'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qform_j_orientation = 'Posterior-to-Anterior'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  qform_k_orientation = 'Inferior-to-Superior'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:  num_ext = '0'
190603-21:53:36,499 interface INFO:
	 stderr 2019-06-03T21:53:36.497117:/>
mincconvert -clobber -2 /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/tmp_mnc_201906032153353881302959.mnc /data/out/preproc/mri/_args_run.task.ses01.sid01/segmentation_ants/sub-01_ses-01_T1w_normalized_brain_labeled.mnc
190603-21:53:38,58 workflow INFO:
	 Runtime memory and threads stats unavailable
190603-21:53:38,61 workflow INFO:
	 Executing node transform_brain_mask.a0 in dir: /data/out/preproc/mri/_args_run.task.ses01.sid01/transform_brain_mask
190603-21:53:38,67 workflow INFO:
	 Running: mincresample -clobber -invert_transformation -like /data/in/sub-01/ses-01/anat/sub-01_ses-01_T1w.mnc -nearest_neighbour -transformation /data/out/preproc/mri/_args_run.task.ses01.sid01/mri_normalize/sub-01_ses-01_T1w_normalized.xfm /data/out/preproc/mri/_args_run.task.ses01.sid01/t1_mni_brain_mask/sub-01_ses-01_T1w_normalized_brain_mask.mnc sub-01_ses-01_T1w_normalized_brain_mask_resample.mnc
190603-21:53:38,594 interface INFO:
	 stderr 2019-06-03T21:53:38.594296:Transforming slices:................................................................................................................................................................................................................................................................Done
190603-21:53:39,103 workflow INFO:
	 ***********************************
190603-21:53:39,103 workflow ERROR:
	 could not run node: preproc.initialization.petVolume.a0
190603-21:53:39,103 workflow INFO:
	 crashfile: /opt/crash-20190603-214823-root-petVolume.a0-44a9a5e9-8108-4dc6-8be1-e760f91bcd7b.pklz
190603-21:53:39,103 workflow INFO:
	 ***********************************
Traceback (most recent call last):
  File "/opt/APPIAN/Launcher.py", line 43, in <module>
    run_scan_level(opts,args)
  File "/opt/APPIAN/scanLevel.py", line 31, in run_scan_level
    scan_level_workflow.workflow.run()
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine/workflows.py", line 597, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/linear.py", line 57, in run
    report_nodes_not_run(notrun)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
    raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details

The input images we used are from ADNI Database. Here is a link to the folder structure we are currently getting the error: https://we.tl/t-DeNOSM4gRU (this link is temporary, let us know if you have any trouble downloading)

Finally, can you send us the 3D images and folder structures you used to test the latest versions of APPIAN? We suspect the error may be coming from the header structure of our image files.

Thank you very much for your time. We hope to hear from you soon.

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@guilhermepovala @tfunck @jcazeredo