mkdir: cannot create directory ‘/rigel/psych/users/av2902/sb_cpac/preproc/’: File exists
[33mWARNING:[0m skipping mount of /rigel/psych/users/av2902/sb_cpac/scratch: no such file or directory
Running BIDS validator
#### Running C-PAC for sub-206
Number of participants to run in parallel: 1
Input directory: /bids_dataset
Output directory: /outputs/output
Working directory: /outputs/tmp
Crash directory: /outputs/crash
Log directory: /outputs/log
Remove working directory: False
Available memory: 100.0 (GB)
Available threads: 1
Number of threads for ANTs: 1
Parsing /bids_dataset..
Starting participant level processing
Run called with config file /outputs/cpac_pipeline_config_2020-11-12T22-11-31Z.yml
201112-22:11:43,572 nipype.workflow INFO:
C-PAC version: 1.7.2
Setting maximum number of cores per participant to 1
Setting number of participants at once to 1
Setting OMP_NUM_THREADS to 1
Setting MKL_NUM_THREADS to 1
Setting ANTS/ITK thread usage to 1
Maximum potential number of cores that might be used during this run: 1
201112-22:11:48,943 nipype.workflow INFO:
Pipeline building completed.
201112-22:11:48,943 nipype.workflow INFO:
Strategy forks:
- cpac_fmriprep-options
201112-22:11:51,570 nipype.workflow INFO:
Workflow resting_preproc_sub-206_ses-1 settings: ['check', 'execution', 'logging', 'monitoring']
201112-22:11:53,72 nipype.workflow INFO:
Running serially.
201112-22:11:53,83 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-2/select_scan_params".
201112-22:11:53,116 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:11:53,116 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:11:53,127 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-2/s3_scan_params".
201112-22:11:53,158 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:11:53,158 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:11:53,162 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/scan_params_0".
201112-22:11:53,217 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:11:53,217 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:11:53,219 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-2/selectrest".
201112-22:11:53,263 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:11:53,263 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:11:53,273 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-2/check_for_s3".
201112-22:11:53,302 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:11:53,302 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:11:53,304 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-2/func_get_idx".
201112-22:11:53,330 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:11:53,331 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:11:53,332 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-2/func_drop_trs".
201112-22:11:53,356 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" - collecting precomputed outputs
201112-22:11:53,357 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" found cached.
201112-22:11:53,360 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique".
201112-22:11:53,376 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique" - collecting precomputed outputs
201112-22:11:53,377 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique" found cached.
201112-22:11:53,379 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient".
201112-22:11:53,409 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient" - collecting precomputed outputs
201112-22:11:53,409 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient" found cached.
201112-22:11:53,412 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_RPI".
201112-22:11:53,428 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" - collecting precomputed outputs
201112-22:11:53,428 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" found cached.
201112-22:11:53,430 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_generate_ref" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_generate_ref".
201112-22:11:53,458 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_generate_ref" - collecting precomputed outputs
201112-22:11:53,458 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_generate_ref" found cached.
201112-22:11:53,461 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_motion".
201112-22:11:53,495 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" - collecting precomputed outputs
201112-22:11:53,495 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" found cached.
201112-22:11:53,497 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_motion_correct_mcflirt".
201112-22:11:53,791 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" - collecting precomputed outputs
201112-22:11:53,791 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" found cached.
201112-22:11:53,800 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FDJ" in "/outputs/tmp/resting_preproc_sub-206_ses-1/gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/calculate_FDJ".
201112-22:11:53,819 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FDJ" - collecting precomputed outputs
201112-22:11:53,820 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FDJ" found cached.
201112-22:11:53,822 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_jenkinson" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_frame_wise_displacement_jenkinson".
201112-22:11:53,881 nipype.workflow INFO:
[Node] Running "sinker_0_frame_wise_displacement_jenkinson" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:54,128 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_jenkinson".
201112-22:11:54,130 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_max_displacement" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_max_displacement".
201112-22:11:54,174 nipype.workflow INFO:
[Node] Running "sinker_0_max_displacement" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:54,412 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_max_displacement".
201112-22:11:54,414 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_coordinate_transformation" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_coordinate_transformation".
201112-22:11:54,473 nipype.workflow INFO:
[Node] Running "sinker_0_coordinate_transformation" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:54,719 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_coordinate_transformation".
201112-22:11:54,732 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/func_mean_skull".
201112-22:11:54,800 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" - collecting precomputed outputs
201112-22:11:54,800 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" found cached.
201112-22:11:54,802 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_pass".
201112-22:11:54,841 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" - collecting precomputed outputs
201112-22:11:54,842 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" found cached.
201112-22:11:54,844 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_dilate".
201112-22:11:54,868 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" - collecting precomputed outputs
201112-22:11:54,868 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" found cached.
201112-22:11:54,870 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_mask".
201112-22:11:54,912 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" - collecting precomputed outputs
201112-22:11:54,912 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" found cached.
201112-22:11:54,914 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/unifize".
201112-22:11:54,931 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" - collecting precomputed outputs
201112-22:11:54,931 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" found cached.
201112-22:11:54,934 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_second_pass".
201112-22:11:54,949 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" - collecting precomputed outputs
201112-22:11:54,949 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" found cached.
201112-22:11:54,952 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/combine_masks".
201112-22:11:54,998 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" - collecting precomputed outputs
201112-22:11:54,998 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" found cached.
201112-22:11:55,0 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.cal_DVARS" in "/outputs/tmp/resting_preproc_sub-206_ses-1/gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/cal_DVARS".
201112-22:11:55,22 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.cal_DVARS" - collecting precomputed outputs
201112-22:11:55,23 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.cal_DVARS" found cached.
201112-22:11:55,24 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/func_extract_brain".
201112-22:11:55,53 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" - collecting precomputed outputs
201112-22:11:55,53 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" found cached.
201112-22:11:55,56 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_normalize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize".
201112-22:11:55,73 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_normalize" - collecting precomputed outputs
201112-22:11:55,73 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_normalize" found cached.
201112-22:11:55,76 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mask_normalize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mask_normalize".
201112-22:11:55,110 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mask_normalize" - collecting precomputed outputs
201112-22:11:55,111 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mask_normalize" found cached.
201112-22:11:55,113 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mean".
201112-22:11:55,146 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean" - collecting precomputed outputs
201112-22:11:55,146 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean" found cached.
201112-22:11:55,148 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.norm_motion_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/norm_motion_params".
201112-22:11:55,185 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.norm_motion_params" - collecting precomputed outputs
201112-22:11:55,185 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.norm_motion_params" found cached.
201112-22:11:55,187 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.qc_motion_0.motion_plot" in "/outputs/tmp/resting_preproc_sub-206_ses-1/qc_motion_0/_scan_tgng_run-2/motion_plot".
201112-22:11:55,228 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.qc_motion_0.motion_plot" - collecting precomputed outputs
201112-22:11:55,228 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.qc_motion_0.motion_plot" found cached.
201112-22:11:55,232 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_trans_plot" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_qc___movement_trans_plot".
201112-22:11:55,279 nipype.workflow INFO:
[Node] Running "sinker_0_qc___movement_trans_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:55,493 nipype.interface INFO:
sub: /outputs/output/pipeline_cpac_fmriprep-options/sub-206_ses-1/qc___movement_trans_plot/_scan_tgng_run-2/motion_trans_plot.png -> /outputs/output/pipeline_cpac_fmriprep-options/sub-206_ses-1/qc/movement_trans_plot/_scan_tgng_run-2/motion_trans_plot.png
201112-22:11:55,521 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_trans_plot".
201112-22:11:55,523 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_rot_plot" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_qc___movement_rot_plot".
201112-22:11:55,567 nipype.workflow INFO:
[Node] Running "sinker_0_qc___movement_rot_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:55,782 nipype.interface INFO:
sub: /outputs/output/pipeline_cpac_fmriprep-options/sub-206_ses-1/qc___movement_rot_plot/_scan_tgng_run-2/motion_rot_plot.png -> /outputs/output/pipeline_cpac_fmriprep-options/sub-206_ses-1/qc/movement_rot_plot/_scan_tgng_run-2/motion_rot_plot.png
201112-22:11:55,807 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_rot_plot".
201112-22:11:55,809 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_motion_parameters" in "/outputs/tmp/resting_preproc_sub-206_ses-1/gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/calc_motion_parameters".
201112-22:11:55,840 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_motion_parameters" - collecting precomputed outputs
201112-22:11:55,841 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_motion_parameters" found cached.
201112-22:11:55,843 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_motion_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_motion_params".
201112-22:11:55,890 nipype.workflow INFO:
[Node] Running "sinker_0_motion_params" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:56,133 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_params".
201112-22:11:56,135 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FD" in "/outputs/tmp/resting_preproc_sub-206_ses-1/gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/calculate_FD".
201112-22:11:56,188 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FD" - collecting precomputed outputs
201112-22:11:56,188 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FD" found cached.
201112-22:11:56,190 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_power" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_frame_wise_displacement_power".
201112-22:11:56,235 nipype.workflow INFO:
[Node] Running "sinker_0_frame_wise_displacement_power" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:56,472 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_power".
201112-22:11:56,474 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_power_parameters" in "/outputs/tmp/resting_preproc_sub-206_ses-1/gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/calc_power_parameters".
201112-22:11:56,507 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_power_parameters" - collecting precomputed outputs
201112-22:11:56,507 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_power_parameters" found cached.
201112-22:11:56,509 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_power_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_power_params".
201112-22:11:56,555 nipype.workflow INFO:
[Node] Running "sinker_0_power_params" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:56,791 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_power_params".
201112-22:11:56,794 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_movement_parameters" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_movement_parameters".
201112-22:11:56,834 nipype.workflow INFO:
[Node] Running "sinker_0_movement_parameters" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:57,71 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_movement_parameters".
201112-22:11:57,73 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_despiked_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/func_despiked_0".
201112-22:11:57,108 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_despiked_0" - collecting precomputed outputs
201112-22:11:57,108 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_despiked_0" found cached.
201112-22:11:57,111 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_slice_timing_correction_0.slice_timing" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_slice_timing_correction_0/_scan_tgng_run-2/slice_timing".
201112-22:11:57,131 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_slice_timing_correction_0.slice_timing" - collecting precomputed outputs
201112-22:11:57,132 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_slice_timing_correction_0.slice_timing" found cached.
201112-22:11:57,134 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_deoblique" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique".
201112-22:11:57,166 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_deoblique" - collecting precomputed outputs
201112-22:11:57,166 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_deoblique" found cached.
201112-22:11:57,168 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_reorient" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient".
201112-22:11:57,201 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_reorient" - collecting precomputed outputs
201112-22:11:57,201 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_reorient" found cached.
201112-22:11:57,204 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_RPI".
201112-22:11:57,221 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" - collecting precomputed outputs
201112-22:11:57,222 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI" found cached.
201112-22:11:57,224 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_generate_ref" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_generate_ref".
201112-22:11:57,241 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_generate_ref" - collecting precomputed outputs
201112-22:11:57,241 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_generate_ref" found cached.
201112-22:11:57,244 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_motion".
201112-22:11:57,279 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" - collecting precomputed outputs
201112-22:11:57,279 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_motion" found cached.
201112-22:11:57,281 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_motion_correct_mcflirt".
201112-22:11:57,550 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" - collecting precomputed outputs
201112-22:11:57,551 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt" found cached.
201112-22:11:57,559 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_motion_correct" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_motion_correct".
201112-22:11:57,601 nipype.workflow INFO:
[Node] Running "sinker_0_motion_correct" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:57,841 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_correct".
201112-22:11:57,843 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/func_mean_skull".
201112-22:11:57,876 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" - collecting precomputed outputs
201112-22:11:57,876 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull" found cached.
201112-22:11:57,878 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_pass".
201112-22:11:57,915 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" - collecting precomputed outputs
201112-22:11:57,915 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass" found cached.
201112-22:11:57,918 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_dilate".
201112-22:11:57,935 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" - collecting precomputed outputs
201112-22:11:57,936 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate" found cached.
201112-22:11:57,938 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_first_mask".
201112-22:11:57,963 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" - collecting precomputed outputs
201112-22:11:57,963 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask" found cached.
201112-22:11:57,965 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/unifize".
201112-22:11:57,980 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" - collecting precomputed outputs
201112-22:11:57,981 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.unifize" found cached.
201112-22:11:57,983 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/skullstrip_second_pass".
201112-22:11:58,0 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" - collecting precomputed outputs
201112-22:11:58,1 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass" found cached.
201112-22:11:58,3 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/combine_masks".
201112-22:11:58,20 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" - collecting precomputed outputs
201112-22:11:58,20 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks" found cached.
201112-22:11:58,23 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_merge_masks" in "/outputs/tmp/resting_preproc_sub-206_ses-1/nuisance_regressor_0_0/_scan_tgng_run-2/_selector_WM-2mm-M-SDB_CSF-2mm-M-SDB_G-M-SDB_M-SDB_P-2_BP-B0.01-T0.08/GlobalSignal_merge_masks".
201112-22:11:58,37 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_merge_masks" - collecting precomputed outputs
201112-22:11:58,37 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_merge_masks" found cached.
201112-22:11:58,39 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_union_masks" in "/outputs/tmp/resting_preproc_sub-206_ses-1/nuisance_regressor_0_0/_scan_tgng_run-2/_selector_WM-2mm-M-SDB_CSF-2mm-M-SDB_G-M-SDB_M-SDB_P-2_BP-B0.01-T0.08/GlobalSignal_union_masks".
201112-22:11:58,55 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_union_masks" - collecting precomputed outputs
201112-22:11:58,56 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_union_masks" found cached.
201112-22:11:58,58 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_functional_brain_mask" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_functional_brain_mask".
201112-22:11:58,99 nipype.workflow INFO:
[Node] Running "sinker_0_functional_brain_mask" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:58,336 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_brain_mask".
201112-22:11:58,339 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.functional_brain_mask_derivative_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/functional_brain_mask_derivative_0".
201112-22:11:58,357 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.functional_brain_mask_derivative_0" - collecting precomputed outputs
201112-22:11:58,357 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.functional_brain_mask_derivative_0" found cached.
201112-22:11:58,360 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/func_preproc_fsl_afni_mean_mcflirt_0_skullstrip/_scan_tgng_run-2/func_extract_brain".
201112-22:11:58,378 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" - collecting precomputed outputs
201112-22:11:58,378 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain" found cached.
201112-22:11:58,380 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_normalize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize".
201112-22:11:58,398 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_normalize" - collecting precomputed outputs
201112-22:11:58,398 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_normalize" found cached.
201112-22:11:58,401 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_mean" in "/outputs/tmp/resting_preproc_sub-206_ses-1/nuisance_regressor_0_0/_scan_tgng_run-2/_selector_WM-2mm-M-SDB_CSF-2mm-M-SDB_G-M-SDB_M-SDB_P-2_BP-B0.01-T0.08/GlobalSignal_mean".
201112-22:11:58,424 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_mean" - collecting precomputed outputs
201112-22:11:58,424 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_mean" found cached.
201112-22:11:58,426 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.functional_mean" in "/outputs/tmp/resting_preproc_sub-206_ses-1/nuisance_regressor_0_0/_scan_tgng_run-2/_selector_WM-2mm-M-SDB_CSF-2mm-M-SDB_G-M-SDB_M-SDB_P-2_BP-B0.01-T0.08/functional_mean".
201112-22:11:58,448 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.functional_mean" - collecting precomputed outputs
201112-22:11:58,448 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.functional_mean" found cached.
201112-22:11:58,451 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.qc_snr_0.std_dev" in "/outputs/tmp/resting_preproc_sub-206_ses-1/qc_snr_0/_scan_tgng_run-2/std_dev".
201112-22:11:58,472 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.qc_snr_0.std_dev" - collecting precomputed outputs
201112-22:11:58,473 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.qc_snr_0.std_dev" found cached.
201112-22:11:58,474 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_functional_preprocessed".
201112-22:11:58,523 nipype.workflow INFO:
[Node] Running "sinker_0_functional_preprocessed" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:58,763 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed".
201112-22:11:58,765 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mask_normalize" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mask_normalize".
201112-22:11:58,789 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mask_normalize" - collecting precomputed outputs
201112-22:11:58,789 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mask_normalize" found cached.
201112-22:11:58,791 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed_mask" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_functional_preprocessed_mask".
201112-22:11:58,840 nipype.workflow INFO:
[Node] Running "sinker_0_functional_preprocessed_mask" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:59,80 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed_mask".
201112-22:11:59,83 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mean" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mean".
201112-22:11:59,128 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mean" - collecting precomputed outputs
201112-22:11:59,129 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mean" found cached.
201112-22:11:59,131 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_mean_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_mean_functional".
201112-22:11:59,197 nipype.workflow INFO:
[Node] Running "sinker_0_mean_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:59,437 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_mean_functional".
201112-22:11:59,439 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.norm_motion_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/norm_motion_params".
201112-22:11:59,471 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.norm_motion_params" - collecting precomputed outputs
201112-22:11:59,471 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.norm_motion_params" found cached.
201112-22:11:59,473 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_slice_time_corrected" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_slice_time_corrected".
201112-22:11:59,532 nipype.workflow INFO:
[Node] Running "sinker_0_slice_time_corrected" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:59,773 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_slice_time_corrected".
201112-22:11:59,775 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/sinker_0_raw_functional".
201112-22:11:59,843 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:00,424 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:00,426 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-2/check_func_scan".
201112-22:12:00,459 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:00,460 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:00,473 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-1/select_scan_params".
201112-22:12:00,513 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:00,514 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:00,527 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-1/s3_scan_params".
201112-22:12:00,553 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:00,554 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:00,559 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-1/scan_params_0".
201112-22:12:00,591 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:00,592 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:00,595 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-1/selectrest".
201112-22:12:00,630 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:00,630 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:00,640 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-1/check_for_s3".
201112-22:12:00,664 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:00,665 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:00,667 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-1/func_get_idx".
201112-22:12:00,699 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:00,699 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:00,701 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-1/func_drop_trs".
201112-22:12:00,776 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-tgng_run-1_bold.nii.gz[0..129] -expr "a" -prefix sub-206_ses-1_task-tgng_run-1_bold_calc.nii.gz
201112-22:12:01,33 nipype.interface INFO:
stderr 2020-11-12T22:12:01.033569:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:01,34 nipype.interface INFO:
stderr 2020-11-12T22:12:01.034026:++ Authored by: A cast of thousands
201112-22:12:06,886 nipype.interface INFO:
stderr 2020-11-12T22:12:06.886108:++ Output dataset ./sub-206_ses-1_task-tgng_run-1_bold_calc.nii.gz
201112-22:12:07,85 nipype.workflow ERROR:
Node func_drop_trs.b6 failed to run on host node096.
201112-22:12:07,93 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221207-av2902-func_drop_trs.b6-e61d344c-1709-48bf-99c0-60bddb1cd59a.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 566, in move
os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-1/func_drop_trs/_0x5a8096a39d65ecc3fcfbf3d89b63d0c0_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-1/func_drop_trs/_0x5a8096a39d65ecc3fcfbf3d89b63d0c0.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
hashfile_unfinished.replace('_unfinished', ''))
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 580, in move
copy_function(src, real_dst)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 266, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_tgng_run-1/func_drop_trs/_0x5a8096a39d65ecc3fcfbf3d89b63d0c0_unfinished.json'
201112-22:12:07,99 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-1/sinker_0_raw_functional".
201112-22:12:07,171 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:07,583 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:07,585 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_tgng_run-1/check_func_scan".
201112-22:12:07,615 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:07,615 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:07,624 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_rest_run-1/select_scan_params".
201112-22:12:07,656 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:07,656 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:07,668 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_rest_run-1/s3_scan_params".
201112-22:12:07,693 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:07,693 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:07,696 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_rest_run-1/scan_params_0".
201112-22:12:07,728 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:07,728 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:07,732 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_rest_run-1/selectrest".
201112-22:12:07,783 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:07,784 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:07,795 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_rest_run-1/check_for_s3".
201112-22:12:07,824 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:07,824 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:07,825 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_rest_run-1/func_get_idx".
201112-22:12:07,851 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:07,851 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:07,854 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_rest_run-1/func_drop_trs".
201112-22:12:07,910 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-rest_run-1_bold.nii.gz[0..179] -expr "a" -prefix sub-206_ses-1_task-rest_run-1_bold_calc.nii.gz
201112-22:12:08,160 nipype.interface INFO:
stderr 2020-11-12T22:12:08.160337:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:08,160 nipype.interface INFO:
stderr 2020-11-12T22:12:08.160764:++ Authored by: A cast of thousands
201112-22:12:16,230 nipype.interface INFO:
stderr 2020-11-12T22:12:16.230643:++ Output dataset ./sub-206_ses-1_task-rest_run-1_bold_calc.nii.gz
201112-22:12:16,422 nipype.workflow ERROR:
Node func_drop_trs.b5 failed to run on host node096.
201112-22:12:16,424 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221216-av2902-func_drop_trs.b5-d63c2a8a-f342-4fa0-8232-e61c9a53b4d0.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 566, in move
os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_rest_run-1/func_drop_trs/_0xd766b892dbb9c9f65377ee83266cc40d_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_rest_run-1/func_drop_trs/_0xd766b892dbb9c9f65377ee83266cc40d.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
hashfile_unfinished.replace('_unfinished', ''))
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 580, in move
copy_function(src, real_dst)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 266, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_rest_run-1/func_drop_trs/_0xd766b892dbb9c9f65377ee83266cc40d_unfinished.json'
201112-22:12:16,432 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_rest_run-1/sinker_0_raw_functional".
201112-22:12:16,496 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:16,940 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:16,943 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_rest_run-1/check_func_scan".
201112-22:12:16,976 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:16,977 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:16,989 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_ms_run-1/select_scan_params".
201112-22:12:17,25 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:17,25 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:17,34 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_ms_run-1/s3_scan_params".
201112-22:12:17,59 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:17,59 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:17,62 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_ms_run-1/scan_params_0".
201112-22:12:17,99 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:17,99 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:17,102 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_ms_run-1/selectrest".
201112-22:12:17,145 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:17,145 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:17,153 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_ms_run-1/check_for_s3".
201112-22:12:17,176 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:17,177 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:17,179 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_ms_run-1/func_get_idx".
201112-22:12:17,209 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:17,209 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:17,211 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_ms_run-1/func_drop_trs".
201112-22:12:17,278 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-ms_run-1_bold.nii.gz[0..142] -expr "a" -prefix sub-206_ses-1_task-ms_run-1_bold_calc.nii.gz
201112-22:12:17,542 nipype.interface INFO:
stderr 2020-11-12T22:12:17.542803:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:17,543 nipype.interface INFO:
stderr 2020-11-12T22:12:17.543244:++ Authored by: A cast of thousands
201112-22:12:23,742 nipype.interface INFO:
stderr 2020-11-12T22:12:23.742839:++ Output dataset ./sub-206_ses-1_task-ms_run-1_bold_calc.nii.gz
201112-22:12:23,926 nipype.workflow ERROR:
Node func_drop_trs.b4 failed to run on host node096.
201112-22:12:23,929 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221223-av2902-func_drop_trs.b4-3c8fca85-b1d5-4540-98e1-69774d6e921f.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 566, in move
os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_ms_run-1/func_drop_trs/_0xef3379eb2e469cb0465e165d39809cca_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_ms_run-1/func_drop_trs/_0xef3379eb2e469cb0465e165d39809cca.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 480, in run
hashfile_unfinished.replace('_unfinished', ''))
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 580, in move
copy_function(src, real_dst)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 266, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/local/miniconda/lib/python3.7/shutil.py", line 120, in copyfile
with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_ms_run-1/func_drop_trs/_0xef3379eb2e469cb0465e165d39809cca_unfinished.json'
201112-22:12:23,936 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_ms_run-1/sinker_0_raw_functional".
201112-22:12:24,1 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:24,425 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:24,427 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_ms_run-1/check_func_scan".
201112-22:12:24,454 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:24,455 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:24,464 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-3/select_scan_params".
201112-22:12:24,489 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:24,489 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:24,502 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-3/s3_scan_params".
201112-22:12:24,547 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:24,548 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:24,551 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/scan_params_0".
201112-22:12:24,585 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:24,586 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:24,589 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-3/selectrest".
201112-22:12:24,623 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:24,623 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:24,635 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-3/check_for_s3".
201112-22:12:24,660 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:24,660 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:24,661 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-3/func_get_idx".
201112-22:12:24,693 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:24,693 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:24,695 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-3/func_drop_trs".
201112-22:12:24,729 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" - collecting precomputed outputs
201112-22:12:24,729 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" found cached.
201112-22:12:24,732 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique".
201112-22:12:24,855 nipype.workflow INFO:
[Node] Running "func_deoblique" ("nipype.interfaces.afni.utils.Refit"), a CommandLine Interface with command:
3drefit -deoblique /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:25,258 nipype.interface INFO:
stderr 2020-11-12T22:12:25.258008:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:25,258 nipype.interface INFO:
stderr 2020-11-12T22:12:25.258417:++ Authored by: RW Cox
201112-22:12:25,316 nipype.interface INFO:
stderr 2020-11-12T22:12:25.316045:++ Processing AFNI dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:25,316 nipype.interface INFO:
stderr 2020-11-12T22:12:25.316853: + deoblique
201112-22:12:25,317 nipype.interface INFO:
stderr 2020-11-12T22:12:25.317106: + loading and re-writing dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz (/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz in NIFTI storage)
201112-22:12:26,247 nipype.interface INFO:
stderr 2020-11-12T22:12:26.247797:++ WARNING: nifti_read_buffer(/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz):
201112-22:12:26,251 nipype.interface INFO:
stderr 2020-11-12T22:12:26.247797: data bytes needed = 278528
201112-22:12:26,251 nipype.interface INFO:
stderr 2020-11-12T22:12:26.247797: data bytes input = 223057
201112-22:12:26,251 nipype.interface INFO:
stderr 2020-11-12T22:12:26.247797: number missing = 55471 (set to 0)
201112-22:12:26,251 nipype.interface INFO:
stderr 2020-11-12T22:12:26.251913:** NIFTI load bricks: cannot read brick 13 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
201112-22:12:26,444 nipype.interface INFO:
stderr 2020-11-12T22:12:26.444904:** NIFTI load bricks: cannot read brick 17 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
201112-22:12:26,445 nipype.interface INFO:
stderr 2020-11-12T22:12:26.445894:[7m** ERROR:[0m Can't write NIfTI file since dataset isn't loaded: /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:26,447 nipype.interface INFO:
stderr 2020-11-12T22:12:26.447137:++ 3drefit processed 1 datasets
201112-22:12:26,681 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique".
201112-22:12:26,683 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient".
201112-22:12:26,712 nipype.workflow INFO:
[Node] Running "func_reorient" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -orient RPI -prefix sub-206_ses-1_task-matching_run-3_bold_calc_resample.nii.gz -inset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:27,224 nipype.interface INFO:
stderr 2020-11-12T22:12:27.224006:++ WARNING: nifti_read_buffer(/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz):
201112-22:12:27,224 nipype.interface INFO:
stderr 2020-11-12T22:12:27.224006: data bytes needed = 278528
201112-22:12:27,224 nipype.interface INFO:
stderr 2020-11-12T22:12:27.224006: data bytes input = 273787
201112-22:12:27,224 nipype.interface INFO:
stderr 2020-11-12T22:12:27.224006: number missing = 4741 (set to 0)
201112-22:12:27,225 nipype.interface INFO:
stderr 2020-11-12T22:12:27.225384:** NIFTI load bricks: cannot read brick 36 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
201112-22:12:27,514 nipype.interface INFO:
stderr 2020-11-12T22:12:27.514562:++ WARNING: nifti_read_buffer(/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz):
201112-22:12:27,514 nipype.interface INFO:
stderr 2020-11-12T22:12:27.514562: data bytes needed = 278528
201112-22:12:27,515 nipype.interface INFO:
stderr 2020-11-12T22:12:27.514562: data bytes input = 267224
201112-22:12:27,515 nipype.interface INFO:
stderr 2020-11-12T22:12:27.514562: number missing = 11304 (set to 0)
201112-22:12:27,515 nipype.interface INFO:
stderr 2020-11-12T22:12:27.515419:** NIFTI load bricks: cannot read brick 41 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
201112-22:12:27,516 nipype.interface INFO:
stderr 2020-11-12T22:12:27.516858:r_fill_resampled_data_brick: failure to compute dataset slice 0
201112-22:12:27,517 nipype.interface INFO:
stderr 2020-11-12T22:12:27.517935:failure to resample dataset, exiting...
201112-22:12:27,691 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient" (/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient)
201112-22:12:27,694 nipype.workflow ERROR:
Node func_reorient.b3 failed to run on host node096.
201112-22:12:27,694 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221227-av2902-func_reorient.b3-b4920587-0bb6-45be-bb57-6c9b01d948c3.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 110, in _run_interface
return super(AFNICommandBase, self)._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1033, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 970, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
3dresample -orient RPI -prefix sub-206_ses-1_task-matching_run-3_bold_calc_resample.nii.gz -inset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
Standard output:
Standard error:
++ WARNING: nifti_read_buffer(/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz):
data bytes needed = 278528
data bytes input = 273787
number missing = 4741 (set to 0)
** NIFTI load bricks: cannot read brick 36 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
++ WARNING: nifti_read_buffer(/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz):
data bytes needed = 278528
data bytes input = 267224
number missing = 11304 (set to 0)
** NIFTI load bricks: cannot read brick 41 from '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_reorient/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz'
r_fill_resampled_data_brick: failure to compute dataset slice 0
failure to resample dataset, exiting...
Return code: 255
201112-22:12:27,696 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_despiked_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0".
201112-22:12:27,705 nipype.workflow INFO:
[Node] Running "func_despiked_0" ("nipype.interfaces.afni.preprocess.Despike"), a CommandLine Interface with command:
3dDespike -prefix sub-206_ses-1_task-matching_run-3_bold_calc_despike.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:28,108 nipype.interface INFO:
stderr 2020-11-12T22:12:28.108554:++ 3dDespike: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:28,109 nipype.interface INFO:
stderr 2020-11-12T22:12:28.108979:++ Authored by: RW Cox
201112-22:12:28,123 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
201112-22:12:28,123 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: such as /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz,
201112-22:12:28,123 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: or viewing/combining it with volumes of differing obliquity,
201112-22:12:28,123 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: you should consider running:
201112-22:12:28,123 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: 3dWarp -deoblique
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: on this and other oblique datasets in the same session.
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.123425: See 3dWarp -help for details.
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.124384:++ Oblique dataset:/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz is 28.699991 degrees from plumb.
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.124592:++ Input dataset is in short format, but output will be in float format
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.124782:++ ignoring first 0 time points, using last 99
201112-22:12:28,124 nipype.interface INFO:
stderr 2020-11-12T22:12:28.124968:++ using 99 time points => -corder 3
201112-22:12:28,125 nipype.interface INFO:
stderr 2020-11-12T22:12:28.125163:++ Loading dataset /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0/sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:28,525 nipype.interface INFO:
stderr 2020-11-12T22:12:28.525422:++ 30000 voxels in the automask [out of 139264 in dataset]
201112-22:12:28,531 nipype.interface INFO:
stderr 2020-11-12T22:12:28.531086:++ 53122 voxels in the dilated automask [out of 139264 in dataset]
201112-22:12:28,541 nipype.interface INFO:
stderr 2020-11-12T22:12:28.541227:++ Procesing time series with OLD model fit algorithm
201112-22:12:28,541 nipype.interface INFO:
stderr 2020-11-12T22:12:28.541411:++ smash edit thresholds: 3.1 .. 5.0 MADs
201112-22:12:28,541 nipype.interface INFO:
stderr 2020-11-12T22:12:28.541577: + [ 3.457% .. 0.072% of normal distribution]
201112-22:12:28,542 nipype.interface INFO:
stderr 2020-11-12T22:12:28.542753: + [ 8.839% .. 3.125% of Laplace distribution]
201112-22:12:28,542 nipype.interface INFO:
stderr 2020-11-12T22:12:28.542938:++ start OpenMP thread #0
201112-22:12:31,354 nipype.interface INFO:
stderr 2020-11-12T22:12:31.354749:........................
201112-22:12:31,355 nipype.interface INFO:
stderr 2020-11-12T22:12:31.355240:++ Elapsed despike time = 2s 812ms
201112-22:12:31,355 nipype.interface INFO:
stderr 2020-11-12T22:12:31.355390:
201112-22:12:31,356 nipype.interface INFO:
stderr 2020-11-12T22:12:31.356106:++ FINAL: 5259078 data points, 338143 edits [6.430%], 35551 big edits [0.676%]
201112-22:12:31,383 nipype.interface INFO:
stderr 2020-11-12T22:12:31.383866:** ERROR (nifti_image_write_hdr_img2): cannot open output file './sub-206_ses-1_task-matching_run-3_bold_calc_despike.nii.gz'
201112-22:12:31,582 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.func_despiked_0" (/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0)
201112-22:12:31,595 nipype.workflow ERROR:
Node func_despiked_0.b3 failed to run on host node096.
201112-22:12:31,601 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221231-av2902-func_despiked_0.b3-bfd58ade-9e0e-434b-992e-609f40a74f69.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 218, in _list_outputs
outputs = super(AFNICommand, self)._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1167, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:12:31,610 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/sinker_0_raw_functional".
201112-22:12:31,626 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:31,950 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:31,952 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-3/check_func_scan".
201112-22:12:31,987 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:32,227 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:32,237 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-2/select_scan_params".
201112-22:12:32,272 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:32,509 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:32,520 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-2/s3_scan_params".
201112-22:12:32,529 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:32,764 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:32,767 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-2/scan_params_0".
201112-22:12:32,779 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:33,14 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:33,17 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-2/selectrest".
201112-22:12:33,49 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:33,287 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:33,298 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-2/check_for_s3".
201112-22:12:33,303 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:33,625 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:33,627 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-2/func_get_idx".
201112-22:12:33,635 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:33,868 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:33,869 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-2/func_drop_trs".
201112-22:12:33,877 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-matching_run-2_bold.nii.gz[0..98] -expr "a" -prefix sub-206_ses-1_task-matching_run-2_bold_calc.nii.gz
201112-22:12:34,134 nipype.interface INFO:
stderr 2020-11-12T22:12:34.134847:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:34,135 nipype.interface INFO:
stderr 2020-11-12T22:12:34.135235:++ Authored by: A cast of thousands
201112-22:12:38,723 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" (/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-2/func_drop_trs)
201112-22:12:38,734 nipype.workflow ERROR:
Node func_drop_trs.b2 failed to run on host node096.
201112-22:12:38,739 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221238-av2902-func_drop_trs.b2-2350c4a8-0fdf-44e3-9429-7ad8a2d5b364.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 218, in _list_outputs
outputs = super(AFNICommand, self)._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1167, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:12:38,748 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-2/sinker_0_raw_functional".
201112-22:12:38,757 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:39,62 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:39,63 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-2/check_func_scan".
201112-22:12:39,98 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:39,335 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:39,347 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-1/select_scan_params".
201112-22:12:39,381 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:39,619 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:39,629 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-1/s3_scan_params".
201112-22:12:39,638 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:39,874 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:39,877 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-1/scan_params_0".
201112-22:12:39,887 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:40,122 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:40,125 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-1/selectrest".
201112-22:12:40,158 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:40,394 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:40,405 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-1/check_for_s3".
201112-22:12:40,410 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:40,701 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:40,703 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-1/func_get_idx".
201112-22:12:40,711 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:40,947 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:40,949 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-1/func_drop_trs".
201112-22:12:40,956 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-matching_run-1_bold.nii.gz[0..98] -expr "a" -prefix sub-206_ses-1_task-matching_run-1_bold_calc.nii.gz
201112-22:12:41,208 nipype.interface INFO:
stderr 2020-11-12T22:12:41.208815:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:41,209 nipype.interface INFO:
stderr 2020-11-12T22:12:41.209270:++ Authored by: A cast of thousands
201112-22:12:43,7 nipype.interface INFO:
stderr 2020-11-12T22:12:43.007749:** ERROR (nifti_image_write_hdr_img2): cannot open output file './sub-206_ses-1_task-matching_run-1_bold_calc.nii.gz'
201112-22:12:43,199 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" (/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-1/func_drop_trs)
201112-22:12:43,213 nipype.workflow ERROR:
Node func_drop_trs.b1 failed to run on host node096.
201112-22:12:43,217 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221243-av2902-func_drop_trs.b1-dc432eb8-164e-4aa9-8d42-feca0291498b.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 218, in _list_outputs
outputs = super(AFNICommand, self)._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1167, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:12:43,227 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-1/sinker_0_raw_functional".
201112-22:12:43,236 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:43,543 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:43,545 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_matching_run-1/check_func_scan".
201112-22:12:43,579 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:43,814 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:43,825 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_conditioning_run-1/select_scan_params".
201112-22:12:43,856 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:44,88 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:44,99 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_conditioning_run-1/s3_scan_params".
201112-22:12:44,107 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:44,336 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:44,339 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.scan_params_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_conditioning_run-1/scan_params_0".
201112-22:12:44,349 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:44,581 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:44,583 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_conditioning_run-1/selectrest".
201112-22:12:44,616 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:44,847 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:44,857 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_conditioning_run-1/check_for_s3".
201112-22:12:44,862 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:45,139 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:45,141 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_conditioning_run-1/func_get_idx".
201112-22:12:45,149 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:45,384 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:45,385 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" in "/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_conditioning_run-1/func_drop_trs".
201112-22:12:45,392 nipype.workflow INFO:
[Node] Running "func_drop_trs" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /bids_dataset/sub-206/ses-1/func/sub-206_ses-1_task-conditioning_run-1_bold.nii.gz[0..150] -expr "a" -prefix sub-206_ses-1_task-conditioning_run-1_bold_calc.nii.gz
201112-22:12:45,639 nipype.interface INFO:
stderr 2020-11-12T22:12:45.639465:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:45,639 nipype.interface INFO:
stderr 2020-11-12T22:12:45.639831:++ Authored by: A cast of thousands
201112-22:12:48,168 nipype.interface INFO:
stderr 2020-11-12T22:12:48.168833:** ERROR (nifti_image_write_hdr_img2): cannot open output file './sub-206_ses-1_task-conditioning_run-1_bold_calc.nii.gz'
201112-22:12:48,359 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs" (/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_conditioning_run-1/func_drop_trs)
201112-22:12:48,373 nipype.workflow ERROR:
Node func_drop_trs.b0 failed to run on host node096.
201112-22:12:48,377 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221248-av2902-func_drop_trs.b0-18019fd8-effe-4708-bede-9733f3498483.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 218, in _list_outputs
outputs = super(AFNICommand, self)._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1167, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:12:48,387 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_raw_functional" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_conditioning_run-1/sinker_0_raw_functional".
201112-22:12:48,397 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:48,748 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:48,749 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_gather_0/_scan_conditioning_run-1/check_func_scan".
201112-22:12:48,782 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:49,17 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:49,27 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/roi_dataflow_0/_mask_Yeo-7_space-MNI152NLin6_res-1x1x1_mask_file_..ndmg_atlases..label..Human..Yeo-7_space-MNI152NLin6_res-1x1x1.nii.gz/check_for_s3".
201112-22:12:49,34 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:49,280 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3".
201112-22:12:49,282 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/roi_dataflow_0/_mask_Yeo-7-liberal_space-MNI152NLin6_res-1x1x1_mask_file_..ndmg_atlases..label..Human..Yeo-7-liberal_space-MNI152NLin6_res-1x1x1.nii.gz/check_for_s3".
201112-22:12:49,286 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:49,590 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3".
201112-22:12:49,592 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.lap_tmpl" in "/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/lap_tmpl".
201112-22:12:49,597 nipype.workflow INFO:
[Node] Running "lap_tmpl" ("CPAC.utils.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 T_template0_maths.nii.gz Laplacian /ants_template/oasis/T_template0.nii.gz 1.5 1
201112-22:12:59,351 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.lap_tmpl" (/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/lap_tmpl)
201112-22:12:59,364 nipype.workflow ERROR:
Node lap_tmpl failed to run on host node096.
201112-22:12:59,369 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221259-av2902-lap_tmpl-6cea2816-eca3-43dc-96c3-ee9463bfe78c.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 523, in run
outputs = self.aggregate_outputs(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 597, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1167, in _list_outputs
outputs[out_name] = os.path.abspath(fname)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:12:59,380 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.res_tmpl" in "/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/res_tmpl".
201112-22:12:59,388 nipype.workflow INFO:
[Node] Running "res_tmpl" ("CPAC.utils.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command:
ResampleImageBySpacing 3 /ants_template/oasis/T_template0.nii.gz T_template0_resampled.nii.gz 4 4 4 1
201112-22:13:00,31 nipype.interface INFO:
stdout 2020-11-12T22:13:00.031377: spacing [1, 1, 1] dim 3
201112-22:13:00,31 nipype.interface INFO:
stdout 2020-11-12T22:13:00.031885: spacing2 [4, 4, 4]
201112-22:13:00,32 nipype.interface INFO:
stdout 2020-11-12T22:13:00.032099: smoothing by : 3 dir 0
201112-22:13:00,370 nipype.interface INFO:
stdout 2020-11-12T22:13:00.370580: smoothing by : 3 dir 1
201112-22:13:00,786 nipype.interface INFO:
stdout 2020-11-12T22:13:00.786714: smoothing by : 3 dir 2
201112-22:13:01,574 nipype.interface INFO:
stdout 2020-11-12T22:13:01.574539: out space [4, 4, 4]
201112-22:13:01,575 nipype.interface INFO:
stdout 2020-11-12T22:13:01.575028: output size [54, 64, 72] spc [4, 4, 4]
201112-22:13:01,810 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.res_tmpl".
201112-22:13:01,812 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.anat_gather_0.check_for_s3" in "/outputs/tmp/resting_preproc_sub-206_ses-1/anat_gather_0/check_for_s3".
201112-22:13:01,818 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:13:02,148 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.anat_gather_0.check_for_s3".
201112-22:13:02,150 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_deoblique" in "/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique".
201112-22:13:02,306 nipype.workflow INFO:
[Node] Running "anat_deoblique" ("nipype.interfaces.afni.utils.Refit"), a CommandLine Interface with command:
3drefit -deoblique /outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/sub-206_ses-1_T1w.nii.gz
201112-22:13:02,557 nipype.interface INFO:
stderr 2020-11-12T22:13:02.557906:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:13:02,558 nipype.interface INFO:
stderr 2020-11-12T22:13:02.558314:++ Authored by: RW Cox
201112-22:13:02,566 nipype.interface INFO:
stderr 2020-11-12T22:13:02.566925:** AFNI converts NIFTI_datatype=4 (INT16) in file /outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/sub-206_ses-1_T1w.nii.gz to FLOAT32
201112-22:13:02,567 nipype.interface INFO:
stderr 2020-11-12T22:13:02.567463: Warnings of this type will be muted for this session.
201112-22:13:02,567 nipype.interface INFO:
stderr 2020-11-12T22:13:02.567463: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
201112-22:13:02,568 nipype.interface INFO:
stderr 2020-11-12T22:13:02.568815:++ Processing AFNI dataset /outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/sub-206_ses-1_T1w.nii.gz
201112-22:13:02,569 nipype.interface INFO:
stderr 2020-11-12T22:13:02.569739: + deoblique
201112-22:13:02,570 nipype.interface INFO:
stderr 2020-11-12T22:13:02.570249: + loading and re-writing dataset /outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/sub-206_ses-1_T1w.nii.gz (/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/sub-206_ses-1_T1w.nii.gz in NIFTI storage)
201112-22:13:05,418 nipype.interface INFO:
stderr 2020-11-12T22:13:05.418325:++ 3drefit processed 1 datasets
201112-22:13:05,614 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_deoblique" (/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique)
201112-22:13:05,628 nipype.workflow ERROR:
Node anat_deoblique failed to run on host node096.
201112-22:13:05,632 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221305-av2902-anat_deoblique-e05da0d8-8000-469c-bd73-bc5ca84bc0d2.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:13:05,654 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_plot" in "/outputs/tmp/resting_preproc_sub-206_ses-1/sinker_0_motion_estimate_filter_info_plot".
201112-22:13:05,663 nipype.workflow INFO:
[Node] Running "sinker_0_motion_estimate_filter_info_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:13:05,891 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_plot".
201112-22:13:05,893 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_design" in "/outputs/tmp/resting_preproc_sub-206_ses-1/sinker_0_motion_estimate_filter_info_design".
201112-22:13:05,899 nipype.workflow INFO:
[Node] Running "sinker_0_motion_estimate_filter_info_design" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:13:06,129 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_design".
201112-22:13:06,132 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_lateral_ventricles_mask" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_lateral_ventricles_mask".
201112-22:13:06,136 nipype.workflow INFO:
[Node] Running "check_for_s3_lateral_ventricles_mask" ("CPAC.utils.interfaces.function.Function")
201112-22:13:06,364 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_lateral_ventricles_mask".
201112-22:13:06,365 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_derivative" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_brain_for_func_derivative".
201112-22:13:06,369 nipype.workflow INFO:
[Node] Running "resampled_template_brain_for_func_derivative" ("CPAC.utils.interfaces.function.Function")
201112-22:13:06,605 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_derivative".
201112-22:13:06,607 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_preproc" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_brain_for_func_preproc".
201112-22:13:06,611 nipype.workflow INFO:
[Node] Running "resampled_template_brain_for_func_preproc" ("CPAC.utils.interfaces.function.Function")
201112-22:13:06,843 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_preproc".
201112-22:13:06,845 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.func_template_edge_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/func_template_edge_0".
201112-22:13:06,849 nipype.workflow INFO:
[Node] Running "func_template_edge_0" ("CPAC.utils.interfaces.function.Function")
201112-22:13:07,385 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_template_edge_0".
201112-22:13:07,386 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.montage_mfi_0.resample_o" in "/outputs/tmp/resting_preproc_sub-206_ses-1/montage_mfi_0/resample_o".
201112-22:13:07,391 nipype.workflow INFO:
[Node] Running "resample_o" ("CPAC.utils.interfaces.function.Function")
201112-22:13:07,828 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.montage_mfi_0.resample_o".
201112-22:13:07,830 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_derivative" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_derivative".
201112-22:13:07,834 nipype.workflow INFO:
[Node] Running "resampled_template_skull_for_func_derivative" ("CPAC.utils.interfaces.function.Function")
201112-22:13:08,45 nipype.workflow INFO:
[Node] Setting-up "template_skull_for_func_derivative" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_derivative/template_skull_for_func_derivative".
201112-22:13:08,50 nipype.workflow INFO:
[Node] Running "template_skull_for_func_derivative" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -prefix tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz -rmode Cu -dxyz 2.000000 2.000000 2.000000 -inset /outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_derivative/template_skull_for_func_derivative/tpl-MNI152NLin2009cAsym_res-02_T1w_reference.nii.gz
201112-22:13:08,789 nipype.workflow INFO:
[Node] Finished "template_skull_for_func_derivative".
201112-22:13:08,806 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_derivative".
201112-22:13:08,807 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_preproc" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc".
201112-22:13:08,815 nipype.workflow INFO:
[Node] Running "resampled_template_skull_for_func_preproc" ("CPAC.utils.interfaces.function.Function")
201112-22:13:09,26 nipype.workflow INFO:
[Node] Setting-up "template_skull_for_func_preproc" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc".
201112-22:13:09,33 nipype.workflow INFO:
[Node] Running "template_skull_for_func_preproc" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -prefix tpl-MNI152NLin2009cAsym_res-02_T1w_reference_resample.nii.gz -rmode Cu -dxyz 2.000000 2.000000 2.000000 -inset /outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc/tpl-MNI152NLin2009cAsym_res-02_T1w_reference.nii.gz
201112-22:13:09,360 nipype.workflow WARNING:
[Node] Error on "template_skull_for_func_preproc" (/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc)
201112-22:13:09,427 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_preproc" (/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc)
201112-22:13:09,444 nipype.workflow ERROR:
Node resampled_template_skull_for_func_preproc failed to run on host node096.
201112-22:13:09,449 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221309-av2902-resampled_template_skull_for_func_preproc-e987dd6e-f55b-4dd4-a35d-c7189137dc45.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/afni/base.py", line 110, in _run_interface
return super(AFNICommandBase, self)._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 1030, in _run_interface
runtime = run_command(runtime, output=self.terminal_output)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 768, in run_command
close_fds=(not sys.platform.startswith('win')),
File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 800, in __init__
restore_signals, start_new_session)
File "/usr/local/miniconda/lib/python3.7/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc': '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 639, in _run_command
_save_resultfile(result, outdir, self.name)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 309, in save_resultfile
savepkl(resultsfile, result)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 720, in savepkl
pkl_file = gzip.open(filename, 'wb')
File "/usr/local/miniconda/lib/python3.7/gzip.py", line 53, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/usr/local/miniconda/lib/python3.7/gzip.py", line 163, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc/result_template_skull_for_func_preproc.pklz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface
out = function_handle(**args)
File "/code/CPAC/utils/datasource.py", line 586, in resolve_resolution
resampled_template = resample.run()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 475, in run
os.remove(hashfile_unfinished)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/template_skull_for_func_preproc/_0x515bd94bea7e6e1cc7ab705d0b32d7d0_unfinished.json'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:13:09,457 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_WHITE" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_PRIORS_WHITE".
201112-22:13:09,466 nipype.workflow INFO:
[Node] Running "check_for_s3_PRIORS_WHITE" ("CPAC.utils.interfaces.function.Function")
201112-22:13:09,733 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_WHITE".
201112-22:13:09,735 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_GRAY" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_PRIORS_GRAY".
201112-22:13:09,741 nipype.workflow INFO:
[Node] Running "check_for_s3_PRIORS_GRAY" ("CPAC.utils.interfaces.function.Function")
201112-22:13:09,973 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_GRAY".
201112-22:13:09,975 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_CSF" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_PRIORS_CSF".
201112-22:13:09,982 nipype.workflow INFO:
[Node] Running "check_for_s3_PRIORS_CSF" ("CPAC.utils.interfaces.function.Function")
201112-22:13:10,258 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_CSF".
201112-22:13:10,259 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_skull_for_anat" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat".
201112-22:13:10,265 nipype.workflow INFO:
[Node] Running "resampled_template_skull_for_anat" ("CPAC.utils.interfaces.function.Function")
201112-22:13:10,512 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.resampled_template_skull_for_anat" (/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat)
201112-22:13:10,524 nipype.workflow ERROR:
Node resampled_template_skull_for_anat failed to run on host node096.
201112-22:13:10,528 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221310-av2902-resampled_template_skull_for_anat-7c5afe82-a9f9-4021-aede-def6d25f1240.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface
out = function_handle(**args)
File "/code/CPAC/utils/datasource.py", line 586, in resolve_resolution
resampled_template = resample.run()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 402, in run
outdir = self.output_dir()
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 269, in output_dir
self._output_dir = op.realpath(op.join(outputdir, self.name))
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 396, in realpath
return abspath(path)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:13:10,536 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.resampled_template_brain_for_anat" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_brain_for_anat".
201112-22:13:10,544 nipype.workflow INFO:
[Node] Running "resampled_template_brain_for_anat" ("CPAC.utils.interfaces.function.Function")
201112-22:13:10,755 nipype.workflow INFO:
[Node] Setting-up "template_brain_for_anat" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_brain_for_anat/template_brain_for_anat".
201112-22:13:10,761 nipype.workflow INFO:
[Node] Running "template_brain_for_anat" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -prefix tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w_resample.nii.gz -rmode Cu -dxyz 1.000000 1.000000 1.000000 -inset /outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_brain_for_anat/template_brain_for_anat/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz
201112-22:13:12,833 nipype.workflow INFO:
[Node] Finished "template_brain_for_anat".
201112-22:13:12,849 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.resampled_template_brain_for_anat".
201112-22:13:12,857 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.anat_template_edge_0" in "/outputs/tmp/resting_preproc_sub-206_ses-1/anat_template_edge_0".
201112-22:13:12,863 nipype.workflow INFO:
[Node] Running "anat_template_edge_0" ("CPAC.utils.interfaces.function.Function")
201112-22:13:14,802 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.anat_template_edge_0" (/outputs/tmp/resting_preproc_sub-206_ses-1/anat_template_edge_0)
201112-22:13:14,816 nipype.workflow ERROR:
Node anat_template_edge_0 failed to run on host node096.
201112-22:13:14,820 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221314-av2902-anat_template_edge_0-03101fbf-8369-4057-9708-df43daac041d.pklz
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
runtime = self._run_interface(runtime)
File "/code/CPAC/utils/interfaces/function.py", line 152, in _run_interface
out = function_handle(**args)
File "/code/CPAC/qc/qc.py", line 451, in afni_Edge3
return os.path.abspath('./skull_edge.nii.gz')
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 569, in run
vals = np.loadtxt(mon_sp.fname, delimiter=',')
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/npyio.py", line 962, in loadtxt
fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 265, in open
ds = DataSource(destpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 322, in __init__
self._destpath = os.path.abspath(destpath)
File "/usr/local/miniconda/lib/python3.7/posixpath.py", line 383, in abspath
cwd = os.getcwd()
FileNotFoundError: [Errno 2] No such file or directory
201112-22:13:14,829 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_brain" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_acpc_template_brain".
201112-22:13:14,837 nipype.workflow INFO:
[Node] Running "check_for_s3_acpc_template_brain" ("CPAC.utils.interfaces.function.Function")
201112-22:13:15,69 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_brain".
201112-22:13:15,71 nipype.workflow INFO:
[Node] Setting-up "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_skull" in "/outputs/tmp/resting_preproc_sub-206_ses-1/check_for_s3_acpc_template_skull".
201112-22:13:15,75 nipype.workflow INFO:
[Node] Running "check_for_s3_acpc_template_skull" ("CPAC.utils.interfaces.function.Function")
201112-22:13:15,337 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_skull".
201112-22:13:15,338 nipype.workflow INFO:
***********************************
201112-22:13:15,338 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b6
201112-22:13:15,338 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221207-av2902-func_drop_trs.b6-e61d344c-1709-48bf-99c0-60bddb1cd59a.pklz
201112-22:13:15,339 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b5
201112-22:13:15,339 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221216-av2902-func_drop_trs.b5-d63c2a8a-f342-4fa0-8232-e61c9a53b4d0.pklz
201112-22:13:15,339 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b4
201112-22:13:15,339 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221223-av2902-func_drop_trs.b4-3c8fca85-b1d5-4540-98e1-69774d6e921f.pklz
201112-22:13:15,339 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient.b3
201112-22:13:15,339 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221227-av2902-func_reorient.b3-b4920587-0bb6-45be-bb57-6c9b01d948c3.pklz
201112-22:13:15,340 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.func_despiked_0.b3
201112-22:13:15,340 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221231-av2902-func_despiked_0.b3-bfd58ade-9e0e-434b-992e-609f40a74f69.pklz
201112-22:13:15,340 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b2
201112-22:13:15,340 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221238-av2902-func_drop_trs.b2-2350c4a8-0fdf-44e3-9429-7ad8a2d5b364.pklz
201112-22:13:15,341 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b1
201112-22:13:15,341 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221243-av2902-func_drop_trs.b1-dc432eb8-164e-4aa9-8d42-feca0291498b.pklz
201112-22:13:15,341 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b0
201112-22:13:15,341 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221248-av2902-func_drop_trs.b0-18019fd8-effe-4708-bede-9733f3498483.pklz
201112-22:13:15,342 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.lap_tmpl
201112-22:13:15,342 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221259-av2902-lap_tmpl-6cea2816-eca3-43dc-96c3-ee9463bfe78c.pklz
201112-22:13:15,343 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_deoblique
201112-22:13:15,343 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221305-av2902-anat_deoblique-e05da0d8-8000-469c-bd73-bc5ca84bc0d2.pklz
201112-22:13:15,343 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_preproc
201112-22:13:15,344 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221309-av2902-resampled_template_skull_for_func_preproc-e987dd6e-f55b-4dd4-a35d-c7189137dc45.pklz
201112-22:13:15,344 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.resampled_template_skull_for_anat
201112-22:13:15,344 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221310-av2902-resampled_template_skull_for_anat-7c5afe82-a9f9-4021-aede-def6d25f1240.pklz
201112-22:13:15,344 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.anat_template_edge_0
201112-22:13:15,344 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221314-av2902-anat_template_edge_0-03101fbf-8369-4057-9708-df43daac041d.pklz
201112-22:13:15,344 nipype.workflow INFO:
***********************************
201112-22:13:15,370 nipype.workflow INFO:
Error of subject workflow resting_preproc_sub-206_ses-1
CPAC run error:
Pipeline configuration: cpac_fmriprep-options
Subject workflow: resting_preproc_sub-206_ses-1
Elapsed run time (minutes): 1.5300026019414266
Timing information saved in /outputs/log/cpac_individual_timing_cpac_fmriprep-options.csv
System time of start: 2020-11-12 22:11:48
Traceback (most recent call last):
File "/code/CPAC/pipeline/cpac_pipeline.py", line 417, in run_workflow
workflow.run(plugin=plugin, plugin_args=plugin_args)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 61, in run
report_nodes_not_run(notrun)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/tools.py", line 82, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details