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-182
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_2020-11-12T22-03-29Z.yml
201112-22:03:41,887 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
201112-22:03:47,750 nipype.workflow INFO:
Pipeline building completed.
201112-22:03:47,751 nipype.workflow INFO:
Strategy forks:
- cpac_fmriprep-options
201112-22:03:50,417 nipype.workflow INFO:
Workflow resting_preproc_sub-206_ses-1 settings: ['check', 'execution', 'logging', 'monitoring']
201112-22:03:51,611 nipype.workflow INFO:
Running serially.
201112-22:03:51,620 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".
201112-22:03:51,650 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:03:51,887 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:03:51,898 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".
201112-22:03:51,905 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:03:52,139 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:03:52,142 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".
201112-22:03:52,151 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:03:52,385 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:03:52,388 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".
201112-22:03:52,420 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:03:52,655 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:03:52,666 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".
201112-22:03:52,671 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:03:52,999 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:03:53,0 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".
201112-22:03:53,7 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:03:53,243 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:03:53,244 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".
201112-22:03:53,251 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-2_bold.nii.gz[0..129] -expr "a" -prefix sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:03:53,498 nipype.interface INFO:
stderr 2020-11-12T22:03:53.498495:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:03:53,499 nipype.interface INFO:
stderr 2020-11-12T22:03:53.499358:++ Authored by: A cast of thousands
201112-22:03:59,335 nipype.interface INFO:
stderr 2020-11-12T22:03:59.334885:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:03:59,515 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs".
201112-22:03:59,516 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".
201112-22:03:59,576 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_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:04:00,15 nipype.interface INFO:
stderr 2020-11-12T22:04:00.015254:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:04:00,15 nipype.interface INFO:
stderr 2020-11-12T22:04:00.015611:++ Authored by: RW Cox
201112-22:04:00,32 nipype.interface INFO:
stderr 2020-11-12T22:04:00.032119:++ Processing AFNI dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:04:00,32 nipype.interface INFO:
stderr 2020-11-12T22:04:00.032808: + deoblique
201112-22:04:00,33 nipype.interface INFO:
stderr 2020-11-12T22:04:00.033014: + loading and re-writing dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz (/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz in NIFTI storage)
201112-22:04:04,2 nipype.interface INFO:
stderr 2020-11-12T22:04:04.002152:++ 3drefit processed 1 datasets
201112-22:04:04,175 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique".
201112-22:04:04,176 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".
201112-22:04:04,184 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-tgng_run-2_bold_calc_resample.nii.gz -inset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:04:08,835 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient".
201112-22:04:08,836 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".
201112-22:04:08,844 nipype.workflow INFO:
[Node] Running "func_get_mean_RPI" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample.nii.gz
201112-22:04:09,192 nipype.interface INFO:
stderr 2020-11-12T22:04:09.192478:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:04:09,192 nipype.interface INFO:
stderr 2020-11-12T22:04:09.192790:++ Authored by: KR Hammett & RW Cox
201112-22:04:09,668 nipype.interface INFO:
stderr 2020-11-12T22:04:09.668827:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_resample_tstat.nii.gz
201112-22:04:09,813 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI".
201112-22:04:09,814 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".
201112-22:04:09,822 nipype.workflow INFO:
[Node] Running "func_generate_ref" ("nipype.interfaces.afni.preprocess.Volreg"), a CommandLine Interface with command:
3dvolreg -twopass -Fourier -1Dfile sub-206_ses-1_task-tgng_run-2_bold_calc_resample.1D -1Dmatrix_save sub-206_ses-1_task-tgng_run-2_bold_calc_resample.aff12.1D -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_volreg.nii.gz -base /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_tstat.nii.gz -zpad 4 -maxdisp1D sub-206_ses-1_task-tgng_run-2_bold_calc_resample_md.1D /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_generate_ref/sub-206_ses-1_task-tgng_run-2_bold_calc_resample.nii.gz
201112-22:04:10,77 nipype.interface INFO:
stderr 2020-11-12T22:04:10.077399:++ 3dvolreg: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:04:10,77 nipype.interface INFO:
stderr 2020-11-12T22:04:10.077697:++ Authored by: RW Cox
201112-22:04:10,96 nipype.interface INFO:
stderr 2020-11-12T22:04:10.096738:++ Coarse del was 10, replaced with 3
201112-22:05:57,476 nipype.interface INFO:
stderr 2020-11-12T22:05:57.476303:++ Max displacement in automask = 0.42 (mm) at sub-brick 74
201112-22:05:57,476 nipype.interface INFO:
stderr 2020-11-12T22:05:57.476843:++ Max delta displ in automask = 0.54 (mm) at sub-brick 73
201112-22:06:01,304 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_generate_ref".
201112-22:06:01,307 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".
201112-22:06:01,315 nipype.workflow INFO:
[Node] Running "func_get_mean_motion" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_volreg_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_volreg.nii.gz
201112-22:06:01,567 nipype.interface INFO:
stderr 2020-11-12T22:06:01.567553:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:06:01,568 nipype.interface INFO:
stderr 2020-11-12T22:06:01.567867:++ Authored by: KR Hammett & RW Cox
201112-22:06:02,35 nipype.interface INFO:
stderr 2020-11-12T22:06:02.035467:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_resample_volreg_tstat.nii.gz
201112-22:06:02,182 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_motion".
201112-22:06:02,183 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".
201112-22:06:02,191 nipype.workflow INFO:
[Node] Running "func_motion_correct_mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient/sub-206_ses-1_task-tgng_run-2_bold_calc_resample.nii.gz -out /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf.nii.gz -reffile /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_volreg_tstat.nii.gz -mats -plots -rmsabs -rmsrel
201112-22:06:25,663 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt".
201112-22:06:25,672 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".
201112-22:06:25,680 nipype.workflow INFO:
[Node] Running "calculate_FDJ" ("CPAC.utils.interfaces.function.Function")
201112-22:06:25,913 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FDJ".
201112-22:06:25,915 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".
201112-22:06:25,924 nipype.workflow INFO:
[Node] Running "sinker_0_frame_wise_displacement_jenkinson" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:06:26,166 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_jenkinson".
201112-22:06:26,168 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".
201112-22:06:26,178 nipype.workflow INFO:
[Node] Running "sinker_0_max_displacement" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:06:26,412 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_max_displacement".
201112-22:06:26,413 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".
201112-22:06:26,432 nipype.workflow INFO:
[Node] Running "sinker_0_coordinate_transformation" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:06:26,703 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_coordinate_transformation".
201112-22:06:26,714 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".
201112-22:06:26,721 nipype.workflow INFO:
[Node] Running "func_mean_skull" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf.nii.gz
201112-22:06:26,976 nipype.interface INFO:
stderr 2020-11-12T22:06:26.976315:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:06:26,976 nipype.interface INFO:
stderr 2020-11-12T22:06:26.976665:++ Authored by: KR Hammett & RW Cox
201112-22:06:27,483 nipype.interface INFO:
stderr 2020-11-12T22:06:27.483439:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat.nii.gz
201112-22:06:27,631 nipype.workflow INFO:
[Node] Finished "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".
201112-22:06:27,633 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".
201112-22:06:27,640 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain.nii.gz -f 0.20 -m
201112-22:06:29,675 nipype.workflow INFO:
[Node] Finished "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".
201112-22:06:29,677 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".
201112-22:06:29,683 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask_dil.nii.gz
201112-22:06:30,356 nipype.workflow INFO:
[Node] Finished "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".
201112-22:06:30,358 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".
201112-22:06:30,366 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain.nii.gz -mas /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask_dil.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_masked.nii.gz
201112-22:06:30,779 nipype.workflow INFO:
[Node] Finished "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".
201112-22:06:30,781 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".
201112-22:06:30,787 nipype.workflow INFO:
[Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command:
3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_masked.nii.gz
201112-22:06:31,88 nipype.interface INFO:
stderr 2020-11-12T22:06:31.087846:++ 3dUnifize: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:07:40,259 nipype.interface INFO:
stderr 2020-11-12T22:07:40.259074: + Pre-processing: IAV..UW[s4182]Im
201112-22:07:40,275 nipype.interface INFO:
stderr 2020-11-12T22:07:40.275457:++ Output dataset ./uni.nii.gz
201112-22:07:40,275 nipype.interface INFO:
stderr 2020-11-12T22:07:40.275734:++ ===== Elapsed = 69.2 sec
201112-22:07:40,445 nipype.workflow INFO:
[Node] Finished "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".
201112-22:07:40,446 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".
201112-22:07:40,452 nipype.workflow INFO:
[Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command:
3dAutomask -apply_prefix uni_masked.nii.gz -dilate 1 -prefix uni_mask.nii.gz /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/uni.nii.gz
201112-22:07:40,885 nipype.interface INFO:
stderr 2020-11-12T22:07:40.885684:++ 3dAutomask: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:07:40,886 nipype.interface INFO:
stderr 2020-11-12T22:07:40.886284:++ Authored by: Emperor Zhark
201112-22:07:40,899 nipype.interface INFO:
stderr 2020-11-12T22:07:40.899150:++ Loading dataset /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/uni.nii.gz
201112-22:07:40,902 nipype.interface INFO:
stderr 2020-11-12T22:07:40.902571:++ Forming automask
201112-22:07:40,905 nipype.interface INFO:
stderr 2020-11-12T22:07:40.905907: + Fixed clip level = 434.580750
201112-22:07:40,911 nipype.interface INFO:
stderr 2020-11-12T22:07:40.911275: + Used gradual clip level = 388.892303 .. 504.911438
201112-22:07:40,911 nipype.interface INFO:
stderr 2020-11-12T22:07:40.911488: + Number voxels above clip level = 25946
201112-22:07:40,911 nipype.interface INFO:
stderr 2020-11-12T22:07:40.911649: + Clustering voxels ...
201112-22:07:40,912 nipype.interface INFO:
stderr 2020-11-12T22:07:40.912689: + Largest cluster has 25937 voxels
201112-22:07:40,914 nipype.interface INFO:
stderr 2020-11-12T22:07:40.913982: + Clustering voxels ...
201112-22:07:40,915 nipype.interface INFO:
stderr 2020-11-12T22:07:40.915017: + Largest cluster has 25462 voxels
201112-22:07:40,918 nipype.interface INFO:
stderr 2020-11-12T22:07:40.918398: + Filled 761 voxels in small holes; now have 26223 voxels
201112-22:07:40,920 nipype.interface INFO:
stderr 2020-11-12T22:07:40.920634: + Filled 4 voxels in large holes; now have 26227 voxels
201112-22:07:40,921 nipype.interface INFO:
stderr 2020-11-12T22:07:40.921819: + Clustering voxels ...
201112-22:07:40,922 nipype.interface INFO:
stderr 2020-11-12T22:07:40.922839: + Largest cluster has 26225 voxels
201112-22:07:40,923 nipype.interface INFO:
stderr 2020-11-12T22:07:40.923077: + Clustering non-brain voxels ...
201112-22:07:40,923 nipype.interface INFO:
stderr 2020-11-12T22:07:40.923224: + Clustering voxels ...
201112-22:07:40,926 nipype.interface INFO:
stderr 2020-11-12T22:07:40.926364: + Largest cluster has 112983 voxels
201112-22:07:40,926 nipype.interface INFO:
stderr 2020-11-12T22:07:40.926703: + Mask now has 26281 voxels
201112-22:07:40,926 nipype.interface INFO:
stderr 2020-11-12T22:07:40.926860:++ Dilating automask
201112-22:07:40,933 nipype.interface INFO:
stderr 2020-11-12T22:07:40.933974: + Clustering voxels ...
201112-22:07:40,936 nipype.interface INFO:
stderr 2020-11-12T22:07:40.936418: + Largest cluster has 107510 voxels
201112-22:07:40,936 nipype.interface INFO:
stderr 2020-11-12T22:07:40.936751:++ 31754 voxels in the mask [out of 139264: 22.80%]
201112-22:07:40,936 nipype.interface INFO:
stderr 2020-11-12T22:07:40.936935:++ first 11 x-planes are zero [from R]
201112-22:07:40,937 nipype.interface INFO:
stderr 2020-11-12T22:07:40.937099:++ last 8 x-planes are zero [from L]
201112-22:07:40,937 nipype.interface INFO:
stderr 2020-11-12T22:07:40.937247:++ first 5 y-planes are zero [from P]
201112-22:07:40,937 nipype.interface INFO:
stderr 2020-11-12T22:07:40.937396:++ last 7 y-planes are zero [from A]
201112-22:07:40,937 nipype.interface INFO:
stderr 2020-11-12T22:07:40.937534:++ first 1 z-planes are zero [from I]
201112-22:07:40,937 nipype.interface INFO:
stderr 2020-11-12T22:07:40.937677:++ last 3 z-planes are zero [from S]
201112-22:07:40,942 nipype.interface INFO:
stderr 2020-11-12T22:07:40.942507:++ Output dataset ./uni_mask.nii.gz
201112-22:07:40,942 nipype.interface INFO:
stderr 2020-11-12T22:07:40.942680:++ applying mask to original data
201112-22:07:40,943 nipype.interface INFO:
stderr 2020-11-12T22:07:40.943347:++ Writing masked data
201112-22:07:40,955 nipype.interface INFO:
stderr 2020-11-12T22:07:40.955749:++ Output dataset ./uni_masked.nii.gz
201112-22:07:40,956 nipype.interface INFO:
stderr 2020-11-12T22:07:40.956211:++ CPU time = 0.000000 sec
201112-22:07:41,100 nipype.workflow INFO:
[Node] Finished "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".
201112-22:07:41,102 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".
201112-22:07:41,109 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask.nii.gz -mul /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/uni_mask.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask_maths.nii.gz
201112-22:07:41,506 nipype.workflow INFO:
[Node] Finished "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".
201112-22:07:41,508 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".
201112-22:07:41,517 nipype.workflow INFO:
[Node] Running "cal_DVARS" ("CPAC.utils.interfaces.function.Function")
201112-22:07:42,344 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.cal_DVARS".
201112-22:07:42,346 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".
201112-22:07:42,354 nipype.workflow INFO:
[Node] Running "func_extract_brain" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf.nii.gz -b /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_tstat_brain_mask_maths.nii.gz -expr "a*b" -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc.nii.gz
201112-22:07:42,598 nipype.interface INFO:
stderr 2020-11-12T22:07:42.598552:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:07:42,598 nipype.interface INFO:
stderr 2020-11-12T22:07:42.598870:++ Authored by: A cast of thousands
201112-22:07:45,286 nipype.interface INFO:
stderr 2020-11-12T22:07:45.286101:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc.nii.gz
201112-22:07:45,456 nipype.workflow INFO:
[Node] Finished "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".
201112-22:07:45,458 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".
201112-22:07:45,465 nipype.workflow INFO:
[Node] Running "func_normalize" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc.nii.gz -ing 10000 /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc_maths.nii.gz -odt float
201112-22:07:47,507 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_normalize".
201112-22:07:47,509 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".
201112-22:07:47,515 nipype.workflow INFO:
[Node] Running "func_mask_normalize" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc_maths.nii.gz -Tmin -bin /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mask_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc_maths_maths.nii.gz -odt char
201112-22:07:48,522 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mask_normalize".
201112-22:07:48,523 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".
201112-22:07:48,529 nipype.workflow INFO:
[Node] Running "func_mean" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc_tstat.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mean/sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc.nii.gz
201112-22:07:48,770 nipype.interface INFO:
stderr 2020-11-12T22:07:48.770841:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:07:48,771 nipype.interface INFO:
stderr 2020-11-12T22:07:48.771240:++ Authored by: KR Hammett & RW Cox
201112-22:07:49,66 nipype.interface INFO:
stderr 2020-11-12T22:07:49.066342:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_resample_mcf_calc_tstat.nii.gz
201112-22:07:49,236 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean".
201112-22:07:49,237 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".
201112-22:07:49,245 nipype.workflow INFO:
[Node] Running "norm_motion_params" ("CPAC.utils.interfaces.function.Function")
201112-22:07:49,479 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.norm_motion_params".
201112-22:07:49,480 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".
201112-22:07:49,486 nipype.workflow INFO:
[Node] Running "motion_plot" ("CPAC.utils.interfaces.function.Function")
201112-22:07:50,105 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.qc_motion_0.motion_plot".
201112-22:07:50,106 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".
201112-22:07:50,113 nipype.workflow INFO:
[Node] Running "sinker_0_qc___movement_trans_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:50,324 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
201112-22:07:50,340 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_trans_plot".
201112-22:07:50,342 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".
201112-22:07:50,349 nipype.workflow INFO:
[Node] Running "sinker_0_qc___movement_rot_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:50,565 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
201112-22:07:50,582 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_qc___movement_rot_plot".
201112-22:07:50,583 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".
201112-22:07:50,591 nipype.workflow INFO:
[Node] Running "calc_motion_parameters" ("CPAC.utils.interfaces.function.Function")
201112-22:07:50,824 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_motion_parameters".
201112-22:07:50,826 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".
201112-22:07:50,833 nipype.workflow INFO:
[Node] Running "sinker_0_motion_params" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:51,63 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_params".
201112-22:07:51,64 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".
201112-22:07:51,69 nipype.workflow INFO:
[Node] Running "calculate_FD" ("CPAC.utils.interfaces.function.Function")
201112-22:07:51,302 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calculate_FD".
201112-22:07:51,303 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".
201112-22:07:51,310 nipype.workflow INFO:
[Node] Running "sinker_0_frame_wise_displacement_power" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:51,541 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_frame_wise_displacement_power".
201112-22:07:51,543 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".
201112-22:07:51,549 nipype.workflow INFO:
[Node] Running "calc_power_parameters" ("CPAC.utils.interfaces.function.Function")
201112-22:07:51,782 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.calc_power_parameters".
201112-22:07:51,784 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".
201112-22:07:51,791 nipype.workflow INFO:
[Node] Running "sinker_0_power_params" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:52,23 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_power_params".
201112-22:07:52,25 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".
201112-22:07:52,33 nipype.workflow INFO:
[Node] Running "sinker_0_movement_parameters" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:07:52,263 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_movement_parameters".
201112-22:07:52,265 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".
201112-22:07:52,272 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-tgng_run-2_bold_calc_despike.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/func_despiked_0/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:07:52,661 nipype.interface INFO:
stderr 2020-11-12T22:07:52.661333:++ 3dDespike: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:07:52,661 nipype.interface INFO:
stderr 2020-11-12T22:07:52.661699:++ Authored by: RW Cox
201112-22:07:52,675 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
201112-22:07:52,675 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: such as /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/func_despiked_0/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz,
201112-22:07:52,675 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: or viewing/combining it with volumes of differing obliquity,
201112-22:07:52,675 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: you should consider running:
201112-22:07:52,675 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: 3dWarp -deoblique
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: on this and other oblique datasets in the same session.
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.675320: See 3dWarp -help for details.
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.676273:++ Oblique dataset:/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/func_despiked_0/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz is 28.699991 degrees from plumb.
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.676479:++ Input dataset is in short format, but output will be in float format
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.676652:++ ignoring first 0 time points, using last 130
201112-22:07:52,676 nipype.interface INFO:
stderr 2020-11-12T22:07:52.676822:++ using 130 time points => -corder 4
201112-22:07:52,677 nipype.interface INFO:
stderr 2020-11-12T22:07:52.677005:++ Loading dataset /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/func_despiked_0/sub-206_ses-1_task-tgng_run-2_bold_calc.nii.gz
201112-22:07:53,139 nipype.interface INFO:
stderr 2020-11-12T22:07:53.139454:++ 30052 voxels in the automask [out of 139264 in dataset]
201112-22:07:53,145 nipype.interface INFO:
stderr 2020-11-12T22:07:53.145127:++ 53226 voxels in the dilated automask [out of 139264 in dataset]
201112-22:07:53,156 nipype.interface INFO:
stderr 2020-11-12T22:07:53.156262:++ Procesing time series with OLD model fit algorithm
201112-22:07:53,156 nipype.interface INFO:
stderr 2020-11-12T22:07:53.156443:++ smash edit thresholds: 3.1 .. 5.0 MADs
201112-22:07:53,156 nipype.interface INFO:
stderr 2020-11-12T22:07:53.156602: + [ 3.457% .. 0.072% of normal distribution]
201112-22:07:53,157 nipype.interface INFO:
stderr 2020-11-12T22:07:53.157783: + [ 8.839% .. 3.125% of Laplace distribution]
201112-22:07:53,158 nipype.interface INFO:
stderr 2020-11-12T22:07:53.158028:++ start OpenMP thread #0
201112-22:07:57,838 nipype.interface INFO:
stderr 2020-11-12T22:07:57.838584:.........................
201112-22:07:57,839 nipype.interface INFO:
stderr 2020-11-12T22:07:57.839054:++ Elapsed despike time = 4s 681ms
201112-22:07:57,839 nipype.interface INFO:
stderr 2020-11-12T22:07:57.839203:
201112-22:07:57,840 nipype.interface INFO:
stderr 2020-11-12T22:07:57.840058:++ FINAL: 6919380 data points, 428914 edits [6.199%], 42629 big edits [0.616%]
201112-22:08:01,475 nipype.interface INFO:
stderr 2020-11-12T22:08:01.475144:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike.nii.gz
201112-22:08:01,664 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_despiked_0".
201112-22:08:01,666 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".
201112-22:08:01,675 nipype.interface WARNING:
Passing a file prefixed by "@" will be deprecated; please use the `slice_timing` input
201112-22:08:01,676 nipype.workflow INFO:
[Node] Running "slice_timing" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command:
3dTshift -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz -tpattern @/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/scan_params_0/tpattern.txt -TR 2.0s /outputs/tmp/resting_preproc_sub-206_ses-1/func_slice_timing_correction_0/_scan_tgng_run-2/slice_timing/sub-206_ses-1_task-tgng_run-2_bold_calc_despike.nii.gz
201112-22:08:01,889 nipype.interface WARNING:
Passing a file prefixed by "@" will be deprecated; please use the `slice_timing` input
201112-22:08:02,108 nipype.interface INFO:
stderr 2020-11-12T22:08:02.108618:++ 3dTshift: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:08:02,125 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
201112-22:08:02,125 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: such as /outputs/tmp/resting_preproc_sub-206_ses-1/func_slice_timing_correction_0/_scan_tgng_run-2/slice_timing/sub-206_ses-1_task-tgng_run-2_bold_calc_despike.nii.gz,
201112-22:08:02,125 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: or viewing/combining it with volumes of differing obliquity,
201112-22:08:02,126 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: you should consider running:
201112-22:08:02,126 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: 3dWarp -deoblique
201112-22:08:02,126 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: on this and other oblique datasets in the same session.
201112-22:08:02,126 nipype.interface INFO:
stderr 2020-11-12T22:08:02.125660: See 3dWarp -help for details.
201112-22:08:02,126 nipype.interface INFO:
stderr 2020-11-12T22:08:02.126485:++ Oblique dataset:/outputs/tmp/resting_preproc_sub-206_ses-1/func_slice_timing_correction_0/_scan_tgng_run-2/slice_timing/sub-206_ses-1_task-tgng_run-2_bold_calc_despike.nii.gz is 28.699991 degrees from plumb.
201112-22:08:06,283 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_slice_timing_correction_0.slice_timing".
201112-22:08:06,285 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".
201112-22:08:06,345 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_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz
201112-22:08:06,598 nipype.interface INFO:
stderr 2020-11-12T22:08:06.597967:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:08:06,598 nipype.interface INFO:
stderr 2020-11-12T22:08:06.598379:++ Authored by: RW Cox
201112-22:08:06,601 nipype.interface INFO:
stderr 2020-11-12T22:08:06.601322:++ Processing AFNI dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz
201112-22:08:06,602 nipype.interface INFO:
stderr 2020-11-12T22:08:06.601996: + deoblique
201112-22:08:06,602 nipype.interface INFO:
stderr 2020-11-12T22:08:06.602201: + loading and re-writing dataset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz (/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_deoblique/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz in NIFTI storage)
201112-22:08:08,614 nipype.interface INFO:
stderr 2020-11-12T22:08:08.614640:++ 3drefit processed 1 datasets
201112-22:08:08,787 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_deoblique".
201112-22:08:08,789 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".
201112-22:08:08,796 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-tgng_run-2_bold_calc_despike_tshift_resample.nii.gz -inset /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift.nii.gz
201112-22:08:11,434 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_reorient".
201112-22:08:11,435 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".
201112-22:08:11,442 nipype.workflow INFO:
[Node] Running "func_get_mean_RPI" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_tstat.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_RPI/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample.nii.gz
201112-22:08:11,691 nipype.interface INFO:
stderr 2020-11-12T22:08:11.691110:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:08:11,691 nipype.interface INFO:
stderr 2020-11-12T22:08:11.691423:++ Authored by: KR Hammett & RW Cox
201112-22:08:12,282 nipype.interface INFO:
stderr 2020-11-12T22:08:12.282352:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_tstat.nii.gz
201112-22:08:12,431 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI".
201112-22:08:12,432 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".
201112-22:08:12,439 nipype.workflow INFO:
[Node] Running "func_generate_ref" ("nipype.interfaces.afni.preprocess.Volreg"), a CommandLine Interface with command:
3dvolreg -twopass -Fourier -1Dfile sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample.1D -1Dmatrix_save sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample.aff12.1D -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_volreg.nii.gz -base /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_RPI/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_tstat.nii.gz -zpad 4 -maxdisp1D sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_md.1D /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_generate_ref/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample.nii.gz
201112-22:08:12,681 nipype.interface INFO:
stderr 2020-11-12T22:08:12.681077:++ 3dvolreg: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:08:12,681 nipype.interface INFO:
stderr 2020-11-12T22:08:12.681378:++ Authored by: RW Cox
201112-22:08:12,688 nipype.interface INFO:
stderr 2020-11-12T22:08:12.688681:++ Coarse del was 10, replaced with 3
201112-22:09:58,700 nipype.interface INFO:
stderr 2020-11-12T22:09:58.700488:++ Max displacement in automask = 0.43 (mm) at sub-brick 76
201112-22:09:58,701 nipype.interface INFO:
stderr 2020-11-12T22:09:58.701306:++ Max delta displ in automask = 0.55 (mm) at sub-brick 73
201112-22:10:03,410 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_generate_ref".
201112-22:10:03,412 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".
201112-22:10:03,420 nipype.workflow INFO:
[Node] Running "func_get_mean_motion" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_volreg_tstat.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_motion/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_volreg.nii.gz
201112-22:10:03,669 nipype.interface INFO:
stderr 2020-11-12T22:10:03.669375:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:10:03,669 nipype.interface INFO:
stderr 2020-11-12T22:10:03.669685:++ Authored by: KR Hammett & RW Cox
201112-22:10:04,462 nipype.interface INFO:
stderr 2020-11-12T22:10:04.462383:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_volreg_tstat.nii.gz
201112-22:10:04,611 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_motion".
201112-22:10:04,613 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".
201112-22:10:04,621 nipype.workflow INFO:
[Node] Running "func_motion_correct_mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_reorient/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample.nii.gz -out /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_motion_correct_mcflirt/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf.nii.gz -reffile /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_get_mean_motion/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_volreg_tstat.nii.gz -mats -plots -rmsabs -rmsrel
201112-22:10:25,717 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt".
201112-22:10:25,731 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".
201112-22:10:25,740 nipype.workflow INFO:
[Node] Running "sinker_0_motion_correct" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:10:25,970 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_correct".
201112-22:10:25,971 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".
201112-22:10:25,980 nipype.workflow INFO:
[Node] Running "func_mean_skull" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf.nii.gz
201112-22:10:26,232 nipype.interface INFO:
stderr 2020-11-12T22:10:26.231803:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:10:26,232 nipype.interface INFO:
stderr 2020-11-12T22:10:26.232432:++ Authored by: KR Hammett & RW Cox
201112-22:10:26,854 nipype.interface INFO:
stderr 2020-11-12T22:10:26.854209:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat.nii.gz
201112-22:10:27,4 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull".
201112-22:10:27,5 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".
201112-22:10:27,11 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain.nii.gz -f 0.20 -m
201112-22:10:28,817 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass".
201112-22:10:28,819 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".
201112-22:10:28,826 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_dil.nii.gz
201112-22:10:29,453 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate".
201112-22:10:29,455 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".
201112-22:10:29,462 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain.nii.gz -mas /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_dil.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_masked.nii.gz
201112-22:10:29,864 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_mask".
201112-22:10:29,866 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".
201112-22:10:29,873 nipype.workflow INFO:
[Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command:
3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_masked.nii.gz
201112-22:10:30,120 nipype.interface INFO:
stderr 2020-11-12T22:10:30.120671:++ 3dUnifize: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:39,359 nipype.interface INFO:
stderr 2020-11-12T22:11:39.359593: + Pre-processing: IAV..UW[s4177]Im
201112-22:11:39,374 nipype.interface INFO:
stderr 2020-11-12T22:11:39.374339:++ Output dataset ./uni.nii.gz
201112-22:11:39,374 nipype.interface INFO:
stderr 2020-11-12T22:11:39.374618:++ ===== Elapsed = 69.3 sec
201112-22:11:39,547 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.unifize".
201112-22:11:39,557 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".
201112-22:11:39,566 nipype.workflow INFO:
[Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command:
3dAutomask -apply_prefix uni_masked.nii.gz -dilate 1 -prefix uni_mask.nii.gz /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/uni.nii.gz
201112-22:11:39,816 nipype.interface INFO:
stderr 2020-11-12T22:11:39.816714:++ 3dAutomask: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:39,817 nipype.interface INFO:
stderr 2020-11-12T22:11:39.817302:++ Authored by: Emperor Zhark
201112-22:11:39,820 nipype.interface INFO:
stderr 2020-11-12T22:11:39.820098:++ Loading dataset /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/uni.nii.gz
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ Forming automask
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Fixed clip level = 434.198334
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Used gradual clip level = 387.472900 .. 506.786133
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Number voxels above clip level = 25928
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering voxels ...
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Largest cluster has 25919 voxels
201112-22:11:39,879 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering voxels ...
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Largest cluster has 25441 voxels
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Filled 765 voxels in small holes; now have 26206 voxels
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Filled 4 voxels in large holes; now have 26210 voxels
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering voxels ...
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Largest cluster has 26208 voxels
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering non-brain voxels ...
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering voxels ...
201112-22:11:39,880 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Largest cluster has 112992 voxels
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Mask now has 26272 voxels
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ Dilating automask
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Clustering voxels ...
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855: + Largest cluster has 107510 voxels
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ 31754 voxels in the mask [out of 139264: 22.80%]
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ first 11 x-planes are zero [from R]
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ last 8 x-planes are zero [from L]
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ first 5 y-planes are zero [from P]
201112-22:11:39,881 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ last 7 y-planes are zero [from A]
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ first 1 z-planes are zero [from I]
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ last 3 z-planes are zero [from S]
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ Output dataset ./uni_mask.nii.gz
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ applying mask to original data
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ Writing masked data
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ Output dataset ./uni_masked.nii.gz
201112-22:11:39,882 nipype.interface INFO:
stderr 2020-11-12T22:11:39.878855:++ CPU time = 0.000000 sec
201112-22:11:40,30 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_second_pass".
201112-22:11:40,31 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".
201112-22:11:40,40 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask.nii.gz -mul /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/uni_mask.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths.nii.gz
201112-22:11:40,433 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.combine_masks".
201112-22:11:40,435 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".
201112-22:11:40,440 nipype.workflow INFO:
[Node] Running "GlobalSignal_merge_masks" ("nipype.interfaces.utility.base.Merge")
201112-22:11:40,670 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_merge_masks".
201112-22:11:40,672 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".
201112-22:11:40,680 nipype.workflow INFO:
[Node] Running "GlobalSignal_union_masks" ("CPAC.utils.interfaces.masktool.MaskTool"), a CommandLine Interface with command:
3dmask_tool -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths_mask.nii.gz -input /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths.nii.gz
201112-22:11:41,88 nipype.interface INFO:
stderr 2020-11-12T22:11:41.088289:++ no -frac option: defaulting to -union
201112-22:11:41,88 nipype.interface INFO:
stderr 2020-11-12T22:11:41.088609:++ processing 1 input dataset(s), NN=2...
201112-22:11:41,88 nipype.interface INFO:
stderr 2020-11-12T22:11:41.088770:++ padding all datasets by 0 (for dilations)
201112-22:11:41,101 nipype.interface INFO:
stderr 2020-11-12T22:11:41.101498:++ frac 0 over 1 volumes gives min count 0
201112-22:11:41,101 nipype.interface INFO:
stderr 2020-11-12T22:11:41.101882:++ voxel limits: 0 clipped, 31714 survived, 107550 were zero
201112-22:11:41,102 nipype.interface INFO:
stderr 2020-11-12T22:11:41.102061:++ writing result sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths_mask.nii.gz...
201112-22:11:41,108 nipype.interface INFO:
stderr 2020-11-12T22:11:41.108299:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths_mask.nii.gz
201112-22:11:41,253 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_union_masks".
201112-22:11:41,254 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".
201112-22:11:41,263 nipype.workflow INFO:
[Node] Running "sinker_0_functional_brain_mask" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:41,498 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_brain_mask".
201112-22:11:41,500 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".
201112-22:11:41,505 nipype.workflow INFO:
[Node] Running "functional_brain_mask_derivative_0" ("CPAC.utils.interfaces.function.Function")
201112-22:11:41,719 nipype.workflow INFO:
[Node] Setting-up "functional_brain_mask_derivative" in "/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/functional_brain_mask_derivative_0/functional_brain_mask_derivative".
201112-22:11:41,725 nipype.workflow INFO:
[Node] Running "functional_brain_mask_derivative" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths_resample.nii.gz -rmode Cu -dxyz 2.000000 2.000000 2.000000 -inset /outputs/tmp/resting_preproc_sub-206_ses-1/_scan_tgng_run-2/functional_brain_mask_derivative_0/functional_brain_mask_derivative/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths.nii.gz
201112-22:11:42,211 nipype.workflow INFO:
[Node] Finished "functional_brain_mask_derivative".
201112-22:11:42,227 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.functional_brain_mask_derivative_0".
201112-22:11:42,229 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".
201112-22:11:42,239 nipype.workflow INFO:
[Node] Running "func_extract_brain" ("nipype.interfaces.afni.utils.Calc"), a CommandLine Interface with command:
3dcalc -a /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_motion_correct_mcflirt/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf.nii.gz -b /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths.nii.gz -expr "a*b" -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc.nii.gz
201112-22:11:42,483 nipype.interface INFO:
stderr 2020-11-12T22:11:42.483310:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:42,483 nipype.interface INFO:
stderr 2020-11-12T22:11:42.483637:++ Authored by: A cast of thousands
201112-22:11:45,464 nipype.interface INFO:
stderr 2020-11-12T22:11:45.463909:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc.nii.gz
201112-22:11:45,637 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain".
201112-22:11:45,638 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".
201112-22:11:45,645 nipype.workflow INFO:
[Node] Running "func_normalize" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc.nii.gz -ing 10000 /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths.nii.gz -odt float
201112-22:11:47,781 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_normalize".
201112-22:11:47,783 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".
201112-22:11:47,790 nipype.workflow INFO:
[Node] Running "GlobalSignal_mean" ("nipype.interfaces.afni.preprocess.ROIStats"), a CommandLine Interface with command:
3dROIstats -mask /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths_mask.nii.gz -1Dformat /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths.nii.gz
201112-22:11:48,840 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.GlobalSignal_mean".
201112-22:11:48,841 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".
201112-22:11:48,847 nipype.workflow INFO:
[Node] Running "functional_mean" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths_tstat.nii.gz /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths.nii.gz
201112-22:11:49,89 nipype.interface INFO:
stderr 2020-11-12T22:11:49.089482:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:49,89 nipype.interface INFO:
stderr 2020-11-12T22:11:49.089876:++ Authored by: KR Hammett & RW Cox
201112-22:11:49,659 nipype.interface INFO:
stderr 2020-11-12T22:11:49.659100:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths_tstat.nii.gz
201112-22:11:49,834 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.nuisance_regressor_0_0.functional_mean".
201112-22:11:49,835 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".
201112-22:11:49,843 nipype.workflow INFO:
[Node] Running "std_dev" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -stdev -mask /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/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_tstat_brain_mask_maths.nii.gz -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths_tstat.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/qc_snr_0/_scan_tgng_run-2/std_dev/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths.nii.gz
201112-22:11:50,82 nipype.interface INFO:
stderr 2020-11-12T22:11:50.082621:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:50,82 nipype.interface INFO:
stderr 2020-11-12T22:11:50.082930:++ Authored by: KR Hammett & RW Cox
201112-22:11:50,591 nipype.interface INFO:
stderr 2020-11-12T22:11:50.591296:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths_tstat.nii.gz
201112-22:11:50,742 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.qc_snr_0.std_dev".
201112-22:11:50,744 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".
201112-22:11:50,751 nipype.workflow INFO:
[Node] Running "sinker_0_functional_preprocessed" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:50,982 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed".
201112-22:11:50,984 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".
201112-22:11:50,991 nipype.workflow INFO:
[Node] Running "func_mask_normalize" ("nipype.interfaces.fsl.utils.ImageMaths"), a CommandLine Interface with command:
fslmaths /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths.nii.gz -Tmin -bin /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mask_normalize/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_maths_maths.nii.gz -odt char
201112-22:11:52,5 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mask_normalize".
201112-22:11:52,7 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".
201112-22:11:52,14 nipype.workflow INFO:
[Node] Running "sinker_0_functional_preprocessed_mask" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:52,253 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_functional_preprocessed_mask".
201112-22:11:52,254 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".
201112-22:11:52,261 nipype.workflow INFO:
[Node] Running "func_mean" ("nipype.interfaces.afni.utils.TStat"), a CommandLine Interface with command:
3dTstat -mean -prefix sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_tstat.nii.gz /outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_fsl_afni_mean_mcflirt_0/_scan_tgng_run-2/func_mean/sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc.nii.gz
201112-22:11:52,515 nipype.interface INFO:
stderr 2020-11-12T22:11:52.515314:++ 3dTstat: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:52,515 nipype.interface INFO:
stderr 2020-11-12T22:11:52.515808:++ Authored by: KR Hammett & RW Cox
201112-22:11:53,81 nipype.interface INFO:
stderr 2020-11-12T22:11:53.081916:++ Output dataset ./sub-206_ses-1_task-tgng_run-2_bold_calc_despike_tshift_resample_mcf_calc_tstat.nii.gz
201112-22:11:53,272 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.func_mean".
201112-22:11:53,273 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".
201112-22:11:53,282 nipype.workflow INFO:
[Node] Running "sinker_0_mean_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:53,523 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_mean_functional".
201112-22:11:53,525 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".
201112-22:11:53,534 nipype.workflow INFO:
[Node] Running "norm_motion_params" ("CPAC.utils.interfaces.function.Function")
201112-22:11:53,776 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_preproc_fsl_afni_mean_mcflirt_0.norm_motion_params".
201112-22:11:53,778 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".
201112-22:11:53,787 nipype.workflow INFO:
[Node] Running "sinker_0_slice_time_corrected" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:54,25 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_slice_time_corrected".
201112-22:11:54,27 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".
201112-22:11:54,39 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:11:54,389 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:11:54,391 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".
201112-22:11:54,426 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:11:54,670 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:11:54,681 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".
201112-22:11:54,712 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:11:54,948 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:11:54,960 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".
201112-22:11:54,969 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:11:55,203 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:11:55,205 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".
201112-22:11:55,216 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:11:55,451 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:11:55,454 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".
201112-22:11:55,491 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:11:55,737 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:11:55,748 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".
201112-22:11:55,753 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:11:56,88 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:11:56,91 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".
201112-22:11:56,102 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:11:56,342 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:11:56,343 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".
201112-22:11:56,351 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
201112-22:11:56,603 nipype.interface INFO:
stderr 2020-11-12T22:11:56.603655:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:11:56,604 nipype.interface INFO:
stderr 2020-11-12T22:11:56.604104:++ Authored by: A cast of thousands
201112-22:12:02,741 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_tgng_run-1/func_drop_trs)
201112-22:12:02,754 nipype.workflow ERROR:
Node func_drop_trs.b6 failed to run on host node167.
201112-22:12:02,761 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221202-av2902-func_drop_trs.b6-1ba6f5fc-fc69-4ced-be0b-018784f1ac0b.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
201112-22:12:02,766 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".
201112-22:12:02,777 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:03,118 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:03,120 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".
201112-22:12:03,155 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:03,393 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:03,404 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".
201112-22:12:03,438 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:03,675 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:03,686 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".
201112-22:12:03,696 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:03,933 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:03,936 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".
201112-22:12:03,947 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:04,182 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:04,184 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".
201112-22:12:04,215 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:04,454 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:04,464 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".
201112-22:12:04,470 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:04,785 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:04,786 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".
201112-22:12:04,795 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:05,30 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:05,31 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".
201112-22:12:05,39 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
201112-22:12:05,287 nipype.interface INFO:
stderr 2020-11-12T22:12:05.287596:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:05,288 nipype.interface INFO:
stderr 2020-11-12T22:12:05.288937:++ Authored by: A cast of thousands
201112-22:12:08,213 nipype.interface INFO:
stderr 2020-11-12T22:12:08.213724:** ERROR (nifti_image_write_hdr_img2): cannot open output file './sub-206_ses-1_task-rest_run-1_bold_calc.nii.gz'
201112-22:12:08,403 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_rest_run-1/func_drop_trs)
201112-22:12:08,416 nipype.workflow ERROR:
Node func_drop_trs.b5 failed to run on host node167.
201112-22:12:08,419 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221208-av2902-func_drop_trs.b5-6f83fea8-bb92-4e5c-b7b3-63e795943b4b.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
201112-22:12:08,425 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".
201112-22:12:08,434 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:08,803 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:08,805 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".
201112-22:12:08,838 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:09,74 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:09,84 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".
201112-22:12:09,119 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:09,354 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:09,365 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".
201112-22:12:09,373 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:09,604 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:09,608 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".
201112-22:12:09,619 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:09,852 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:09,855 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".
201112-22:12:09,886 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:10,123 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:10,133 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".
201112-22:12:10,139 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:10,438 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:10,440 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".
201112-22:12:10,449 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:10,683 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:10,684 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".
201112-22:12:10,692 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
201112-22:12:10,938 nipype.interface INFO:
stderr 2020-11-12T22:12:10.938394:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:10,938 nipype.interface INFO:
stderr 2020-11-12T22:12:10.938769:++ Authored by: A cast of thousands
201112-22:12:17,218 nipype.interface INFO:
stderr 2020-11-12T22:12:17.217879:++ Output dataset ./sub-206_ses-1_task-ms_run-1_bold_calc.nii.gz
201112-22:12:17,405 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_ms_run-1/func_drop_trs)
201112-22:12:17,420 nipype.workflow ERROR:
Node func_drop_trs.b4 failed to run on host node167.
201112-22:12:17,425 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221217-av2902-func_drop_trs.b4-81b793e7-a7c1-4b81-b388-3697e3ab4114.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
201112-22:12:17,432 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_ms_run-1/sinker_0_raw_functional".
201112-22:12:17,443 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:17,795 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:17,796 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".
201112-22:12:17,831 nipype.workflow INFO:
[Node] Running "check_func_scan" ("CPAC.utils.interfaces.function.Function")
201112-22:12:18,64 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan".
201112-22:12:18,74 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".
201112-22:12:18,104 nipype.workflow INFO:
[Node] Running "select_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:18,336 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params".
201112-22:12:18,348 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".
201112-22:12:18,356 nipype.workflow INFO:
[Node] Running "s3_scan_params" ("CPAC.utils.interfaces.function.Function")
201112-22:12:18,589 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params".
201112-22:12:18,594 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".
201112-22:12:18,605 nipype.workflow INFO:
[Node] Running "scan_params_0" ("CPAC.utils.interfaces.function.Function")
201112-22:12:18,839 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.scan_params_0".
201112-22:12:18,842 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".
201112-22:12:18,875 nipype.workflow INFO:
[Node] Running "selectrest" ("CPAC.utils.interfaces.function.Function")
201112-22:12:19,116 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.selectrest".
201112-22:12:19,126 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".
201112-22:12:19,131 nipype.workflow INFO:
[Node] Running "check_for_s3" ("CPAC.utils.interfaces.function.Function")
201112-22:12:19,472 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3".
201112-22:12:19,473 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".
201112-22:12:19,481 nipype.workflow INFO:
[Node] Running "func_get_idx" ("nipype.interfaces.utility.wrappers.Function")
201112-22:12:19,714 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx".
201112-22:12:19,716 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".
201112-22:12:19,723 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-3_bold.nii.gz[0..98] -expr "a" -prefix sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:19,968 nipype.interface INFO:
stderr 2020-11-12T22:12:19.968850:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:19,969 nipype.interface INFO:
stderr 2020-11-12T22:12:19.969219:++ Authored by: A cast of thousands
201112-22:12:24,388 nipype.interface INFO:
stderr 2020-11-12T22:12:24.388686:++ Output dataset ./sub-206_ses-1_task-matching_run-3_bold_calc.nii.gz
201112-22:12:24,567 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs".
201112-22:12:24,570 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".
201112-22:12:24,615 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
201112-22:12:24,892 nipype.interface INFO:
stderr 2020-11-12T22:12:24.892357:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:24,892 nipype.interface INFO:
stderr 2020-11-12T22:12:24.892707:++ Authored by: RW Cox
201112-22:12:24,913 nipype.interface INFO:
stderr 2020-11-12T22:12:24.913840:++ 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
201112-22:12:24,915 nipype.interface INFO:
stderr 2020-11-12T22:12:24.915049: + deoblique
201112-22:12:24,916 nipype.interface INFO:
stderr 2020-11-12T22:12:24.916284: + 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)
201112-22:12:29,224 nipype.interface INFO:
stderr 2020-11-12T22:12:29.224349:++ 3drefit processed 1 datasets
201112-22:12:29,409 nipype.workflow WARNING:
[Node] Error on "resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique" (/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique)
201112-22:12:29,414 nipype.workflow ERROR:
Node func_deoblique.b3 failed to run on host node167.
201112-22:12:29,417 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221229-av2902-func_deoblique.b3-74dec37b-13e3-4f89-8743-99af819ad22e.pklz
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 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/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 475, in run
os.remove(hashfile_unfinished)
FileNotFoundError: [Errno 2] No such file or directory: '/outputs/tmp/resting_preproc_sub-206_ses-1/func_preproc_before_stc_fsl_afni_mean_mcflirt_0/_scan_matching_run-3/func_deoblique/_0x4a1bbe3ab9772ece9e57b3eb4dcb5332_unfinished.json'
201112-22:12:29,423 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".
201112-22:12:29,500 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
201112-22:12:29,756 nipype.interface INFO:
stderr 2020-11-12T22:12:29.756176:++ 3dDespike: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:29,756 nipype.interface INFO:
stderr 2020-11-12T22:12:29.756605:++ Authored by: RW Cox
201112-22:12:29,760 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080:[7m*+ WARNING:[0m If you are performing spatial transformations on an oblique dset,
201112-22:12:29,760 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: 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,
201112-22:12:29,761 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: or viewing/combining it with volumes of differing obliquity,
201112-22:12:29,761 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: you should consider running:
201112-22:12:29,761 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: 3dWarp -deoblique
201112-22:12:29,761 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: on this and other oblique datasets in the same session.
201112-22:12:29,761 nipype.interface INFO:
stderr 2020-11-12T22:12:29.760080: See 3dWarp -help for details.
201112-22:12:29,762 nipype.interface INFO:
stderr 2020-11-12T22:12:29.762306:++ 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.
201112-22:12:29,762 nipype.interface INFO:
stderr 2020-11-12T22:12:29.762306:++ Input dataset is in short format, but output will be in float format
201112-22:12:29,762 nipype.interface INFO:
stderr 2020-11-12T22:12:29.762306:++ ignoring first 0 time points, using last 99
201112-22:12:29,762 nipype.interface INFO:
stderr 2020-11-12T22:12:29.762306:++ using 99 time points => -corder 3
201112-22:12:29,763 nipype.interface INFO:
stderr 2020-11-12T22:12:29.762306:++ 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
201112-22:12:30,116 nipype.interface INFO:
stderr 2020-11-12T22:12:30.116563:++ 30000 voxels in the automask [out of 139264 in dataset]
201112-22:12:30,122 nipype.interface INFO:
stderr 2020-11-12T22:12:30.122461:++ 53122 voxels in the dilated automask [out of 139264 in dataset]
201112-22:12:30,130 nipype.interface INFO:
stderr 2020-11-12T22:12:30.130778:++ Procesing time series with OLD model fit algorithm
201112-22:12:30,130 nipype.interface INFO:
stderr 2020-11-12T22:12:30.130966:++ smash edit thresholds: 3.1 .. 5.0 MADs
201112-22:12:30,131 nipype.interface INFO:
stderr 2020-11-12T22:12:30.131126: + [ 3.457% .. 0.072% of normal distribution]
201112-22:12:30,131 nipype.interface INFO:
stderr 2020-11-12T22:12:30.131275: + [ 8.839% .. 3.125% of Laplace distribution]
201112-22:12:30,131 nipype.interface INFO:
stderr 2020-11-12T22:12:30.131431:++ start OpenMP thread #0
201112-22:12:32,920 nipype.interface INFO:
stderr 2020-11-12T22:12:32.919970:........................
201112-22:12:32,920 nipype.interface INFO:
stderr 2020-11-12T22:12:32.920422:++ Elapsed despike time = 2s 789ms
201112-22:12:32,920 nipype.interface INFO:
stderr 2020-11-12T22:12:32.920572:
201112-22:12:32,921 nipype.interface INFO:
stderr 2020-11-12T22:12:32.921282:++ FINAL: 5259078 data points, 338143 edits [6.430%], 35551 big edits [0.676%]
201112-22:12:35,674 nipype.interface INFO:
stderr 2020-11-12T22:12:35.674217:++ Output dataset ./sub-206_ses-1_task-matching_run-3_bold_calc_despike.nii.gz
201112-22:12:35,883 nipype.workflow ERROR:
Node func_despiked_0.b3 failed to run on host node167.
201112-22:12:35,888 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221235-av2902-func_despiked_0.b3-7002bef9-900d-4e9a-90f0-871cb1d19ce0.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/_scan_matching_run-3/func_despiked_0/_0x4773861d5ca71ed1c068df76199f1b87_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/_scan_matching_run-3/func_despiked_0/_0x4773861d5ca71ed1c068df76199f1b87.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/_scan_matching_run-3/func_despiked_0/_0x4773861d5ca71ed1c068df76199f1b87_unfinished.json'
201112-22:12:35,896 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".
201112-22:12:35,976 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:36,348 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:36,351 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".
201112-22:12:36,385 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:36,385 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:36,398 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".
201112-22:12:36,431 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:36,431 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:36,439 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".
201112-22:12:36,465 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:36,465 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:36,469 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".
201112-22:12:36,501 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:36,501 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:36,503 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".
201112-22:12:36,534 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:36,534 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:36,542 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".
201112-22:12:36,566 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:36,566 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:36,568 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".
201112-22:12:36,598 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:36,598 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:36,600 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".
201112-22:12:36,684 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
201112-22:12:36,934 nipype.interface INFO:
stderr 2020-11-12T22:12:36.934300:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:36,934 nipype.interface INFO:
stderr 2020-11-12T22:12:36.934649:++ Authored by: A cast of thousands
201112-22:12:41,236 nipype.interface INFO:
stderr 2020-11-12T22:12:41.236092:++ Output dataset ./sub-206_ses-1_task-matching_run-2_bold_calc.nii.gz
201112-22:12:41,442 nipype.workflow ERROR:
Node func_drop_trs.b2 failed to run on host node167.
201112-22:12:41,444 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221241-av2902-func_drop_trs.b2-afb3559a-fab9-4578-95dd-a6cf37177c42.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_matching_run-2/func_drop_trs/_0x265361140859b18ca308c35671cfd90f_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-2/func_drop_trs/_0x265361140859b18ca308c35671cfd90f.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_matching_run-2/func_drop_trs/_0x265361140859b18ca308c35671cfd90f_unfinished.json'
201112-22:12:41,454 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".
201112-22:12:41,534 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:41,911 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:41,913 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".
201112-22:12:41,948 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:41,948 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:41,979 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".
201112-22:12:42,18 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:42,18 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:42,26 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".
201112-22:12:42,50 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:42,50 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:42,53 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".
201112-22:12:42,83 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:42,83 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:42,86 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".
201112-22:12:42,118 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:42,118 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:42,130 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".
201112-22:12:42,153 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:42,154 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:42,157 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".
201112-22:12:42,187 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:42,187 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:42,189 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".
201112-22:12:42,251 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
201112-22:12:42,499 nipype.interface INFO:
stderr 2020-11-12T22:12:42.499312:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:42,499 nipype.interface INFO:
stderr 2020-11-12T22:12:42.499710:++ Authored by: A cast of thousands
201112-22:12:46,820 nipype.interface INFO:
stderr 2020-11-12T22:12:46.820288:++ Output dataset ./sub-206_ses-1_task-matching_run-1_bold_calc.nii.gz
201112-22:12:47,15 nipype.workflow ERROR:
Node func_drop_trs.b1 failed to run on host node167.
201112-22:12:47,18 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221247-av2902-func_drop_trs.b1-f433c5de-659d-41fd-ae9f-d69e55b67ecd.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_matching_run-1/func_drop_trs/_0xe9db47bf693cb7e3f9a4592e4653433e_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_matching_run-1/func_drop_trs/_0xe9db47bf693cb7e3f9a4592e4653433e.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_matching_run-1/func_drop_trs/_0xe9db47bf693cb7e3f9a4592e4653433e_unfinished.json'
201112-22:12:47,28 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".
201112-22:12:47,107 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:47,481 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:47,482 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".
201112-22:12:47,516 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:47,516 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:47,524 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".
201112-22:12:47,560 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" - collecting precomputed outputs
201112-22:12:47,560 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.select_scan_params" found cached.
201112-22:12:47,568 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".
201112-22:12:47,602 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" - collecting precomputed outputs
201112-22:12:47,602 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.s3_scan_params" found cached.
201112-22:12:47,607 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".
201112-22:12:47,638 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.scan_params_0" - collecting precomputed outputs
201112-22:12:47,639 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.scan_params_0" found cached.
201112-22:12:47,642 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".
201112-22:12:47,677 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" - collecting precomputed outputs
201112-22:12:47,677 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.selectrest" found cached.
201112-22:12:47,690 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".
201112-22:12:47,714 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:12:47,714 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_for_s3" found cached.
201112-22:12:47,716 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".
201112-22:12:47,743 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" - collecting precomputed outputs
201112-22:12:47,743 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.edit_func_0.func_get_idx" found cached.
201112-22:12:47,745 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".
201112-22:12:47,801 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
201112-22:12:48,48 nipype.interface INFO:
stderr 2020-11-12T22:12:48.048625:++ 3dcalc: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:12:48,49 nipype.interface INFO:
stderr 2020-11-12T22:12:48.048995:++ Authored by: A cast of thousands
201112-22:12:54,595 nipype.interface INFO:
stderr 2020-11-12T22:12:54.595439:++ Output dataset ./sub-206_ses-1_task-conditioning_run-1_bold_calc.nii.gz
201112-22:12:54,785 nipype.workflow ERROR:
Node func_drop_trs.b0 failed to run on host node167.
201112-22:12:54,787 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221254-av2902-func_drop_trs.b0-37572eb5-f475-40e4-afef-6f975b21ee35.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_conditioning_run-1/func_drop_trs/_0x0fff5acec6306c0ee680a91c4783fcc4_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/edit_func_0/_scan_conditioning_run-1/func_drop_trs/_0x0fff5acec6306c0ee680a91c4783fcc4.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_conditioning_run-1/func_drop_trs/_0x0fff5acec6306c0ee680a91c4783fcc4_unfinished.json'
201112-22:12:54,797 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".
201112-22:12:54,867 nipype.workflow INFO:
[Node] Running "sinker_0_raw_functional" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:12:55,317 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_raw_functional".
201112-22:12:55,319 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".
201112-22:12:55,351 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" - collecting precomputed outputs
201112-22:12:55,351 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_gather_0.check_func_scan" found cached.
201112-22:12:55,358 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".
201112-22:12:55,391 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" - collecting precomputed outputs
201112-22:12:55,391 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" found cached.
201112-22:12:55,393 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".
201112-22:12:55,420 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" - collecting precomputed outputs
201112-22:12:55,420 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.roi_dataflow_0.check_for_s3" found cached.
201112-22:12:55,422 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".
201112-22:12:55,514 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
201112-22:13:04,872 nipype.workflow ERROR:
Node lap_tmpl failed to run on host node167.
201112-22:13:04,876 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221304-av2902-lap_tmpl-1950dcd9-381c-41a8-8515-db864a7f96f1.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/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/lap_tmpl/_0xdff2077e42c097e3a3c18048e6f4551b_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/lap_tmpl/_0xdff2077e42c097e3a3c18048e6f4551b.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/anat_preproc_niworkflows_ants_0/anat_preproc_niworkflows_ants_0_skullstrip/anat_skullstrip_ants/lap_tmpl/_0xdff2077e42c097e3a3c18048e6f4551b_unfinished.json'
201112-22:13:04,888 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".
201112-22:13:04,919 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.res_tmpl" - collecting precomputed outputs
201112-22:13:04,920 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.res_tmpl" found cached.
201112-22:13:04,922 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".
201112-22:13:04,954 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.anat_gather_0.check_for_s3" - collecting precomputed outputs
201112-22:13:04,954 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.anat_gather_0.check_for_s3" found cached.
201112-22:13:04,957 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".
201112-22:13:05,71 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
201112-22:13:05,319 nipype.interface INFO:
stderr 2020-11-12T22:13:05.319385:++ 3drefit: AFNI version=AFNI_20.2.19 (Sep 27 2020) [64-bit]
201112-22:13:05,319 nipype.interface INFO:
stderr 2020-11-12T22:13:05.319744:++ Authored by: RW Cox
201112-22:13:05,326 nipype.interface INFO:
stderr 2020-11-12T22:13:05.326593:** 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
201112-22:13:05,326 nipype.interface INFO:
stderr 2020-11-12T22:13:05.326820: Warnings of this type will be muted for this session.
201112-22:13:05,327 nipype.interface INFO:
stderr 2020-11-12T22:13:05.326820: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
201112-22:13:05,328 nipype.interface INFO:
stderr 2020-11-12T22:13:05.328348:++ 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
201112-22:13:05,329 nipype.interface INFO:
stderr 2020-11-12T22:13:05.329293: + deoblique
201112-22:13:05,329 nipype.interface INFO:
stderr 2020-11-12T22:13:05.329581: + 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)
201112-22:13:08,157 nipype.interface INFO:
stderr 2020-11-12T22:13:08.157344:++ 3drefit processed 1 datasets
201112-22:13:08,364 nipype.workflow ERROR:
Node anat_deoblique failed to run on host node167.
201112-22:13:08,368 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221308-av2902-anat_deoblique-ad144eaf-efc8-4668-9630-1ea231a811f2.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/anat_preproc_niworkflows_ants_0/anat_deoblique/_0x308f5fcaa69b0e676653fb21bef917a6_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/anat_preproc_niworkflows_ants_0/anat_deoblique/_0x308f5fcaa69b0e676653fb21bef917a6.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/anat_preproc_niworkflows_ants_0/anat_deoblique/_0x308f5fcaa69b0e676653fb21bef917a6_unfinished.json'
201112-22:13:08,388 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".
201112-22:13:08,457 nipype.workflow INFO:
[Node] Running "sinker_0_motion_estimate_filter_info_plot" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:13:08,705 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_plot".
201112-22:13:08,707 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".
201112-22:13:08,771 nipype.workflow INFO:
[Node] Running "sinker_0_motion_estimate_filter_info_design" ("CPAC.utils.interfaces.datasink.DataSink")
201112-22:13:09,5 nipype.workflow INFO:
[Node] Finished "resting_preproc_sub-206_ses-1.sinker_0_motion_estimate_filter_info_design".
201112-22:13:09,6 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".
201112-22:13:09,34 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_lateral_ventricles_mask" - collecting precomputed outputs
201112-22:13:09,34 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_lateral_ventricles_mask" found cached.
201112-22:13:09,36 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".
201112-22:13:09,62 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_derivative" - collecting precomputed outputs
201112-22:13:09,62 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_derivative" found cached.
201112-22:13:09,64 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".
201112-22:13:09,90 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_preproc" - collecting precomputed outputs
201112-22:13:09,90 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.resampled_template_brain_for_func_preproc" found cached.
201112-22:13:09,92 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".
201112-22:13:09,127 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.func_template_edge_0" - collecting precomputed outputs
201112-22:13:09,127 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.func_template_edge_0" found cached.
201112-22:13:09,130 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".
201112-22:13:09,168 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.montage_mfi_0.resample_o" - collecting precomputed outputs
201112-22:13:09,168 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.montage_mfi_0.resample_o" found cached.
201112-22:13:09,170 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".
201112-22:13:09,206 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_derivative" - collecting precomputed outputs
201112-22:13:09,207 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_derivative" found cached.
201112-22:13:09,209 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".
201112-22:13:09,337 nipype.workflow INFO:
[Node] Running "resampled_template_skull_for_func_preproc" ("CPAC.utils.interfaces.function.Function")
201112-22:13:09,556 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".
201112-22:13:09,575 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
201112-22:13:10,251 nipype.workflow INFO:
[Node] Finished "template_skull_for_func_preproc".
201112-22:13:10,282 nipype.workflow ERROR:
Node resampled_template_skull_for_func_preproc failed to run on host node167.
201112-22:13:10,285 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221310-av2902-resampled_template_skull_for_func_preproc-859ce541-3d5d-4e18-9907-c6977b8721da.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/resampled_template_skull_for_func_preproc/_0xf705cab77a4aca355794f4ca8fefe6a7_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_func_preproc/_0xf705cab77a4aca355794f4ca8fefe6a7.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/resampled_template_skull_for_func_preproc/_0xf705cab77a4aca355794f4ca8fefe6a7_unfinished.json'
201112-22:13:10,295 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".
201112-22:13:10,320 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_WHITE" - collecting precomputed outputs
201112-22:13:10,320 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_WHITE" found cached.
201112-22:13:10,323 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".
201112-22:13:10,348 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_GRAY" - collecting precomputed outputs
201112-22:13:10,348 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_GRAY" found cached.
201112-22:13:10,350 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".
201112-22:13:10,374 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_CSF" - collecting precomputed outputs
201112-22:13:10,374 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_PRIORS_CSF" found cached.
201112-22:13:10,376 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".
201112-22:13:10,434 nipype.workflow INFO:
[Node] Running "resampled_template_skull_for_anat" ("CPAC.utils.interfaces.function.Function")
201112-22:13:10,657 nipype.workflow INFO:
[Node] Setting-up "template_skull_for_anat" in "/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat/template_skull_for_anat".
201112-22:13:10,676 nipype.workflow INFO:
[Node] Running "template_skull_for_anat" ("nipype.interfaces.afni.utils.Resample"), a CommandLine Interface with command:
3dresample -prefix mni_icbm152_t1_tal_nlin_asym_09c_resample.nii.gz -rmode Cu -dxyz 1.000000 1.000000 1.000000 -inset /outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat/template_skull_for_anat/mni_icbm152_t1_tal_nlin_asym_09c.nii
201112-22:13:10,934 nipype.interface INFO:
stderr 2020-11-12T22:13:10.934086:** AFNI converts NIFTI_datatype=4 (INT16) in file /outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat/template_skull_for_anat/mni_icbm152_t1_tal_nlin_asym_09c.nii to FLOAT32
201112-22:13:10,934 nipype.interface INFO:
stderr 2020-11-12T22:13:10.934657: Warnings of this type will be muted for this session.
201112-22:13:10,934 nipype.interface INFO:
stderr 2020-11-12T22:13:10.934657: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
201112-22:13:13,518 nipype.workflow INFO:
[Node] Finished "template_skull_for_anat".
201112-22:13:13,544 nipype.workflow ERROR:
Node resampled_template_skull_for_anat failed to run on host node167.
201112-22:13:13,549 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221313-av2902-resampled_template_skull_for_anat-5f85e745-6b8f-42d3-941d-9eb820e138be.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/resampled_template_skull_for_anat/_0x66ccbe1150e4c53dbb06b60b12aa0fe8_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/resampled_template_skull_for_anat/_0x66ccbe1150e4c53dbb06b60b12aa0fe8.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/resampled_template_skull_for_anat/_0x66ccbe1150e4c53dbb06b60b12aa0fe8_unfinished.json'
201112-22:13:13,559 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".
201112-22:13:13,588 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.resampled_template_brain_for_anat" - collecting precomputed outputs
201112-22:13:13,588 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.resampled_template_brain_for_anat" found cached.
201112-22:13:13,599 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".
201112-22:13:13,655 nipype.workflow INFO:
[Node] Running "anat_template_edge_0" ("CPAC.utils.interfaces.function.Function")
201112-22:13:15,832 nipype.workflow ERROR:
Node anat_template_edge_0 failed to run on host node167.
201112-22:13:15,837 nipype.workflow ERROR:
Saving crash info to /outputs/crash/crash-20201112-221315-av2902-anat_template_edge_0-4cfa398f-0746-4018-8a6f-36d4bca6d962.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/anat_template_edge_0/_0xbe485e190a2ae7fa6eddcba9e13855fc_unfinished.json' -> '/outputs/tmp/resting_preproc_sub-206_ses-1/anat_template_edge_0/_0xbe485e190a2ae7fa6eddcba9e13855fc.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/anat_template_edge_0/_0xbe485e190a2ae7fa6eddcba9e13855fc_unfinished.json'
201112-22:13:15,847 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".
201112-22:13:15,868 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_brain" - collecting precomputed outputs
201112-22:13:15,868 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_brain" found cached.
201112-22:13:15,870 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".
201112-22:13:15,917 nipype.workflow INFO:
[Node] Cached "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_skull" - collecting precomputed outputs
201112-22:13:15,918 nipype.workflow INFO:
[Node] "resting_preproc_sub-206_ses-1.check_for_s3_acpc_template_skull" found cached.
201112-22:13:15,921 nipype.workflow INFO:
***********************************
201112-22:13:15,921 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b6
201112-22:13:15,921 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221202-av2902-func_drop_trs.b6-1ba6f5fc-fc69-4ced-be0b-018784f1ac0b.pklz
201112-22:13:15,922 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b5
201112-22:13:15,922 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221208-av2902-func_drop_trs.b5-6f83fea8-bb92-4e5c-b7b3-63e795943b4b.pklz
201112-22:13:15,922 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b4
201112-22:13:15,922 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221217-av2902-func_drop_trs.b4-81b793e7-a7c1-4b81-b388-3697e3ab4114.pklz
201112-22:13:15,923 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique.b3
201112-22:13:15,923 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221229-av2902-func_deoblique.b3-74dec37b-13e3-4f89-8743-99af819ad22e.pklz
201112-22:13:15,923 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.func_despiked_0.b3
201112-22:13:15,924 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221235-av2902-func_despiked_0.b3-7002bef9-900d-4e9a-90f0-871cb1d19ce0.pklz
201112-22:13:15,924 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b2
201112-22:13:15,924 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221241-av2902-func_drop_trs.b2-afb3559a-fab9-4578-95dd-a6cf37177c42.pklz
201112-22:13:15,925 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b1
201112-22:13:15,925 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221247-av2902-func_drop_trs.b1-f433c5de-659d-41fd-ae9f-d69e55b67ecd.pklz
201112-22:13:15,925 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.edit_func_0.func_drop_trs.b0
201112-22:13:15,926 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221254-av2902-func_drop_trs.b0-37572eb5-f475-40e4-afef-6f975b21ee35.pklz
201112-22:13:15,926 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
201112-22:13:15,926 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221304-av2902-lap_tmpl-1950dcd9-381c-41a8-8515-db864a7f96f1.pklz
201112-22:13:15,928 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.anat_preproc_niworkflows_ants_0.anat_deoblique
201112-22:13:15,928 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221308-av2902-anat_deoblique-ad144eaf-efc8-4668-9630-1ea231a811f2.pklz
201112-22:13:15,928 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.resampled_template_skull_for_func_preproc
201112-22:13:15,928 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221310-av2902-resampled_template_skull_for_func_preproc-859ce541-3d5d-4e18-9907-c6977b8721da.pklz
201112-22:13:15,929 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.resampled_template_skull_for_anat
201112-22:13:15,929 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221313-av2902-resampled_template_skull_for_anat-5f85e745-6b8f-42d3-941d-9eb820e138be.pklz
201112-22:13:15,929 nipype.workflow ERROR:
could not run node: resting_preproc_sub-206_ses-1.anat_template_edge_0
201112-22:13:15,929 nipype.workflow INFO:
crashfile: /outputs/crash/crash-20201112-221315-av2902-anat_template_edge_0-4cfa398f-0746-4018-8a6f-36d4bca6d962.pklz
201112-22:13:15,929 nipype.workflow INFO:
***********************************
201112-22:13:15,963 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): 9.56800194978714
Timing information saved in /outputs/log/cpac_individual_timing_cpac_fmriprep-options.csv
System time of start: 2020-11-12 22:03:47
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