FMRIPREP takes over 48h to process 2-3 subjects

[chrisgorgo]

--nthreads 1
--omp-nthreads 4

• 13 GB available on the system
• no errors

https://openneuro.org/datasets/ds000148/versions/00001?app=FMRIPREP&version=36&job=74e4888f-4707-47d9-af9a-dd39c08d13a4

Running fMRIPREP version 1.0.0-rc11:
  * BIDS dataset path: /snapshot/data.
  * Participant list: ['20', '40'].
  * Run identifier: 20171125-163415_5972434f-1e2e-418a-b0f5-16f8e46d5330.

171125-16:34:16,673 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-01_bold.nii.gz" (0.07 GB / 263 TRs).
171125-16:34:17,177 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-01_bold.nii.gz.
171125-16:34:17,532 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:34:18,659 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-02_bold.nii.gz" (0.07 GB / 263 TRs).
171125-16:34:19,133 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-02_bold.nii.gz.
171125-16:34:19,405 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:34:20,596 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-03_bold.nii.gz" (0.07 GB / 263 TRs).
171125-16:34:21,71 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-20/func/sub-20_task-figure2backwith1backlures_run-03_bold.nii.gz.
171125-16:34:21,344 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:34:23,545 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-01_bold.nii.gz" (0.07 GB / 263 TRs).
171125-16:34:24,25 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-01_bold.nii.gz.
171125-16:34:24,302 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:34:25,523 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-02_bold.nii.gz" (0.07 GB / 265 TRs).
171125-16:34:25,999 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-02_bold.nii.gz.
171125-16:34:26,274 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:34:27,402 workflow IMPORTANT:
	 Creating bold processing workflow for "/snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-03_bold.nii.gz" (0.07 GB / 262 TRs).
171125-16:34:27,985 workflow WARNING:
	 No fieldmaps found or they were ignored, building base workflow for dataset /snapshot/data/sub-40/func/sub-40_task-figure2backwith1backlures_run-03_bold.nii.gz.
171125-16:34:28,285 workflow IMPORTANT:
	 Creating BOLD surface-sampling workflow.
171125-16:40:44,872 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-16:40:44,872 niworkflows INFO:
	 Generating visual report
171125-16:41:08,363 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-16:42:10,726 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:42:30,590 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:48:34,85 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-16:48:34,85 niworkflows INFO:
	 Generating visual report
171125-16:48:57,934 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-16:50:00,527 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:50:20,335 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:56:22,639 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-16:56:22,639 niworkflows INFO:
	 Generating visual report
171125-16:56:46,453 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-16:57:49,310 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:58:09,367 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-16:58:09,472 interface WARNING:
	 No 'fmap' images found for sub-<undefined>
171125-16:58:09,472 interface WARNING:
	 No 'sbref' images found for sub-<undefined>
171125-17:53:57,395 niworkflows INFO:
	 Generating report for ANTS BrainExtraction. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_BrainExtractionMask.nii.gz"
171125-17:54:14,366 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/report.html)
171125-17:54:20,318 niworkflows INFO:
	 Estimating initial transform using AffineInitializer
171125-18:04:24,96 niworkflows INFO:
	 Terminal outputs of initialization saved (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/stderr.nipype-init).
171125-18:04:24,97 niworkflows INFO:
	 Loading settings from file /usr/local/miniconda/lib/python3.6/site-packages/niworkflows/data/t1-mni_registration_precise_000.json.
171125-18:04:24,100 niworkflows INFO:
	 Retry #0, commandline: 
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.05 ] --metric Mattes[ /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 100x100, 1e-06, 20 ] --smoothing-sigmas 2.0x1.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 100x100, 1e-06, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 4, None, 1 ] --convergence [ 100x70x50x20, 1e-06, 10 ] --smoothing-sigmas 3.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
171125-20:13:02,955 niworkflows INFO:
	 Successful spatial normalization (retry #0).
171125-20:13:02,957 niworkflows INFO:
	 Report - setting fixed (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mni_Warped.nii.gz) images
171125-20:13:02,957 niworkflows INFO:
	 Generating visual report
171125-20:13:27,272 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_2_mni/report.svg)
171125-20:16:53,980 niworkflows INFO:
	 Generating report for FAST (in_files ['/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain.nii.gz'], segmentation /root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg.nii.gz, individual tissue classes ['/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_0.nii.gz', '/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_1.nii.gz', '/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_2.nii.gz']).
171125-20:17:25,533 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_20_wf/anat_preproc_wf/t1_seg/report.html)
171125-20:24:37,61 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-20:24:37,61 niworkflows INFO:
	 Generating visual report
171125-20:25:00,792 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-20:25:58,67 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:26:17,612 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:32:22,391 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-20:32:22,392 niworkflows INFO:
	 Generating visual report
171125-20:32:46,28 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-20:33:43,313 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:34:02,875 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:40:06,146 niworkflows INFO:
	 Report - setting before (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/pos_tsnr/stdev.nii.gz) and after (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/pre_tsnr/stdev.nii.gz) images
171125-20:40:06,146 niworkflows INFO:
	 Generating visual report
171125-20:40:30,795 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_preproc_report_wf/bold_rpt/report.svg)
171125-20:41:28,965 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:41:49,8 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/mask_reportlet/report.html)
171125-20:41:49,126 interface WARNING:
	 No 'fmap' images found for sub-<undefined>
171125-20:41:49,126 interface WARNING:
	 No 'sbref' images found for sub-<undefined>
171125-21:37:26,932 niworkflows INFO:
	 Generating report for ANTS BrainExtraction. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_N4Corrected0.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/highres001_BrainExtractionMask.nii.gz"
171125-21:38:28,952 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/report.html)
171125-21:38:34,824 niworkflows INFO:
	 Estimating initial transform using AffineInitializer
171125-21:48:34,187 niworkflows INFO:
	 Terminal outputs of initialization saved (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/stderr.nipype-init).
171125-21:48:34,187 niworkflows INFO:
	 Loading settings from file /usr/local/miniconda/lib/python3.6/site-packages/niworkflows/data/t1-mni_registration_precise_000.json.
171125-21:48:34,190 niworkflows INFO:
	 Retry #0, commandline: 
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.05 ] --metric Mattes[ /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 100x100, 1e-06, 20 ] --smoothing-sigmas 2.0x1.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 100x100, 1e-06, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz, /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/moving_masked.nii.gz, 1, 4, None, 1 ] --convergence [ 100x70x50x20, 1e-06, 10 ] --smoothing-sigmas 3.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
171125-23:56:54,864 niworkflows INFO:
	 Successful spatial normalization (retry #0).
171125-23:56:54,865 niworkflows INFO:
	 Report - setting fixed (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/fixed_masked.nii.gz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mni_Warped.nii.gz) images
171125-23:56:54,865 niworkflows INFO:
	 Generating visual report
171125-23:57:19,745 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_2_mni/report.svg)
171126-00:00:10,218 niworkflows INFO:
	 Generating report for FAST (in_files ['/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain.nii.gz'], segmentation /root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg.nii.gz, individual tissue classes ['/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_0.nii.gz', '/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_1.nii.gz', '/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/highres001_BrainExtractionBrain_seg_2.nii.gz']).
171126-00:00:20,588 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:00:28,651 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:00:52,76 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:01:00,214 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:01:24,347 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:01:32,439 cli WARNING:
	 Captured warning (<class 'UserWarning'>): Casting data from int32 to float32
171126-00:01:46,882 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/t1_seg/report.html)
171126-18:49:17,743 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz) images
171126-18:49:17,743 niworkflows INFO:
	 Generating visual report
171126-18:49:55,275 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reg_wf/bbreg_wf/mri_coreg/report.svg)
171126-18:50:25,387 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz) images
171126-18:50:25,387 niworkflows INFO:
	 Generating visual report
171126-18:51:03,8 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_reg_wf/bbreg_wf/bbregister/report.svg)
171126-18:51:05,658 niworkflows INFO:
	 Generating report for tCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_confounds_wf/tcompcor/mask_000.nii.gz"
171126-18:51:20,412 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_confounds_wf/tcompcor/report.html)
171126-18:51:21,963 niworkflows INFO:
	 Generating report for aCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_confounds_wf/acc_tfm/highres001_BrainExtractionBrain_prob_0_tpmsum_roi_trans_boldmsk.nii.gz"
171126-18:51:36,928 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_03_wf/bold_confounds_wf/acompcor/report.html)
171126-19:01:48,905 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz) images
171126-19:01:48,905 niworkflows INFO:
	 Generating visual report
171126-19:02:26,897 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reg_wf/bbreg_wf/mri_coreg/report.svg)
171126-19:03:13,701 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz) images
171126-19:03:13,702 niworkflows INFO:
	 Generating visual report
171126-19:03:51,885 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_reg_wf/bbreg_wf/bbregister/report.svg)
171126-19:03:54,633 niworkflows INFO:
	 Generating report for tCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_confounds_wf/tcompcor/mask_000.nii.gz"
171126-19:04:09,566 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_confounds_wf/tcompcor/report.html)
171126-19:04:11,137 niworkflows INFO:
	 Generating report for aCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_confounds_wf/acc_tfm/highres001_BrainExtractionBrain_prob_0_tpmsum_roi_trans_boldmsk.nii.gz"
171126-19:04:26,314 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_02_wf/bold_confounds_wf/acompcor/report.html)
171126-19:14:45,326 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz) images
171126-19:14:45,326 niworkflows INFO:
	 Generating visual report
171126-19:15:23,612 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/report.svg)
171126-19:16:31,441 niworkflows INFO:
	 Report - setting fixed (/output/data/freesurfer/sub-40/mri/brainmask.mgz) and moving (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz) images
171126-19:16:31,441 niworkflows INFO:
	 Generating visual report
171126-19:17:09,877 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/report.svg)
171126-19:17:12,674 niworkflows INFO:
	 Generating report for tCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_confounds_wf/tcompcor/mask_000.nii.gz"
171126-19:17:27,792 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_confounds_wf/tcompcor/report.html)
171126-19:17:29,372 niworkflows INFO:
	 Generating report for aCompCor. file "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_bold_trans_wf/merge/vol0000_xform-00000_merged.nii.gz", mask "/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_confounds_wf/acc_tfm/highres001_BrainExtractionBrain_prob_0_tpmsum_roi_trans_boldmsk.nii.gz"
171126-19:17:44,632 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/func_preproc_task_figure2backwith1backlures_run_01_wf/bold_confounds_wf/acompcor/report.html)
171126-19:55:54,698 niworkflows INFO:
	 Generating report for ReconAll (subject sub-40)
171126-19:55:54,698 niworkflows INFO:
	 Generating visual report
171126-19:56:14,176 niworkflows INFO:
	 Successfully created report (/root/src/fmriprep/work/fmriprep_wf/single_subject_40_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/recon_report/report.html)

[chrisgorgo]

When rerunning with one subject I run into #776

[oesteban]

Hopefully, this will be fixed when we close #833 and you can run with MultiProc safely. I've also opened #855.

Regarding the new error: were you reusing the work directory?

[chrisgorgo]

No - it was on OpenNeuro with clean start.

[oesteban]

Let's retry with the latest release. If we have the SVD error, let's follow up in #776. If we keep seeing it blocked, then let's go through #848. Since this is a duplicate of either of them, I'll close it.

[chrisgorgo]

It's better, but it still takes more than 48h to process two particiapants in some cases: https://openneuro.org/datasets/ds000148/versions/00001?app=FMRIPREP&version=44&job=7717b6df-dce8-4377-a329-753d5587d5f7

Is there a way to check if high res freesurfer was run?

[effigies]

If you check the scripts directory, you should be able to see if the -hires option was passed.

[effigies]

From a quick look at sub-15 and sub-39, hires wasn't run. (The very top of scripts/recon-all.log has the -autorecon1 command, which doesn't have -hires in it.)

[chrisgorgo]

Potentially related to nipy/nipype#2548

[oesteban]

This is very likely a duplicate of #848. Since this one was last updated, I'll bring the information from that one here:

https://openneuro.org/datasets/ds001161/versions/00001?app=FMRIPREP&version=32&job=5a12b82a921b110001c24505

Also check: DS148/sub-20

[oesteban]

Since nipy/nipype#2548 is closed now, I will go ahead and close this one as well. Please reopen if this happens again.