app-C-PAC-brainlife.io v0.0.0.dev - fmriprep-options

C-PAC Run Info


Description	https://brainlife.io/project/5f299e1fbeafe973f362a972/process/5f996dd282260675eb0a4254 will be removed 2020 November 22
Version	1.7.1
Container	Singularity
System	brainlife.io
Data Size	899 TRs (74 × 74 × 40)
Results	run complete with 2 crash files: `crash-20201028-131530-user-tCompCor_tr_string2float.a0.b0-630b6dd0-b915-4830-99fa-3887756fc4a5.pklz` and `crash-20201028-131531-user-aCompCor_tr_string2float.a0.b0-ed134f4e-2936-4663-9d12-e2663b39fa82.pklz

crash details

Each of the crash files has the same complaint:

Node inputs:
function_str = def TR_string_to_float(tr):
    if 'ms' in tr:
        tr = float(tr.replace('ms',''))/1000
    else:
        tr = float(tr.replace('s',''))
    return tr
tr = None
Traceback: 
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 521, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py", line 144, in _run_interface
    out = function_handle(**args)
  File "<string>", line 2, in TR_string_to_float
TypeError: argument of type 'NoneType' is not iterable

The data config (generated) looks like

- anat: /bids/sub-A00021039/ses-DS2/anat/sub-A00021039_ses-DS2_T1w.nii.gz
  creds_path: null
  func:
    rest_acq-645:
      scan: /bids/sub-A00021039/ses-DS2/func/sub-A00021039_ses-DS2_task-rest_acq-645_bold.nii.gz
      scan_parameters: {}
  site_id: site-none
  subject_id: sub-A00021039
  unique_id: ses-DS2

Include:

[x] Run Command:

anat/t1w:
  NKI: A00021039 / DS2 | DS2
func/task: 
  NKI: A00021039 / DS2 rest | DS2,rest,645
preconfig: fmriprep-options

[x] Pipeline Config: fmriprep-options
[x] Data Config: BIDS

Developers only:

[x] Screenshots of brain extraction and registration wireframe overlays from QC pages (if available):

[x] Node timing information:


(('resting_preproc_sub-A00021039_ses-DS2.anat_mni_ants_register_0.calc_ants_warp', 12721.0)

('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.norm', 3796.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_generate_ref', 1264.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_generate_ref', 1255.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_motion_correct_to_standardt1_0', 987.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_functional_to_standard__t1_1', 972.0) ('resting_preproc_sub-A00021039_ses-DS2.write_composite_xfm_functional_to_standardt1_1', 970.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_functional_to_standardt1_0', 955.0) ('resting_preproc_sub-A00021039_ses-DS2.write_composite_xfm_functional_to_standard__t1_0', 926.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt', 276.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.segment', 272.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_motion_correct_mcflirt', 206.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.Functional_2mm_flirt', 169.0) ('resting_preproc_sub-A00021039_ses-DS2.func_to_anat_bbreg_0.bbreg_func_to_anat', 144.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.unifize', 111.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.unifize', 106.0) ('resting_preproc_sub-A00021039_ses-DS2.edit_func_0.func_drop_trs', 57.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.01_atropos', 51.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_reorient', 43.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_reorient', 41.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_deoblique', 40.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_deoblique', 38.0) ('resting_preproc_sub-A00021039_ses-DS2.func_slice_timing_correction_0.slice_timing', 38.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.tcompcor.std', 35.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.map_brainmask', 34.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain', 30.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.CerebrospinalFluid_mean', 29.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_extract_brain', 28.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.WhiteMatter_mean', 27.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.tcompcor.detrend', 22.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_functional_to_standard', 22.0) ('resting_preproc_sub-A00021039_ses-DS2.spatial_map_timeseries_1.spatial_regression', 22.0) ('resting_preproc_sub-A00021039_ses-DS2.spatial_map_timeseries_0.spatial_regression', 21.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_normalize', 20.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_normalize', 19.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_brain_for_func_preproc', 17.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_anat_0.resample_u', 16.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_anat_1.resample_u', 15.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_mean_n4_corrected', 12.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_edge_1', 12.0) ('resting_preproc_sub-A00021039_ses-DS2.carpet_seg_1.carpet_plot', 12.0) ('resting_preproc_sub-A00021039_ses-DS2.carpet_seg_0.carpet_plot', 12.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mask_normalize', 11.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_skull_for_anat', 11.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_mask_normalize', 10.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.lap_tmpl', 10.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.07_fill_gm', 9.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.19_fill_7', 9.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.copy_xform', 9.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_1.snr', 9.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.05_get_wm', 8.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_1qcmean_func_with_t1_edge_s', 8.0) ('resting_preproc_sub-A00021039_ses-DS2.gen_motion_stats_before_stc_fsl_afni_mean_mcflirt_0.cal_DVARS', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.functional_mean', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_0.std_dev', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_0.montage_snr.resample_o', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.erode_skullstrip_mask_WM', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_1.resample_o_csf', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_anat_1.resample_o', 7.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_get_mean_motion', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_RPI', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_get_mean_motion', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.func_mean_skull', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.GlobalSignal_mean', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_1.std_dev', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.lap_target', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.init_aff', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_to_anat_FLIRT_0.linear_func_to_anat', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.anat_to_func_linear_xfm', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_1.std_dev_anat', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_1.montage_snr.resample_o', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.GM.binarize_GM', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.binarize_WM', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_edge_0', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_brain_for_func_derivative', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_skull_for_func_preproc', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_brain_for_anat', 6.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean_n4_corrected', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.10_me_csf', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_0.std_dev_anat', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_1.montage_s', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_1.montage_a', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.resample_o_csf', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mfi_1.resample_o', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.resampled_template_skull_for_func_derivative', 5.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_mean', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_mean', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_skullstrip_1.skull_edge', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.11_add_gm', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.13_add_gm_wm', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.15_add_7', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.16_me_7', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.20_add_7_2', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.22_me_7_2', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.nuisance_regressor_0_0.Anatomical_2mm_flirt', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.seg_preproc_0.WM.threshold_segmentmap_WM', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.montage_s', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_csf_gm_wm_0.montage_a', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_anat_0.resample_o', 4.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_skullstrip_0.skull_edge', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.atropos_wf.copy_xform', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_1.dp_snr', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.qc_snr_0.snr', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.sinker_0_qc_mean_func_with_t1_edge_a', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.func_template_edge_1', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.func_template_edge_0', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mfi_0.resample_o', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mni_anat_1.resample_u', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.montage_mni_anat_0.resample_u', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_mean_functional_to_standard_derivativet1_0', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_mean_functional_to_standardt1_0', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.apply_ants_warp_functional_brain_mask_to_standard_derivativet1_0', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_template_edge_1', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_template_edge_0', 3.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_before_stc_fsl_afni_mean_mcflirt_0.func_preproc_before_stc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_dilate', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.func_preproc_fsl_afni_mean_mcflirt_0.func_preproc_fsl_afni_mean_mcflirt_0_skullstrip.skullstrip_first_pass', 2.0) ('resting_preproc_sub-A00021039_ses-DS2.anat_preproc_niworkflows_ants_0.anat_preproc_niworkflows_ants_0_skullstrip.anat_skullstrip_ants.res_tmpl', 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runtime

FCP-INDI / cpac_run_logs

app-C-PAC-brainlife.io v0.0.0.dev - fmriprep-options #3

C-PAC Run Info

crash details