Fmriprep stopping during skull stripping without errors

#1

fmriprep is stopping during skull stropping but there are no errors in the log or anywhere that I can find in the working directory so I cannot figure out how to fix the problem. Any ideas? I cannot attach my log as I am a new user and I cannot paste my entire log so I’m pasting what I believe are the most relevant sections below. Note: I have had several errors when running it and I’m only pasting the log information from the most recent attempt.

1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)

Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.


    Summary:                  Available Tasks:        Available Modalities: 
    18 Files, 732.92MB        rest                    FLAIR                 
    1 - Subject                                       T1w                   
    1 - Session                                       bold                  
                                                      fieldmap              


If you have any questions, please post on https://neurostars.org/tags/bids.

Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
190904-18:49:16,516 nipype.workflow IMPORTANT:

Running fMRIPREP version 1.4.1:
  * BIDS dataset path: /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/data_BIDS.
  * Participant list: ['00213'].
  * Run identifier: 20190904-184916_42373601-d789-40d9-9d3b-4f710f4227d4.

190904-18:49:19,509 nipype.workflow IMPORTANT:
Creating bold processing workflow for “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/data_BIDS/sub-00213/ses-baseline/func/sub-00213_ses-baseline_task-rest_run-01_bold.nii.gz” (0.31 GB / 240 TRs). Memory resampled/largemem=1.23/1.97 GB.
190904-18:49:19,510 nipype.workflow IMPORTANT:
No single-band-reference found for sub-00213_ses-baseline_task-rest_run-01_bold.nii.gz
190904-18:49:23,318 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
190904-18:49:23,644 nipype.workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/data_BIDS/sub-00213/ses-baseline/func/sub-00213_ses-baseline_task-rest_run-01_bold.nii.gz found.
190904-18:49:24,600 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
190904-18:49:27,290 nipype.workflow IMPORTANT:
Creating bold processing workflow for “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/data_BIDS/sub-00213/ses-baseline/func/sub-00213_ses-baseline_task-rest_run-02_bold.nii.gz” (0.31 GB / 240 TRs). Memory resampled/largemem=1.23/1.97 GB.
190904-18:49:27,291 nipype.workflow IMPORTANT:
No single-band-reference found for sub-00213_ses-baseline_task-rest_run-02_bold.nii.gz
190904-18:49:29,268 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
190904-18:49:29,586 nipype.workflow IMPORTANT:
SDC: fieldmap estimation of type “epi” intended for /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/data_BIDS/sub-00213/ses-baseline/func/sub-00213_ses-baseline_task-rest_run-02_bold.nii.gz found.
190904-18:49:30,808 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
190904-18:49:35,639 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the following boilerplate:

190904-19:19:02,303 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_surf_wf.sampler” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_rh/sampler”.
190904-19:19:02,501 nipype.workflow INFO:
[Node] Setting-up “_sampler0” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0”.
190904-19:19:02,554 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_surf_wf.sampler” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_lh/sampler”.
190904-19:19:02,784 nipype.workflow INFO:
[Node] Running “_sampler0” (“nipype.interfaces.freesurfer.utils.SampleToSurface”), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii --srcsubject sub-00213 --reg /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
190904-19:19:02,805 nipype.workflow INFO:
[Node] Setting-up “_sampler0” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0”.
190904-19:19:03,32 nipype.workflow INFO:
[Node] Running “_sampler0” (“nipype.interfaces.freesurfer.utils.SampleToSurface”), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii --srcsubject sub-00213 --reg /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
190904-19:19:03,466 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref”.
190904-19:19:07,387 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct”.
190904-19:19:07,500 nipype.workflow INFO:
[Node] Running “n4_correct” (“nipype.interfaces.ants.segmentation.N4BiasFieldCorrection”), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_bold_corrected_trans_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz
190904-19:19:30,77 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct”.
190904-19:19:31,411 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass”.
190904-19:19:31,528 nipype.workflow INFO:
[Node] Running “skullstrip_first_pass” (“nipype.interfaces.fsl.preprocess.BET”), a CommandLine Interface with command:
bet /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m
190904-19:19:38,179 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass”.
190904-19:19:39,666 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate”.
190904-19:19:39,758 nipype.workflow INFO:
[Node] Running “skullstrip_first_dilate” (“nipype.interfaces.fsl.maths.DilateImage”), a CommandLine Interface with command:
fslmaths -dt char /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz
190904-19:19:53,842 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate”.
190904-19:19:55,606 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask”.
190904-19:19:55,716 nipype.workflow INFO:
[Node] Running “skullstrip_first_mask” (“nipype.interfaces.fsl.maths.ApplyMask”), a CommandLine Interface with command:
fslmaths /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz
190904-19:19:57,115 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask”.
190904-19:19:59,517 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize”.
190904-19:19:59,705 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 /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz
190904-19:20:14,968 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize”.
190904-19:20:20,51 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize”.
190904-19:20:20,140 nipype.workflow INFO:
[Node] Running “fixhdr_unifize” (“niworkflows.interfaces.utils.CopyXForm”)
190904-19:20:20,862 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize”.
190904-19:20:23,321 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass”.
190904-19:20:23,532 nipype.workflow INFO:
[Node] Running “skullstrip_second_pass” (“nipype.interfaces.afni.preprocess.Automask”), a CommandLine Interface with command:
3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
190904-19:20:25,253 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass”.
190904-19:20:32,398 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2”.
190904-19:20:32,497 nipype.workflow INFO:
[Node] Running “fixhdr_skullstrip2” (“niworkflows.interfaces.utils.CopyXForm”)
190904-19:20:32,988 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2”.
190904-19:20:35,746 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks”.
190904-19:20:35,858 nipype.workflow INFO:
[Node] Running “combine_masks” (“nipype.interfaces.fsl.maths.BinaryMaths”), a CommandLine Interface with command:
fslmaths /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz
190904-19:20:36,948 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks”.
190904-19:20:39,471 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask”.
190904-19:20:39,586 nipype.workflow INFO:
[Node] Running “apply_mask” (“nipype.interfaces.fsl.maths.ApplyMask”), a CommandLine Interface with command:
fslmaths /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
190904-19:20:40,628 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask”.
190904-19:20:57,463 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_to_t1w_transform”.
190904-19:21:12,464 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.merge” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/merge”.
190904-19:21:15,19 nipype.workflow INFO:
[Node] Running “merge” (“fmriprep.interfaces.nilearn.Merge”)
190904-19:22:23,367 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.merge”.
190904-19:22:25,367 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.resampling_xfm” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/resampling_xfm”.
190904-19:22:25,471 nipype.workflow INFO:
[Node] Running “resampling_xfm” (“niworkflows.interfaces.freesurfer.PatchedLTAConvert”), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/resampling_xfm/out.lta --src /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/merge/vol0000_xform-00000_merged.nii --trg /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-00213_ses-baseline_T1w_ras_valid_corrected_xform.nii.gz
190904-19:22:26,141 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.resampling_xfm”.
190904-19:22:26,622 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.validate” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/validate”.
190904-19:22:26,694 nipype.workflow INFO:
[Node] Running “validate” (“niworkflows.interfaces.images.ValidateImage”)
190904-19:22:27,49 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.validate”.
190904-19:22:27,460 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.set_xfm_source” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/set_xfm_source”.
190904-19:22:27,543 nipype.workflow INFO:
[Node] Running “set_xfm_source” (“niworkflows.interfaces.freesurfer.PatchedConcatenateLTA”), a CommandLine Interface with command:
mri_concatenate_lta -out_type 1 /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/resampling_xfm/out.lta /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta out_concat.lta
190904-19:22:28,178 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.set_xfm_source”.
190904-19:22:29,510 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.sampler” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_rh/sampler”.
190904-19:22:29,696 nipype.workflow INFO:
[Node] Setting-up “_sampler0” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0”.
190904-19:22:29,737 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_surf_wf.sampler” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_lh/sampler”.
190904-19:22:29,799 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref”.
190904-19:22:29,884 nipype.workflow INFO:
[Node] Running “gen_ref” (“niworkflows.interfaces.registration.EstimateReferenceImage”)
190904-19:22:29,941 nipype.workflow INFO:
[Node] Setting-up “_sampler0” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0”.
190904-19:22:29,947 nipype.workflow INFO:
[Node] Running “_sampler0” (“nipype.interfaces.freesurfer.utils.SampleToSurface”), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii --srcsubject sub-00213 --reg /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
190904-19:22:30,184 nipype.workflow INFO:
[Node] Running “_sampler0” (“nipype.interfaces.freesurfer.utils.SampleToSurface”), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii --srcsubject sub-00213 --reg /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
190904-19:22:31,523 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref”.
190904-19:22:35,408 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct”.
190904-19:22:35,493 nipype.workflow INFO:
[Node] Running “n4_correct” (“nipype.interfaces.ants.segmentation.N4BiasFieldCorrection”), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_bold_corrected_trans_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz
190904-19:22:51,713 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct”.
190904-19:22:53,343 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass”.
190904-19:22:53,451 nipype.workflow INFO:
[Node] Running “skullstrip_first_pass” (“nipype.interfaces.fsl.preprocess.BET”), a CommandLine Interface with command:
bet /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m
190904-19:22:57,892 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass”.
190904-19:22:59,811 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_00213_wf.func_preproc_ses_baseline_task_rest_run_02_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate” in “/mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate”.
190904-19:22:59,899 nipype.workflow INFO:
[Node] Running “skullstrip_first_dilate” (“nipype.interfaces.fsl.maths.DilateImage”), a CommandLine Interface with command:
fslmaths -dt char /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /mnt/munin/Meade/ConnNeuro.01/Analysis/BIDS/fmriprep_workingdir/fmriprep_wf/single_subject_00213_wf/func_preproc_ses_baseline_task_rest_run_02_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz

#2

Can you confirm that no processes are running with top or htop or similar? It may simply be that you’re not seeing output because no cores are available to run the jobs that are ready, or there are no jobs ready except those that are running at this point.

You can also try running with -v, to increase the verbosity, which should give you periodic status updates as to what jobs are running. (If not, -vv or -vvv will work. Each v increases the verbosity, which can help identify problems when things hang, but also produces a lot more text to sift through.)