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