'All iterfields of a MapNode have to have the same length.' #496
Description
What happened?
Nibabies 25.0.1 crashed not long after starting with ValueError: All iterfields of a MapNode have to have the same length. More context provided below.
What command did you use?
docker run --rm -i -u 2254:10 -v /usr/local/pkg/freesurfer7.3/.license:/opt/freesurfer/license.txt:ro -v /data/sylvester/data1/datasets/precbaby/bids/rawdata:/data:ro -v /data/sylvester/data1/datasets/precbaby/bids/derivatives/nibabies:/out -v /export/scratch1/precbaby_nibabies_work/sub-5000_ses-nb0:/work -v /data/sylvester/data1/datasets/precbaby/bids/derivatives/bibsnet:/deriv1 nipreps/nibabies:25.0.1 /data /out participant --participant-label 5000 --session-id nb0 -w /work --verbose --derivatives /deriv1 --anat-only --fd-spike-threshold 0.1 --age-months 1 --surface-recon-method mcribs --cifti-output 91k --debug registration --project-goodvoxels --multi-step-reg --norm-csf --omp-nthreads 8 --mem 300000 --nprocs 8 --stop-on-first-crash --output-spaces fsLR MNIInfant:cohort-1 MNI152NLin6Asym:res-2 T2w MNI152NLin2009cAsym --age-months 1What version of NiBabies are you using?
25.0.1
Relevant log output
251020-15:46:04,593 cli INFO:
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
[email protected]
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
2: [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:
3413 Files, 189.74GB MRI
14 - Subjects
23 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
251020-15:47:16,949 nipype.workflow WARNING:
Previous output generated by version 0+unknown found.
251020-15:47:16,954 nipype.workflow IMPORTANT:
Running nibabies version 25.0.1:
* BIDS dataset path: /data.
* Participant list: [['5000', 'nb0']].
* Run identifier: 20251020-154557_7db9e346-53ad-4444-9af3-bf023c4868ce.
* Output spaces: fsLR MNIInfant:cohort-1:res-native MNI152NLin6Asym:res-2 T2w MNI152NLin2009cAsym:res-native.
* Derivatives: {'deriv1': PosixPath('/deriv1')}.
* Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
251020-15:47:17,375 cli WARNING:
`--age-months` is deprecated and will be removed in a future release.Please use a `sessions.tsv` or `participants.tsv` file to track participants age.
251020-15:47:30,562 nipype.workflow INFO:
ANAT: Using T2w as the reference anatomical
251020-15:47:31,673 nipype.workflow INFO:
ANAT Stage 1: Adding T1w template workflow
251020-15:47:31,683 nipype.workflow INFO:
ANAT Stage 1: Adding T2w template workflow
251020-15:47:31,689 nipype.workflow INFO:
ANAT Found T1w brain mask
251020-15:47:31,690 nipype.workflow INFO:
ANAT Skipping skull-strip, INU-correction only
251020-15:47:31,704 nipype.workflow INFO:
ANAT Found T2w brain mask
251020-15:47:31,705 nipype.workflow INFO:
ANAT Skipping skull-strip, INU-correction only
251020-15:47:31,707 nipype.workflow INFO:
ANAT Coregistering anatomicals
251020-15:47:31,720 nipype.workflow INFO:
ANAT Found precomputed anatomical segmentation
251020-15:47:31,721 nipype.workflow INFO:
ANAT Stage 4: Tissue segmentation
251020-15:47:31,723 nipype.workflow INFO:
ANAT Segmentation: Using existing segmentation
251020-15:47:31,734 nipype.workflow INFO:
ANAT Stage 5a: Preparing normalization workflow for ['MNIInfant:cohort-1', 'MNI152NLin2009cAsym']
251020-15:47:31,750 nipype.workflow INFO:
ANAT Stage 5b: Concatenating normalization for ['MNI152NLin6Asym']
251020-15:47:31,769 nipype.workflow INFO:
ANAT Stage 6: Preparing M-CRIB-S reconstruction workflow
251020-15:47:31,795 nipype.workflow INFO:
ANAT Skipping mask refinement workflow
251020-15:47:31,795 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
251020-15:47:31,816 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
251020-15:47:31,825 nipype.workflow INFO:
ANAT Stage 8a: Creating cortical ribbon mask
251020-15:47:31,830 nipype.workflow INFO:
ANAT Stage 9: Creating dhcp-fsLR registration sphere
251020-15:47:31,912 nipype.workflow INFO:
ANAT - using precomputed aseg
251020-15:47:34,358 nipype.workflow INFO:
NiBabies workflow graph with 313 nodes built successfully.
251020-15:47:35,134 cli INFO:
Generating an HTML version of the citation boilerplate...
251020-15:47:36,18 cli INFO:
Generating a LaTeX version of the citation boilerplate...
251020-15:47:37,251 nipype.workflow IMPORTANT:
nibabies started!
251020-15:47:38,990 nipype.workflow INFO:
Workflow nibabies_25_0_wf settings: ['check', 'execution', 'logging', 'monitoring']
251020-15:47:39,128 nipype.workflow INFO:
Running in parallel.
251020-15:47:39,135 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 17 jobs ready. Free memory (GB): 300.00/300.00, Free processors: 8/8.
251020-15:47:39,622 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.fsdir_run_20251020_154557_7db9e346_53ad_4444_9af3_bf023c4868ce" in "/work/nibabies_25_0_wf/fsdir_run_20251020_154557_7db9e346_53ad_4444_9af3_bf023c4868ce".
251020-15:47:39,628 nipype.workflow INFO:
[Node] Executing "fsdir_run_20251020_154557_7db9e346_53ad_4444_9af3_bf023c4868ce" <niworkflows.interfaces.bids.BIDSFreeSurferDir>
251020-15:47:39,684 nipype.workflow INFO:
[Node] Finished "fsdir_run_20251020_154557_7db9e346_53ad_4444_9af3_bf023c4868ce", elapsed time 0.054695s.
251020-15:47:39,689 nipype.workflow INFO:
[Job 0] Completed (nibabies_25_0_wf.fsdir_run_20251020_154557_7db9e346_53ad_4444_9af3_bf023c4868ce).
251020-15:47:40,86 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.about" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/about".
251020-15:47:40,89 nipype.workflow INFO:
[Node] Executing "about" <nibabies.interfaces.reports.AboutSummary>
251020-15:47:40,90 nipype.workflow INFO:
[Node] Finished "about", elapsed time 0.000573s.
251020-15:47:40,92 nipype.workflow INFO:
[Job 2] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.about).
251020-15:47:40,393 nipype.workflow INFO:
[Node] Setting-up "_split_desc0" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/concat_registrations_wf/split_desc/mapflow/_split_desc0".
251020-15:47:40,395 nipype.workflow INFO:
[Node] Executing "_split_desc0" <smriprep.interfaces.templateflow.TemplateDesc>
251020-15:47:40,397 nipype.workflow INFO:
[Node] Finished "_split_desc0", elapsed time 0.000179s.
251020-15:47:40,400 nipype.workflow INFO:
[Job 6] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.concat_registrations_wf.split_desc).
251020-15:47:40,758 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.split_desc" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNIInfantcohort-1/split_desc".
251020-15:47:40,762 nipype.workflow INFO:
[Node] Executing "split_desc" <smriprep.interfaces.templateflow.TemplateDesc>
251020-15:47:40,763 nipype.workflow INFO:
[Node] Finished "split_desc", elapsed time 0.00024s.
251020-15:47:40,765 nipype.workflow INFO:
[Job 9] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.split_desc).
251020-15:47:41,339 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.split_desc" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/split_desc".
251020-15:47:41,343 nipype.workflow INFO:
[Node] Executing "split_desc" <smriprep.interfaces.templateflow.TemplateDesc>
251020-15:47:41,344 nipype.workflow INFO:
[Node] Finished "split_desc", elapsed time 0.00027s.
251020-15:47:41,347 nipype.workflow INFO:
[Job 10] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.split_desc).
251020-15:47:41,698 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/spacesource".
251020-15:47:41,702 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:41,703 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.000213s.
251020-15:47:41,705 nipype.workflow INFO:
[Job 11] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource).
251020-15:47:41,935 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/spacesource".
251020-15:47:41,937 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:41,938 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.00015s.
251020-15:47:41,939 nipype.workflow INFO:
[Job 12] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource).
251020-15:47:42,179 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/spacesource".
251020-15:47:42,182 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:42,183 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.000241s.
251020-15:47:42,184 nipype.workflow INFO:
[Job 13] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.spacesource).
251020-15:47:42,606 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/spacesource".
251020-15:47:42,610 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:42,611 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.00037s.
251020-15:47:42,613 nipype.workflow INFO:
[Job 14] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource).
251020-15:47:43,80 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/spacesource".
251020-15:47:43,82 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:43,83 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.00017s.
251020-15:47:43,84 nipype.workflow INFO:
[Job 15] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource).
251020-15:47:43,419 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/spacesource".
251020-15:47:43,423 nipype.workflow INFO:
[Node] Executing "spacesource" <niworkflows.interfaces.space.SpaceDataSource>
251020-15:47:43,425 nipype.workflow INFO:
[Node] Finished "spacesource", elapsed time 0.000295s.
251020-15:47:43,427 nipype.workflow INFO:
[Job 16] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.spacesource).
251020-15:47:43,707 nipype.workflow INFO:
[MultiProc] Running 6 tasks, and 17 jobs ready. Free memory (GB): 298.80/300.00, Free processors: 2/8.
Currently running:
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.mask_dil
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.fs_to_mcribs
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.segmentation_wf.to_dseg
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.refine_mask
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.reg_mask
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.bidssrc
251020-15:47:43,929 nipype.workflow INFO:
[Node] Setting-up "_fmt_cohort0" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/concat_registrations_wf/fmt_cohort/mapflow/_fmt_cohort0".
251020-15:47:43,931 nipype.workflow INFO:
[Node] Executing "_fmt_cohort0" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:43,932 nipype.workflow INFO:
[Node] Finished "_fmt_cohort0", elapsed time 0.000363s.
251020-15:47:43,935 nipype.workflow INFO:
[Job 23] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.concat_registrations_wf.fmt_cohort).
251020-15:47:44,131 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.tf_select" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNIInfantcohort-1/tf_select".
251020-15:47:44,134 nipype.workflow INFO:
[Node] Executing "tf_select" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:44,201 nipype.workflow INFO:
[Node] Finished "tf_select", elapsed time 0.066524s.
251020-15:47:44,203 nipype.workflow INFO:
[Job 26] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.tf_select).
251020-15:47:44,463 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.fmt_cohort" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNIInfantcohort-1/fmt_cohort".
251020-15:47:44,466 nipype.workflow INFO:
[Node] Executing "fmt_cohort" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:44,468 nipype.workflow INFO:
[Node] Finished "fmt_cohort", elapsed time 0.000475s.
251020-15:47:44,469 nipype.workflow INFO:
[Job 27] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.fmt_cohort).
251020-15:47:44,934 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.tf_select" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/tf_select".
251020-15:47:44,939 nipype.workflow INFO:
[Node] Executing "tf_select" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:45,79 nipype.workflow INFO:
[Node] Finished "tf_select", elapsed time 0.139169s.
251020-15:47:45,82 nipype.workflow INFO:
[Job 28] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.tf_select).
251020-15:47:45,546 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.fmt_cohort" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/fmt_cohort".
251020-15:47:45,551 nipype.workflow INFO:
[Node] Executing "fmt_cohort" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:45,552 nipype.workflow INFO:
[Node] Finished "fmt_cohort", elapsed time 0.000546s.
251020-15:47:45,555 nipype.workflow INFO:
[Job 29] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.register_template_wf.fmt_cohort).
251020-15:47:45,732 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.reg_mask" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/coregistration_wf/reg_mask".
251020-15:47:45,734 nipype.workflow INFO:
[Node] Executing "reg_mask" <niworkflows.interfaces.nibabel.BinaryDilation>
251020-15:47:45,908 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/gen_tplid".
251020-15:47:45,912 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:45,914 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.000537s.
251020-15:47:45,916 nipype.workflow INFO:
[Job 30] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid).
251020-15:47:46,32 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.refine_mask" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/coregistration_wf/refine_mask".
251020-15:47:46,58 nipype.workflow INFO:
[Node] Executing "refine_mask" <niworkflows.interfaces.nibabel.BinaryDilation>
251020-15:47:46,152 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.fs_to_mcribs" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/mcribs_surface_recon_wf/fs_to_mcribs".
251020-15:47:46,156 nipype.workflow INFO:
[Node] Executing "fs_to_mcribs" <niworkflows.interfaces.nibabel.MapLabels>
251020-15:47:46,161 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.segmentation_wf.to_dseg" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/segmentation_wf/to_dseg".
251020-15:47:46,167 nipype.workflow INFO:
[Node] Executing "to_dseg" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:46,252 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/select_tpl".
251020-15:47:46,259 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:46,273 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.mask_dil" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/mcribs_surface_recon_wf/mask_dil".
251020-15:47:46,278 nipype.workflow INFO:
[Node] Executing "mask_dil" <niworkflows.interfaces.morphology.BinaryDilation>
251020-15:47:46,401 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.140643s.
251020-15:47:46,412 nipype.workflow INFO:
[Job 31] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl).
251020-15:47:46,880 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/gen_tplid".
251020-15:47:46,883 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:46,885 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.00064s.
251020-15:47:46,886 nipype.workflow INFO:
[Job 32] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid).
251020-15:47:47,319 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/select_tpl".
251020-15:47:47,326 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:47,453 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.12572s.
251020-15:47:47,456 nipype.workflow INFO:
[Job 33] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl).
251020-15:47:47,611 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.bidssrc" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/bidssrc".
251020-15:47:47,655 nipype.workflow INFO:
[Node] Executing "bidssrc" <niworkflows.interfaces.bids.BIDSDataGrabber>
251020-15:47:47,658 nipype.interface INFO:
No "flair" images found for sub-5000
251020-15:47:47,659 nipype.interface INFO:
No "roi" images found for sub-5000
251020-15:47:47,659 nipype.interface INFO:
No "pet" images found for sub-5000
251020-15:47:47,659 nipype.interface INFO:
No "asl" images found for sub-5000
251020-15:47:47,660 nipype.workflow INFO:
[Node] Finished "bidssrc", elapsed time 0.001373s.
251020-15:47:47,704 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_tplid".
251020-15:47:47,706 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:47,707 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.00039s.
251020-15:47:47,709 nipype.workflow INFO:
[Job 34] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.gen_tplid).
251020-15:47:47,935 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/select_tpl".
251020-15:47:47,939 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:48,46 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.106911s.
251020-15:47:48,49 nipype.workflow INFO:
[Job 35] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.template_iterator_wf.select_tpl).
251020-15:47:48,538 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/gen_tplid".
251020-15:47:48,545 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:48,548 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.00103s.
251020-15:47:48,550 nipype.workflow INFO:
[Job 36] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid).
251020-15:47:49,79 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNIInfantcohort-1.cohort1.resnative/select_tpl".
251020-15:47:49,81 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:49,166 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.083442s.
251020-15:47:49,168 nipype.workflow INFO:
[Job 37] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl).
251020-15:47:49,483 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/gen_tplid".
251020-15:47:49,486 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:49,488 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.000637s.
251020-15:47:49,490 nipype.workflow INFO:
[Job 38] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid).
251020-15:47:49,732 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin6Asym.res2/select_tpl".
251020-15:47:49,737 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:49,830 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.092293s.
251020-15:47:49,832 nipype.workflow INFO:
[Job 39] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl).
251020-15:47:50,253 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/gen_tplid".
251020-15:47:50,260 nipype.workflow INFO:
[Node] Executing "gen_tplid" <nipype.interfaces.utility.wrappers.Function>
251020-15:47:50,263 nipype.workflow INFO:
[Node] Finished "gen_tplid", elapsed time 0.000822s.
251020-15:47:50,266 nipype.workflow INFO:
[Job 40] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.gen_tplid).
251020-15:47:50,714 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/anat_reports_wf/template_iterator_wf/_in_tuple_MNI152NLin2009cAsym.resnative/select_tpl".
251020-15:47:50,718 nipype.workflow INFO:
[Node] Executing "select_tpl" <smriprep.interfaces.templateflow.TemplateFlowSelect>
251020-15:47:50,840 nipype.workflow INFO:
[Node] Finished "select_tpl", elapsed time 0.120817s.
251020-15:47:50,843 nipype.workflow INFO:
[Job 41] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.anat_reports_wf.template_iterator_wf.select_tpl).
251020-15:47:51,324 nipype.workflow INFO:
[Job 1] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.bidssrc).
251020-15:47:51,328 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 6 jobs ready. Free memory (GB): 299.00/300.00, Free processors: 3/8.
Currently running:
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.mask_dil
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.fs_to_mcribs
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.segmentation_wf.to_dseg
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.refine_mask
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.reg_mask
251020-15:47:51,606 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.bids_info" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/bids_info".
251020-15:47:51,609 nipype.workflow INFO:
[Node] Executing "bids_info" <niworkflows.interfaces.bids.BIDSInfo>
251020-15:47:51,615 nipype.workflow INFO:
[Node] Finished "bids_info", elapsed time 0.005392s.
251020-15:47:51,621 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.t1w_template_wf.anat_ref_dimensions" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/t1w_template_wf/anat_ref_dimensions".
251020-15:47:51,623 nipype.workflow INFO:
[Node] Executing "anat_ref_dimensions" <niworkflows.interfaces.images.TemplateDimensions>
251020-15:47:51,898 nipype.workflow INFO:
[Node] Finished "anat_ref_dimensions", elapsed time 0.274111s.
251020-15:47:51,900 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.t2w_template_wf.anat_ref_dimensions" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/infant_anat_fit_wf/t2w_template_wf/anat_ref_dimensions".
251020-15:47:51,904 nipype.workflow INFO:
[Node] Executing "anat_ref_dimensions" <niworkflows.interfaces.images.TemplateDimensions>
251020-15:47:52,473 nipype.workflow INFO:
[Node] Finished "anat_ref_dimensions", elapsed time 0.56766s.
251020-15:47:53,325 nipype.workflow INFO:
[Job 17] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.bids_info).
251020-15:47:53,325 nipype.workflow INFO:
[Job 18] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.t1w_template_wf.anat_ref_dimensions).
251020-15:47:53,326 nipype.workflow INFO:
[Job 19] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.t2w_template_wf.anat_ref_dimensions).
251020-15:47:53,328 nipype.workflow INFO:
[MultiProc] Running 5 tasks, and 10 jobs ready. Free memory (GB): 299.00/300.00, Free processors: 3/8.
Currently running:
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.mask_dil
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.fs_to_mcribs
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.segmentation_wf.to_dseg
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.refine_mask
* nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.infant_anat_fit_wf.coregistration_wf.reg_mask
251020-15:47:53,680 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.ds_report_about" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/ds_report_about".
251020-15:47:53,688 nipype.workflow INFO:
[Node] Executing "ds_report_about" <nibabies.interfaces.DerivativesDataSink>
251020-15:47:53,853 nipype.workflow INFO:
[Node] Finished "ds_report_about", elapsed time 0.163937s.
251020-15:47:53,856 nipype.workflow INFO:
[Job 20] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.ds_report_about).
251020-15:47:54,152 nipype.workflow INFO:
[Node] Setting-up "nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.summary" in "/work/nibabies_25_0_wf/single_subject_sub-5000_ses-nb0_wf/summary".
251020-15:47:54,374 nipype.workflow INFO:
[Node] Executing "summary" <nibabies.interfaces.reports.SubjectSummary>
251020-15:47:54,400 nipype.workflow INFO:
[Node] Finished "summary", elapsed time 0.02446s.
251020-15:47:54,405 nipype.workflow INFO:
[Job 42] Completed (nibabies_25_0_wf.single_subject_sub-5000_ses-nb0_wf.summary).
251020-15:47:55,113 nipype.workflow ERROR:
Node ds_anat_ref_xfms failed to run on host bbf96e98ed3e.
251020-15:47:55,179 nipype.workflow ERROR:
Saving crash info to /out/sub-5000/ses-nb0/log/20251020-154557_7db9e346-53ad-4444-9af3-bf023c4868ce/crash-20251020-154755-UID2254-ds_anat_ref_xfms-ea2ca5ce-9a25-417c-9ec3-a6f9e9dd84ff.txt
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 291, in _send_procs_to_workers
num_subnodes = self.procs[jobid].num_subnodes()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1307, in num_subnodes
self._check_iterfield()
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1337, in _check_iterfield
raise ValueError(
ValueError: All iterfields of a MapNode have to have the same length.
acquisition = <undefined>
atlas = <undefined>
base_directory = /out
ceagent = <undefined>
check_hdr = True
cohort = <undefined>
compress = <undefined>
data_dtype = <undefined>
datatype = <undefined>
density = <undefined>
desc = <undefined>
direction = <undefined>
dismiss_entities = <undefined>
echo = <undefined>
extension = txt
flip = <undefined>
fmap = <undefined>
fmapid = <undefined>
from = orig
hemi = <undefined>
in_file = [['/opt/conda/envs/nibabies/lib/python3.11/site-packages/smriprep/data/itkIdentityTransform.txt']]
inv = <undefined>
label = <undefined>
meta_dict = <undefined>
modality = <undefined>
mode = image
model = <undefined>
mt = <undefined>
part = <undefined>
proc = <undefined>
reconstruction = <undefined>
recording = <undefined>
resolution = <undefined>
roi = <undefined>
run = <undefined>
scans = <undefined>
session = <undefined>
source_file = [['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-01_T2w.nii.gz'], ['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-02_T2w.nii.gz']]
space = <undefined>
subject = <undefined>
subset = <undefined>
suffix = xfm
task = <undefined>
to = T2w
When creating this crashfile, the results file corresponding
to the node could not be found.
251020-15:47:55,360 nipype.workflow CRITICAL:
nibabies failed: Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 291, in _send_procs_to_workers
num_subnodes = self.procs[jobid].num_subnodes()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1307, in num_subnodes
self._check_iterfield()
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1337, in _check_iterfield
raise ValueError(
ValueError: All iterfields of a MapNode have to have the same length.
acquisition = <undefined>
atlas = <undefined>
base_directory = /out
ceagent = <undefined>
check_hdr = True
cohort = <undefined>
compress = <undefined>
data_dtype = <undefined>
datatype = <undefined>
density = <undefined>
desc = <undefined>
direction = <undefined>
dismiss_entities = <undefined>
echo = <undefined>
extension = txt
flip = <undefined>
fmap = <undefined>
fmapid = <undefined>
from = orig
hemi = <undefined>
in_file = [['/opt/conda/envs/nibabies/lib/python3.11/site-packages/smriprep/data/itkIdentityTransform.txt']]
inv = <undefined>
label = <undefined>
meta_dict = <undefined>
modality = <undefined>
mode = image
model = <undefined>
mt = <undefined>
part = <undefined>
proc = <undefined>
reconstruction = <undefined>
recording = <undefined>
resolution = <undefined>
roi = <undefined>
run = <undefined>
scans = <undefined>
session = <undefined>
source_file = [['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-01_T2w.nii.gz'], ['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-02_T2w.nii.gz']]
space = <undefined>
subject = <undefined>
subset = <undefined>
suffix = xfm
task = <undefined>
to = T2w
When creating this crashfile, the results file corresponding
to the node could not be found.
251020-15:49:06,544 nipype.workflow INFO:
[Node] Finished "reg_mask", elapsed time 80.804189s.
251020-15:49:17,59 nipype.workflow INFO:
[Node] Finished "mask_dil", elapsed time 90.774115s.
251020-15:49:25,121 nipype.workflow INFO:
[Node] Finished "refine_mask", elapsed time 99.026367s.
251020-15:50:01,877 nipype.workflow INFO:
[Node] Finished "to_dseg", elapsed time 135.703118s.
251020-15:50:23,330 nipype.workflow INFO:
[Node] Finished "fs_to_mcribs", elapsed time 157.169651s.
You are using NiBabies-25.0.1, and a newer version of NiBabies is available: 25.2.0.
Please check out our documentation about how and when to upgrade:
https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading
(node:10) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz
0%| | 0.00/13.3M [00:00<?, ?B/s]
5%|▍ | 629k/13.3M [00:00<00:02, 5.39MB/s]
38%|███▊ | 5.00M/13.3M [00:00<00:00, 26.5MB/s]
59%|█████▊ | 7.80M/13.3M [00:00<00:00, 21.9MB/s]
90%|█████████ | 12.0M/13.3M [00:00<00:00, 28.7MB/s]
100%|██████████| 13.3M/13.3M [00:00<00:00, 25.9MB/s]
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 291, in _send_procs_to_workers
num_subnodes = self.procs[jobid].num_subnodes()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1307, in num_subnodes
self._check_iterfield()
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1337, in _check_iterfield
raise ValueError(
ValueError: All iterfields of a MapNode have to have the same length.
acquisition = <undefined>
atlas = <undefined>
base_directory = /out
ceagent = <undefined>
check_hdr = True
cohort = <undefined>
compress = <undefined>
data_dtype = <undefined>
datatype = <undefined>
density = <undefined>
desc = <undefined>
direction = <undefined>
dismiss_entities = <undefined>
echo = <undefined>
extension = txt
flip = <undefined>
fmap = <undefined>
fmapid = <undefined>
from = orig
hemi = <undefined>
in_file = [['/opt/conda/envs/nibabies/lib/python3.11/site-packages/smriprep/data/itkIdentityTransform.txt']]
inv = <undefined>
label = <undefined>
meta_dict = <undefined>
modality = <undefined>
mode = image
model = <undefined>
mt = <undefined>
part = <undefined>
proc = <undefined>
reconstruction = <undefined>
recording = <undefined>
resolution = <undefined>
roi = <undefined>
run = <undefined>
scans = <undefined>
session = <undefined>
source_file = [['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-01_T2w.nii.gz'], ['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-02_T2w.nii.gz']]
space = <undefined>
subject = <undefined>
subset = <undefined>
suffix = xfm
task = <undefined>
to = T2w
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/bin/nibabies", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/cli/run.py", line 104, in main
nibabies_wf.run(**_plugin)
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/workflows.py", line 625, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/base.py", line 198, in run
self._send_procs_to_workers(updatehash=updatehash, graph=graph)
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 294, in _send_procs_to_workers
self._clean_queue(
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/base.py", line 255, in _clean_queue
raise RuntimeError("".join(result["traceback"]))
RuntimeError: Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 291, in _send_procs_to_workers
num_subnodes = self.procs[jobid].num_subnodes()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1307, in num_subnodes
self._check_iterfield()
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 1337, in _check_iterfield
raise ValueError(
ValueError: All iterfields of a MapNode have to have the same length.
acquisition = <undefined>
atlas = <undefined>
base_directory = /out
ceagent = <undefined>
check_hdr = True
cohort = <undefined>
compress = <undefined>
data_dtype = <undefined>
datatype = <undefined>
density = <undefined>
desc = <undefined>
direction = <undefined>
dismiss_entities = <undefined>
echo = <undefined>
extension = txt
flip = <undefined>
fmap = <undefined>
fmapid = <undefined>
from = orig
hemi = <undefined>
in_file = [['/opt/conda/envs/nibabies/lib/python3.11/site-packages/smriprep/data/itkIdentityTransform.txt']]
inv = <undefined>
label = <undefined>
meta_dict = <undefined>
modality = <undefined>
mode = image
model = <undefined>
mt = <undefined>
part = <undefined>
proc = <undefined>
reconstruction = <undefined>
recording = <undefined>
resolution = <undefined>
roi = <undefined>
run = <undefined>
scans = <undefined>
session = <undefined>
source_file = [['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-01_T2w.nii.gz'], ['/data/sub-5000/ses-nb0/anat/sub-5000_ses-nb0_run-02_T2w.nii.gz']]
space = <undefined>
subject = <undefined>
subset = <undefined>
suffix = xfm
task = <undefined>
to = T2wAdd any additional information or context about the problem here.
No response