ValueError: BinaryDilation requires a value for input 'in_file' (using MCRIBS recon w/ precomputed mask) #309
Description
What happened?
The below error occured testing the t1-t2-derivatives branch, in a subject that previously ran w/o error with 23.1.0rc0, with the only differences in the input data being:
- precomputed mask/aseg derivatives in both T1w and T2w space were included (instead of T2w only)
- the precomputed derivatives were changed from "space-orig" to "space-T1w" / "space-T2w" naming convention
What command did you use?
singularity run <...> \
nibabies_t1-t2-derivatives.sif /bids_dir /output_dir participant \
--project-goodvoxels \
--surface-recon-method mcribs \
--omp-nthreads 3 \
--derivatives /derivatives/bibsnet \
--resource-monitor \
--cifti-output 91k \
-vv \
-w /wd \
--fd-radius 35 \What version of NiBabies are you using?
t1-t2-derivatives branch - https://hub.docker.com/layers/nipreps/nibabies/t1-t2-derivatives/images/sha256-1d1272a751e94214569edd69185cab522039242887707f78fc6d19a8758f5b95
Relevant log output
---
Slurm .err
---
(node:4104010) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
[WARNING] Citeproc: citation templateflow not found
exception calling callback for <Future at 0x7f113a6ffd90 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
result = self._interface.run(cwd=outdir, ignore_exception=True)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 388, in run
self._check_mandatory_inputs()
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: BinaryDilation requires a value for input 'in_file'. For a list of required inputs, see BinaryDilation.help()
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 70, in run_node
result["result"] = node.result
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 223, in result
return _load_resultfile(
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py", line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /wd/nibabies_23_2_wf/single_subject_SUB_SES_wf/infant_anat_wf/coregistration_wf/refine_mask/result_refine_mask.pklz
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 342, in _invoke_callbacks
callback(self)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
result = args.result()
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
FileNotFoundError: /wd/nibabies_23_2_wf/single_subject_SUB_SES_wf/infant_anat_wf/coregistration_wf/refine_mask/result_refine_mask.pklz
exception calling callback for <Future at 0x7f113a6ffdf0 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
result = self._interface.run(cwd=outdir, ignore_exception=True)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 388, in run
self._check_mandatory_inputs()
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: BinaryDilation requires a value for input 'in_file'. For a list of required inputs, see BinaryDilation.help()
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 70, in run_node
result["result"] = node.result
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 223, in result
return _load_resultfile(
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py", line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /wd/nibabies_23_2_wf/single_subject_SUB_SES_wf/infant_anat_wf/coregistration_wf/reg_mask/result_reg_mask.pklz
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 342, in _invoke_callbacks
callback(self)
File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
result = args.result()
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 451, in result
return self.__get_result()
File "/opt/conda/envs/nibabies/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
raise self._exception
FileNotFoundError: /wd/nibabies_23_2_wf/single_subject_SUB_SES_wf/infant_anat_wf/coregistration_wf/reg_mask/result_reg_mask.pklz
slurmstepd: error: *** JOB 75319551 ON acl22 CANCELLED AT 2023-08-18T23:53:05 DUE TO TIME LIMIT ***
---
Slurm .log (up to "nibabies started!"):
---
230818-17:53:24,124 cli INFO:
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
[email protected]
[33m1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)[39m
[36m Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.[39m
[34m[4mSummary:[24m[39m [34m[4mAvailable Tasks:[24m[39m [34m[4mAvailable Modalities:[24m[39m
20 Files, 1.2GB rest MRI
1 - Subject
1 - Session
[36m If you have any questions, please post on https://neurostars.org/tags/bids.[39m
230818-17:53:30,326 nipype.workflow IMPORTANT:
Running nibabies version 23.2.0.dev15+gd48007f:
* BIDS dataset path: /bids_dir.
* Participant list: [['SUB', 'SES']].
* Run identifier: 20230818-175310_afd0442f-47c4-4ce0-ab6b-e3f6cf68a9ad.
* Output spaces: MNIInfant.
* Pre-run FreeSurfer's SUBJECTS_DIR: /output_dir/sourcedata/freesurfer.
230818-17:53:31,156 nipype.workflow INFO:
Searching for derivatives in /derivatives/bibsnet
230818-17:53:31,680 nipype.workflow INFO:
Found precomputed derivatives t2w_aseg
t1w_aseg
t1w_mask
t2w_mask
230818-17:53:31,892 nipype.workflow INFO:
Derivatives used:
<T1 mask False>
<T1 aseg False>
<T2 mask True>
<T2 aseg True>
230818-17:53:32,795 nipype.workflow INFO:
No single-band-reference found for sub-SUB_ses-SES_task-rest_acq-AP_run-03_bold.nii.gz.
230818-17:53:32,796 nipype.workflow INFO:
Found usable B0-map (fieldmap) estimator(s) <auto_00001> to correct </bids_dir/sub-SUB/ses-SES/func/sub-SUB_ses-SES_task-rest_acq-AP_run-03_bold.nii.gz> for susceptibility-derived distortions.
230818-17:53:32,909 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.311s.
230818-17:53:35,103 nipype.workflow INFO:
No single-band-reference found for sub-SUB_ses-SES_task-rest_acq-PA_run-01_bold.nii.gz.
230818-17:53:35,104 nipype.workflow INFO:
Found usable B0-map (fieldmap) estimator(s) <auto_00000> to correct </bids_dir/sub-SUB/ses-SES/func/sub-SUB_ses-SES_task-rest_acq-PA_run-01_bold.nii.gz> for susceptibility-derived distortions.
230818-17:53:35,194 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.311s.
230818-17:53:35,563 nipype.workflow INFO:
No single-band-reference found for sub-SUB_ses-SES_task-rest_acq-PA_run-02_bold.nii.gz.
230818-17:53:35,563 nipype.workflow INFO:
Found usable B0-map (fieldmap) estimator(s) <auto_00001> to correct </bids_dir/sub-SUB/ses-SES/func/sub-SUB_ses-SES_task-rest_acq-PA_run-02_bold.nii.gz> for susceptibility-derived distortions.
230818-17:53:35,655 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.311s.
230818-17:53:35,974 nipype.workflow INFO:
Fieldmap estimators found: [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>]
230818-17:53:37,269 nipype.workflow INFO:
Setting-up fieldmap "auto_00000" (EstimatorType.PEPOLAR) with <sub-SUB_ses-SES_dir-AP_run-02_epi.nii.gz, sub-SUB_ses-SES_dir-PA_run-01_epi.nii.gz>
230818-17:53:37,292 nipype.workflow INFO:
Setting-up fieldmap "auto_00001" (EstimatorType.PEPOLAR) with <sub-SUB_ses-SES_dir-AP_run-04_epi.nii.gz, sub-SUB_ses-SES_dir-PA_run-03_epi.nii.gz>
230818-17:53:38,4 nipype.workflow INFO:
NiBabies workflow graph with 1058 nodes built successfully.
230818-17:53:38,15 cli INFO:
Generating an HTML version of the citation boilerplate...
230818-17:53:40,625 cli INFO:
Generating a LaTeX version of the citation boilerplate...
230818-17:53:41,164 nipype.workflow VERBOSE:
nibabies config:
[environment]
cpu_count = 128
exec_env = "singularity"
free_mem = 1641.3
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "23.0.0"
version = "23.2.0.dev15+gd48007f"
[execution]
bids_dir = "/bids_dir"
bids_database_dir = "/wd/20230818-175310_afd0442f-47c4-4ce0-ab6b-e3f6cf68a9ad/bids_db"
bids_description_hash = "cb2b9d74d3ee45030afbed8b010af9a61270952f6b0dde28ed1718d7199a57df"
boilerplate_only = false
sloppy = false
debug = []
derivatives = [ "/derivatives/bibsnet",]
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/output_dir/sourcedata/freesurfer"
layout = "BIDS Layout: .../bids_dir | Subjects: 1 | Sessions: 1 | Runs: 4"
log_dir = "/output_dir/logs"
log_level = 15
low_mem = false
mcribs_dir = "/output_dir/sourcedata/mcribs"
md_only_boilerplate = false
nibabies_dir = "/output_dir"
notrack = false
output_dir = "/output_dir"
me_output_echos = false
output_layout = "bids"
reports_only = false
run_uuid = "20230818-175310_afd0442f-47c4-4ce0-ab6b-e3f6cf68a9ad"
participant_label = [ "SUB",]
templateflow_home = "/home/feczk001/tmadison/.cache/templateflow"
unique_labels = [ [ "SUB", "SES",],]
work_dir = "/wd"
write_graph = false
[workflow]
analysis_level = "participant"
anat_only = false
aroma_err_on_warn = false
aroma_melodic_dim = -200
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = "91k"
fd_radius = 35.0
fmap_bspline = false
force_syn = false
hires = true
ignore = []
longitudinal = false
medial_surface_nan = false
project_goodvoxels = true
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "UNCInfant:cohort-1"
skull_strip_t1w = "force"
slice_time_ref = 0.5
surface_recon_method = "mcribs"
use_aroma = false
use_bbr = false
use_syn_sdc = false
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 24
omp_nthreads = 3
plugin = "MultiProc"
resource_monitor = true
stop_on_first_crash = false
[seeds]
master = 21728
ants = 62702
numpy = 23605
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
230818-17:53:41,164 nipype.workflow IMPORTANT:
nibabies started!Add any additional information or context about the problem here.
The MCRIBS recon still completed for this subject (derivatives/sourcedata/mcribs contains the expected outputs, and the MCRIBS logs reported no errors)