-derivatives flag crash #3580
Description
What happened?
I had a subject with two sessions each with their own anatomy (-subject-anatomical-reference sessionwise ) We have a thurd session with no anatomy and I need to use a specific existing anat:
sub-chrep000001$ ls * ses-19831: anat fmap func ses-22501: anat fmap func ses-22681: fmap func
I used the --derivative flag:
--derivatives anat=/output/sub-chrep000001/ses-22501/anat func=/output/sub-chrep000001/ses-22501/func
and While I did obtain what seems to be complete func resutls, there was a crash and a directory I did not anticipate in the ses level (ses-multi-6732)
What command did you use?
`
/usr/bin/docker service create \
--constraint 'node.hostname==plisskenmri.nyspi.local' \
--replicas 1 \
--reserve-cpu 8 \
--reserve-memory 32g \
--mode replicated \
--restart-condition none \
--mount type=bind,source=$indir,destination=/input,readonly=true \
--mount type=bind,source=$outdir,destination=/output \
--mount type=bind,source=/MRI_DATA/bin/freesurferlicense.txt,destination=/opt/freesurfer/license.txt,readonly=true \
nipreps/fmriprep:25.2.1 /input /output participant \
--participant-label chrep000001 \
--subject-anatomical-reference sessionwise \
--output-spaces MNI152NLin2009cAsym:res-native \
--cifti-output \
--project-goodvoxels \
--ignore slicetiming`
/MRI_DATA/bin/subfmri-arg-25.2.1 -i /MRI_DATA/mritesting/patechrep/rawdata -o /MRI_DATA/mritesting/patechrep/derivatives/fmriprep25.2.1 -l /MRI_DATA/mritesting/patechrep/derivatives/fmriprep25.2.1/singleanat.log -a "--derivatives
anat=/output/sub-chrep000001/ses-22501/anat
func=/output/sub-chrep000001/ses-22501/func
--participant-label chrep000001 --output-spaces MNI152NLin2009cAsym:res-native --cifti-output --project-goodvoxels --ignore slicetiming"What version of fMRIPrep are you running?
25.2.1
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
Anatomical derivatives
Please copy and paste any relevant log output.
[DSCLAB-6111a:ses-multi-6732/log/20251202-154729_6bbcd289-6037-4902-af40-8cd574febc63] juan% cat fmriprep.toml
[environment]
cpu_count = 24
exec_env = "singularity"
free_mem = 123.3
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.10.0"
templateflow_version = "25.0.4"
version = "25.2.1"
[execution]
bids_dir = "/input"
bids_database_dir = "/tmp/work/20251202-154729_6bbcd289-6037-4902-af40-8cd574febc63/bids_db"
bids_description_hash = "bfc1d37ead66565cf73e4d48a4a0bb5677d58892191953d109550aa063e1b034"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/output"
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/output/sourcedata/freesurfer"
layout = "BIDS Layout: .../input | Subjects: 1 | Sessions: 3 | Runs: 4"
log_dir = "/output/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/output"
me_output_echos = false
aggr_ses_reports = 4
output_layout = "bids"
output_spaces = "MNI152NLin2009cAsym:res-native"
reports_only = false
run_uuid = "20251202-154729_6bbcd289-6037-4902-af40-8cd574febc63"
processing_groups = [ "sub-chrep000001_ses-19831,22501,22681",]
participant_label = [ "chrep000001",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/tmp/work"
write_graph = false
[workflow]
anat_only = false
bold2anat_dof = 6
bold2anat_init = "t2w"
cifti_output = "91k"
fmap_bspline = false
force_syn = false
hires = true
fs_no_resume = false
ignore = [ "slicetiming",]
force = []
level = "full"
run_msmsulc = true
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 = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "MNI152NLin2009cAsym:res-native MNI152NLin6Asym:res-2"
subject_anatomical_reference = "first-lex"
use_syn_sdc = false
me_t2s_fit_method = "curvefit"
[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 24
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false
[seeds]
master = 45134
ants = 57333
numpy = 44849
[execution.derivatives]
anat = "/output/sub-chrep000001/ses-22501/anat"
func = "/output/sub-chrep000001/ses-22501/func"
[execution.dataset_links]
raw = "/input"
templateflow = "/home/fmriprep/.cache/templateflow"
anat = "/output/sub-chrep000001/ses-22501/anat"
func = "/output/sub-chrep000001/ses-22501/func"
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
Node inputs:
args = <undefined>
bad_vertex_roi_file = <undefined>
column = <undefined>
corrected_areas = <undefined>
data_roi_file = <undefined>
distance = 10.0
environ = {'OMP_NUM_THREADS': '8'}
exponent = <undefined>
in_file = <undefined>
legacy_cutoff = <undefined>
linear = <undefined>
nearest = True
num_threads = 8
out_file = <undefined>
surf_file = <undefined>
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node dilate_curv.
Cmdline:
wb_command -metric-dilate /tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_L/invert_curv/sub-chrep000001_ses-19831.L.curv.native.shape.gii /output/sub-chrep000001/ses-22501/anat/sub-chrep000001_ses-22501_hemi-L_midthickness.surf.gii 10.000000 sub-chrep000001_ses-19831.L.curv.native.shape.func.gii -nearest
Stdout:
Stderr:
While running:
wb_command -metric-dilate /tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_L/invert_curv/sub-chrep000001_ses-19831.L.curv.native.shape.gii /output/sub-chrep000001/ses-22501/anat/sub-chrep000001_ses-22501_hemi-L_midthickness.surf.gii 10.000000 sub-chrep000001_ses-19831.L.curv.native.shape.func.gii -nearest
ERROR: surface and metric number of vertices do not match
Traceback:
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 457, in aggregate_outputs
setattr(outputs, key, val)
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 325, in validate
value = super().validate(objekt, name, value, return_pathlike=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of a MetricDilateOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_L/dilate_curv/sub-chrep000001_ses-19831.L.curv.native.shape.func.gii' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 404, in run
outputs = self.aggregate_outputs(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 464, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_L/dilate_curv/sub-chrep000001_ses-19831.L.curv.native.shape.func.gii' for output 'out_file' of a MetricDilate interface
cat crash-20251202-163609-root-dilate_curv.a1-2d31e540-fc97-4c49-bb4f-0b823e1930cf.txt
Node: fmriprep_25_2_wf.sub_chrep000001_ses_multi-6732_wf.hcp_morphometrics_wf.dilate_curv
Working directory: /tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_R/dilate_curv
Node inputs:
args = <undefined>
bad_vertex_roi_file = <undefined>
column = <undefined>
corrected_areas = <undefined>
data_roi_file = <undefined>
distance = 10.0
environ = {'OMP_NUM_THREADS': '8'}
exponent = <undefined>
in_file = <undefined>
legacy_cutoff = <undefined>
linear = <undefined>
nearest = True
num_threads = 8
out_file = <undefined>
surf_file = <undefined>
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node dilate_curv.
Cmdline:
wb_command -metric-dilate /tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_R/invert_curv/sub-chrep000001_ses-19831.R.curv.native.shape.gii /output/sub-chrep000001/ses-22501/anat/sub-chrep000001_ses-22501_hemi-R_midthickness.surf.gii 10.000000 sub-chrep000001_ses-19831.R.curv.native.shape.func.gii -nearest
Stdout:
Stderr:
While running:
wb_command -metric-dilate /tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_R/invert_curv/sub-chrep000001_ses-19831.R.curv.native.shape.gii /output/sub-chrep000001/ses-22501/anat/sub-chrep000001_ses-22501_hemi-R_midthickness.surf.gii 10.000000 sub-chrep000001_ses-19831.R.curv.native.shape.func.gii -nearest
ERROR: surface and metric number of vertices do not match
Traceback:
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 457, in aggregate_outputs
setattr(outputs, key, val)
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 325, in validate
value = super().validate(objekt, name, value, return_pathlike=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'out_file' trait of a MetricDilateOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_R/dilate_curv/sub-chrep000001_ses-19831.R.curv.native.shape.func.gii' <class 'str'> was specified.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 404, in run
outputs = self.aggregate_outputs(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/fmriprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 464, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/tmp/work/fmriprep_25_2_wf/sub_chrep000001_ses_multi-6732_wf/hcp_morphometrics_wf/_hemi_R/dilate_curv/sub-chrep000001_ses-19831.R.curv.native.shape.func.gii' for output 'out_file' of a MetricDilate interfaceAdditional information / screenshots
No response