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Failure when combining confounds #349

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mgxd opened this issue Mar 8, 2024 · 0 comments
Open

Failure when combining confounds #349

mgxd opened this issue Mar 8, 2024 · 0 comments
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@mgxd
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mgxd commented Mar 8, 2024

Node: nibabies_24_0_wf.single_subject_x_wf.func_preproc_task_rest_dir_PA_run_2_wf.bold_confounds_wf.concat
Working directory: /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/concat
Node inputs:
acompcor = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/acompcor/acompcor.tsv
aroma = <undefined>
cos_basis = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/tcompcor/pre_filter.tsv
dvars = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_dvars_header/vol0000_unwarped_merged_dvars_nstd_motion.tsv
fd = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/fdisp/fd_power_2012.txt
motion = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_motion_headers/motion_params_motion.tsv
rmsd = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_rmsd_header/sub-x_task-rest_dir-PA_run-2_bold_mcf.nii.gz_rel_motion.tsv
signals = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/signals/signals.tsv
std_dvars = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/add_std_dvars_header/vol0000_unwarped_merged_dvars_std_motion.tsv
tcompcor = /scratch/nibabies_24_0_wf/single_subject_x_wf/func_preproc_task_rest_dir_PA_run_2_wf/bold_confounds_wf/tcompcor/tcompcor.tsv
Traceback (most recent call last):
  File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].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 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node concat.
Traceback:
    Traceback (most recent call last):
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
        runtime = self._run_interface(runtime)
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/interfaces/confounds.py", line 121, in _run_interface
        combined_out, confounds_list = _gather_confounds(
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/nibabies/interfaces/confounds.py", line 250, in _gather_confounds
        new = pd.read_csv(file_name, sep="\t")
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
        return _read(filepath_or_buffer, kwds)
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 577, in _read
        parser = TextFileReader(filepath_or_buffer, **kwds)
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
        self._engine = self._make_engine(f, self.engine)
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1679, in _make_engine
        return mapping[engine](f, **self.options)
      File "/opt/conda/envs/nibabies/lib/python3.10/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
        self._reader = parsers.TextReader(src, **kwds)
      File "pandas/_libs/parsers.pyx", line 557, in pandas._libs.parsers.TextReader.__cinit__
    pandas.errors.EmptyDataError: No columns to parse from file

24.0.0a1, perhaps similar to nipreps/fmriprep#2761

@mgxd mgxd added the bug Something isn't working label Mar 8, 2024
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