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ds003721-fmriprep: "Only one time point!" #83

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jbwexler opened this issue Jun 4, 2024 · 1 comment
Open

ds003721-fmriprep: "Only one time point!" #83

jbwexler opened this issue Jun 4, 2024 · 1 comment
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@effigies
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fmriprep Affects fMRIPrep

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@jbwexler
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jbwexler commented Jun 4, 2024 •
edited
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Occurred for all subjects in dataset. I checked the bolds for one subject and found them to have many time points.

Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocessing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/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/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
Node: fmriprep_23_2_wf.sub_03_wf.syn_preprocessing_auto_00002.epi_reference_wf.epi_merge
Working directory: /node_tmp/work_dir/fmriprep/ds003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocess
ing_auto_00002/epi_reference_wf/epi_merge

Node inputs:

args = <undefined>
auto_detect_sensitivity = True
average_metric = <undefined>
environ = {'SUBJECTS_DIR': '/opt/freesurfer/subjects', 'OMP_NUM_THREADS': '1'}
fixed_timepoint = True
in_files = <undefined>
in_intensity_scales = <undefined>
initial_timepoint = 1
initial_transforms = <undefined>
intensity_scaling = True
no_iteration = True
num_threads = 1
out_file = mri_robust_template_out.mgz
outlier_sensitivity = <undefined>
scaled_intensity_outputs = <undefined>
subjects_dir = /opt/freesurfer/subjects
subsample_threshold = 200
transform_outputs = True

Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", lin
e 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527
, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645
, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/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 epi_merge.

Cmdline:
        echo Only one time point!
Stdout:
        Only one time point!
Stderr:

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", l
ine 453, in aggregate_outputs
            setattr(outputs, key, val)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_exte
nsion.py", line 330, in validate
            value = super(File, self).validate(objekt, name, value, return_pathlike=True)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_exte
nsion.py", line 135, in validate
            self.error(objekt, name, str(value))
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py", lin
e 74, in error
            raise TraitError(
        traits.trait_errors.TraitError: The 'out_lta' trait of a LTAConvertOutputSpec instance must be a
 pathlike object or string representing an existing file, but a value of '/node_tmp/work_dir/fmriprep/ds
003721_sub-03/fmriprep_23_2_wf/sub_03_wf/syn_preprocessing_auto_00002/epi_reference_wf/epi_merge/tp1.lta
' <class 'str'> was specified.

        During handling of the above exception, another exception occurred:

        Traceback (most recent call last):
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", l
ine 400, in run
            outputs = self.aggregate_outputs(runtime)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", l
ine 429, in aggregate_outputs
            predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/freesurfer.
py", line 97, in _list_outputs
            ).run()
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", l
ine 400, in run
            outputs = self.aggregate_outputs(runtime)
          File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", l
ine 460, in aggregate_outputs
            raise FileNotFoundError(msg)
        FileNotFoundError: No such file or directory '/node_tmp/work_dir/fmriprep/ds003721_sub-03/fmripr
ep_23_2_wf/sub_03_wf/syn_preprocessing_auto_00002/epi_reference_wf/epi_merge/tp1.lta' for output 'out_lt
a' of a LTAConvert interface
@jbwexler jbwexler added the fmriprep Affects fMRIPrep label Jun 4, 2024
@effigies effigies self-assigned this Jun 4, 2024
@effigies
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effigies commented Jun 4, 2024

Reproduce locally

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