Open jbwexler opened 4 weeks ago
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
Reproduce locally
effigies
commented
4 weeks ago effigies
commented
4 weeks ago
Occurred for all subjects in dataset. I checked the bolds for one subject and found them to have many time points.