ds002411-fmriprep: transform_Warped.nii.gz not found

[jbwexler]

For about half the subjects:

Node: fmriprep_22_0_wf.single_subject_01_wf.func_preproc_task_ProgramCategorization_run_06_wf.co eff2epi_wf.coregister Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds002411_sub-01/fmriprep_22_0_wf/s ingle_subject_01_wf/func_preproc_task_ProgramCategorization_run_06_wf/coeff2epi_wf/coregister

Node inputs:

args = collapse_output_transforms = True convergence_threshold = [1e-07, 1e-08] convergence_window_size = [5, 3] dimension = 3 environ = {'NSLOTS': '7'} fixed_image = fixed_image_mask = fixed_image_masks = float = initial_moving_transform = initial_moving_transform_com = 1 initialize_transforms_per_stage = False interpolation = LanczosWindowedSinc interpolation_parameters = invert_initial_moving_transform = metric = ['Mattes', 'Mattes'] metric_item_trait = metric_stage_trait = metric_weight = [1.0, 1.0] metric_weight_item_trait = 1.0 metric_weight_stage_trait = moving_image = moving_image_mask = moving_image_masks = num_threads = 7 number_of_iterations = [[50], [20]] output_inverse_warped_image = output_transform_prefix = transform output_warped_image = True radius_bins_item_trait = 5 radius_bins_stage_trait = radius_or_number_of_bins = [32, 32] random_seed = restore_state = restrict_deformation = sampling_percentage = [0.25, 0.5] sampling_percentage_item_trait = sampling_percentage_stage_trait = sampling_strategy = ['Random', 'Random'] sampling_strategy_item_trait = sampling_strategy_stage_trait = save_state = shrink_factors = [[2], [1]] sigma_units = ['mm', 'mm'] smoothing_sigmas = [[8.0], [2.0]] transform_parameters = [(0.1,), (0.1,)] transforms = ['Rigid', 'Rigid'] use_estimate_learning_rate_once = [True, False] use_histogram_matching = [True, True] verbose = False winsorize_lower_quantile = 0.001 winsorize_upper_quantile = 0.999 write_composite_transform = False

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command raise NodeExecutionError( nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node coregister.

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nibabel/loadsave.py", line 90, in load stat_result = os.stat(filename) FileNotFoundError: [Errno 2] No such file or directory: '/scratch1/03201/jbwexler/work_dir/fmriprep/ds002411_sub-01/fmriprep_22_0_wf/single_subject_01_wf/func_preproc_task_ProgramCategorization_run_06_wf/coeff2epi_wf/coregister/transform_Warped.nii.gz'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 398, in run runtime = self._run_interface(runtime) File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/fixes.py", line 110, in _run_interface _copyxform( File "/opt/conda/lib/python3.9/site-packages/niworkflows/utils/images.py", line 79, in _copyxform resampled = nb.load(out_image, mmap=False) File "/opt/conda/lib/python3.9/site-packages/nibabel/loadsave.py", line 92, in load raise FileNotFoundError(f"No such file or no access: '{filename}'") FileNotFoundError: No such file or no access: '/scratch1/03201/jbwexler/work_dir/fmriprep/ds002411_sub-01/fmriprep_22_0_wf/single_subject_01_wf/func_preproc_task_ProgramCategorization_run_06_wf/coeff2epi_wf/coregister/transform_Warped.nii.gz'

[effigies]

This is almost certainly a filesystem sync issue. Rerunning should resolve.

[effigies]

Looks like https://github.com/nipreps/fmriprep/issues/2878. This could be a deeper sdcflows issue.

[liuzhenqi77]

I'm seeing the same error on ds004078 subject-01 using fmriprep 22.0.0.

[jbwexler]

@effigies Do we have a solution for this yet?

[effigies]

No, I haven't figured out what led to this. Did you try rerunning?

[jbwexler]

I haven't, I can try that.

[jbwexler]

Hmm rerunning didn't seem to solve this. Perhaps I need to delete the old work dirs?

[effigies]

I think deleting /scratch1/03201/jbwexler/work_dir/fmriprep/ds002411_sub-01/fmriprep_22_0_wf/single_subject_01_wf/func_preproc_task_ProgramCategorization_run_06_wf/coeff2epi_wf/coregister should be enough.