ds002837-fmriprep: ICA-AROMA issues

[jbwexler]

For majority of subjects (only 19 out of 86 were successful):

Node: fmriprep_23_0_wf.single_subject_5_wf.func_preproc_task_500daysofsummer_run_01_wf.ica_aroma_wf.ica_aroma Working directory: /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/ica_aroma

Node inputs:

TR = 1.0 args = -np compress_report = auto denoise_type = nonaggr dim = environ = {} feat_dir = fnirt_warp_file = in_file = mask = mat_file = melodic_dir = motion_parameters = out_dir = out out_report = ica_aroma_reportlet.svg report_mask =

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 527, in run result = self._run_interface(execute=True) File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface return self._run_command(execute) File "/opt/conda/lib/python3.9/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 ica_aroma.

Cmdline: ICA_AROMA.py -tr 1.000 -np -den nonaggr -i /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/smooth/vol0000_xform-00000_clipped_merged_smooth.nii.gz -m /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/vol0000_unwarped_merged_valid_average_corrected_brain_mask_maths_trans.nii.gz -meldir /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/melodic -mc /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/ica_aroma/out Stdout:

    ------------------------------- RUNNING ICA-AROMA -------------------------------
    --------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------

    Warning! Please check whether the determined TR (of 1.0s) is correct!

    Step 1) MELODIC
      - The existing/specified MELODIC directory will be used.
    Step 2) Automatic classification of the components
      - registering the spatial maps to MNI
      - extracting the CSF & Edge fraction features
      - extracting the Maximum RP correlation feature
      - extracting the High-frequency content feature
      - classification
    Step 3) Data denoising

    ----------------------------------- Finished -----------------------------------

Stderr: Image Exception : #99 :: Out of memory Out of memory Traceback: Traceback (most recent call last): File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs setattr(outputs, key, val) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate value = super(File, self).validate(objekt, name, value, return_pathlike=True) File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate self.error(objekt, name, str(value)) File "/opt/conda/lib/python3.9/site-packages/traits/base_trait_handler.py", line 74, in error raise TraitError( traits.trait_errors.TraitError: The 'nonaggr_denoised_file' trait of a _ICA_AROMAOutputSpecRPT instance must be a pathlike object or string representing an existing file, but a value of '/scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func _preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' <class 'str'> was specified.

    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._post_run_hook(runtime)
      File "/opt/conda/lib/python3.9/site-packages/niworkflows/interfaces/reportlets/segmentation.py", line 231, in _post_run_hook
        outputs = self.aggregate_outputs(runtime=runtime)
      File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
        raise FileNotFoundError(msg)
    FileNotFoundError: No such file or directory '/scratch1/03201/jbwexler/work_dir/fmriprep/ds002837_sub-5/fmriprep_23_0_wf/single_subject_5_wf/func_preproc_task_500daysofsummer_run_01_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' for output 'nonaggr_denoised_file' of a ICA_AROMARPT interface

[effigies]

Image Exception : #99 :: Out of memory
Out of memory

All there is to do there is rerun (possibly with fewer simultaneous BOLD files) or simply not run ICA-AROMA.

[jbwexler]

Sounds good. So you don't think "Warning! Please check whether the determined TR (of 1.0s) is correct!" is an issue?

[effigies]

Unlikely. I think it comes from a time when 1s TR was very fast so likely indicative of an error. This is movie-watching, so they're going for "big", and so a short TR is plausible.

[jbwexler]

Running without ica-aroma solved this.