Error in ica_aroma

wenjun · October 19, 2022, 1:43am

Hello all,

I was using fmriprep v21.0.4 on ubuntu18.04. I added ‘–use-aroma’ in my command, and the following error occurred during the run:

[Node] Running "ica_aroma" ("niworkflows.interfaces.reportlets.segmentation.ICA_AROMARPT"), a CommandLine Interface with command:
ICA_AROMA.py -tr 2.000 -np -den nonaggr -i /work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/smooth/vol0000_xform-00000_clipped_merged_cut_smooth.nii.gz -m /work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/vol0000_xform-00000_clipped_merged_average_corrected_brain_mask_maths_trans.nii.gz -meldir /work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/melodic -mc /work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/ica_aroma/out
221018-17:19:15,768 nipype.workflow WARNING:
	 Storing result file without outputs
221018-17:19:15,771 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_wf.single_subject_001_wf.func_preproc_ses_1_task_rest_wf.ica_aroma_wf.ica_aroma" (/work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/ica_aroma)
221018-17:19:17,478 nipype.workflow ERROR:
	 Node ica_aroma failed to run on host 9712878cbe33.
221018-17:19:18,73 nipype.workflow ERROR:
	 Saving crash info to /out/sub-001/log/20221018-123357_7c238fb6-55a5-4678-9056-0acada24def5/crash-20221018-171917-root-ica_aroma-3ee44c10-5ba6-46bd-ae3c-5433632b4f2d.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 530, in aggregate_outputs
    setattr(outputs, key, val)
  File "/opt/conda/lib/python3.8/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/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/opt/conda/lib/python3.8/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 '/work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_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/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 429, in run
    runtime = self._post_run_hook(runtime)
  File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/reportlets/segmentation.py", line 231, in _post_run_hook
    outputs = self.aggregate_outputs(runtime=runtime)
  File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 537, in aggregate_outputs
    raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory '/work/fmriprep_wf/single_subject_001_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' for output 'nonaggr_denoised_file' of a ICA_AROMARPT interface

221018-17:19:19,406 nipype.workflow ERROR:
	 could not run node: fmriprep_wf.single_subject_001_wf.func_preproc_ses_1_task_rest_wf.ica_aroma_wf.ica_aroma
221018-17:19:19,496 nipype.workflow CRITICAL:
	 fMRIPrep failed: Workflow did not execute cleanly. Check log for details
221018-17:19:24,711 cli ERROR:
	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: 001 (1). Check the HTML reports for details.
221018-17:19:24,711 cli ERROR:
	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: 001 (1). Check the HTML reports for details.

Thank you for any help you can offer!
Jun

Steven · October 19, 2022, 1:47am

Hi Jun,

What is your full fMRIPrep command? Does the error persist when upgrading to the latest fMRIPrep version (22.0.2) and a using fresh working directory?

Best,
Steven

wenjun · October 19, 2022, 12:51pm

Hi Steven,

I changed my output path and working path. Here is my command:

sudo docker run -ti --rm
-v /mnt/hgfs/share/Nifti/project:/data:ro
-v /home/jun/project-derivatives:/out
-v /home/jun/project/work:/work
-v /home/jun/freesurfer/license.txt:/opt/freesurfer/license.txt
nipreps/fmriprep /data /out participant --participant-label 001 -w /work --use-aroma --dummy-scans 4

and an out of memory error has occurred:

Node: fmriprep_wf.single_subject_D040_wf.func_preproc_ses_1_task_rest_wf.ica_aroma_wf.calc_median_val
Working directory: /work/fmriprep_wf/single_subject_D040_wf/func_preproc_ses_1_task_rest_wf/ica_aroma_wf/calc_median_val

Node inputs:

args =
environ = {‘FSLOUTPUTTYPE’: ‘NIFTI_GZ’}
in_file =
index_mask_file =
mask_file =
op_string = -k %s -p 50
output_type = NIFTI_GZ
split_4d =

Traceback (most recent call last):
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 428, in run
runtime = self._run_interface(runtime)
File “/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 822, in _run_interface
self.raise_exception(runtime)
File “/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py”, line 749, in raise_exception
raise RuntimeError(
RuntimeError: Command:
fslstats /work/fmriprep_wf/single_subject_D040_wf/func_preproc_ses_1_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/merge/vol0000_xform-00000_clipped_merged_cut.nii.gz -k /work/fmriprep_wf/single_subject_D040_wf/func_preproc_ses_1_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/vol0000_xform-00000_clipped_merged_average_corrected_brain_mask_maths_trans.nii.gz -p 50
Standard output:

Standard error:
Image Exception : #99 :: Out of memory
Out of memory
Return code: 255

I think it may be due to insufficient memory (docker info: CPUs: 16 Total Memory: 7.765GiB) because it works well on another computer using the same fmriprep version and similar command.
BTW I install fmriprep a few days ago using the command: docker pull nipreps/fmriprep and default tag: latest, but it was not v22.0.2 instead of v21.0.4.

Many thanks!
Jun

Steven · October 19, 2022, 1:04pm

Hi,

You can install 22.0.2 with docker pull nipreps/fmriprep:22.0.2.

Yes, 8 GB is not a lot of memory, especially when you have 16 CPUs working.

Best,
Steven