Remove ICA-AROMA

[effigies]

What would you like to see added in fMRIPrep?

ICA-AROMA is unmaintained, and appears to be incompatible with the version of MELODIC released in FSL 6.0.6.2.

Cmdline:
	ICA_AROMA.py -tr 2.000 -np -den nonaggr -i /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/smooth/vol0000_xform-00000_clipped_merged_smooth.nii.gz -m /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_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 /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/melodic -mc /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out
Stdout:

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

	Step 1) MELODIC
	  - The existing/specified MELODIC directory will be used.
	Step 2) Automatic classification of the components
	  - registering the spatial maps to MNI
Stderr:
	Image Exception : #21 :: Invalid ROI dimensions
	Invalid ROI dimensions
	Image Exception : #21 :: Invalid ROI dimensions
	Invalid ROI dimensions
	Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????
	Aborted (core dumped)
	rm: cannot remove '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????.nii.gz': No such file or directory
	Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr
	Aborted (core dumped)
	Traceback (most recent call last):
	  File "/opt/ICA-AROMA/ICA_AROMA.py", line 210, in <module>
	    aromafunc.register2MNI(fslDir, melIC, melIC_MNI, affmat, warp)
	  File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 161, in register2MNI
	    pixdim1 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim1 | awk \'{print $2}\'' % (fslDir, inFile)))
	ValueError: could not convert string to float: 'Image Exception : #63 :: No image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr\nNo image files match: /scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr'
Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, 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 '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_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 399, 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 461, in aggregate_outputs
	    raise FileNotFoundError(msg)
	FileNotFoundError: No such file or directory '/scratch/fmriprep_23_0_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' for output 'nonaggr_denoised_file' of a ICA_AROMARPT interface

Given that people can request outputs in MNI152NLin6Asym space, it should be possible to run the necessary steps post-preprocessing, and then we will not have our hands tied by unmaintained dependencies.

cc @jdkent

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

No response

[jdkent]

I believe this does appear valid, does not appear to be in conflict with the proposed workflow.

I'm curious if all that's different now is a filename change, which may be straightforward for me to fix. Does not solve the long-term issue of unmaintained software

[michaelhallquist]

I just wanted to put in a plug for keeping ICA-AROMA. I appreciate that it may need to be updated to be compatible with the latest MELODIC, but that seems like a better move than removing it from fmriprep. In addition to folks in my lab, a number of colleagues continue to use ICA-AROMA regularly, and removing it from fmriprep would generate a new problem for us to solve. I tested the base installation of ICA-AROMA on our university cluster with FSL 6.0.6 and did not encounter problems. Do you have a reproducible example of what causes it to crash in fmriprep? I'd be happy to take a look at this if so.

# this works for me.
python ica_aroma/ICA_AROMA.py -overwrite -tr 1.0 \
-in mni_nosmooth_aroma/clock1/nfawuktm_clock1.nii.gz \
-out /pine/scr/m/n/mnhallq/ica_aroma -mc clock1/motion.par \
-warp fonov_mni152_to_fsl_mni152_warpcoef.nii.gz
...
Step 3) Data denoising

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

[effigies]

@michaelhallquist See #2980 (CI output):

230404-21:40:22,922 nipype.workflow INFO:
	 ***********************************
230404-21:40:22,922 nipype.workflow ERROR:
	 could not run node: fmriprep_23_1_wf.single_subject_01_wf.func_preproc_task_mixedgamblestask_run_02_wf.ica_aroma_wf.ica_aroma
230404-21:40:22,926 nipype.workflow INFO:
	 crashfile: /out/fmriprep/sub-01/log/20230404-211412_d4123983-8b9f-43d6-9458-674954fd1c18/crash-20230404-213215-UID1001-ica_aroma-22a68672-708e-4197-8cf8-6ea89ff46711.txt
230404-21:40:22,926 nipype.workflow INFO:
	 ***********************************
230404-21:40:22,970 nipype.workflow CRITICAL:
	 fMRIPrep failed: 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 2.000 -np -den nonaggr -i /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/smooth/vol0000_xform-00000_clipped_merged_smooth.nii.gz -m /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_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 /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/melodic -mc /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out
Stdout:

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

	Step 1) MELODIC
	  - The existing/specified MELODIC directory will be used.
	Step 2) Automatic classification of the components
	  - registering the spatial maps to MNI
Stderr:
	Image Exception : #21 :: Invalid ROI dimensions
	Invalid ROI dimensions
	Image Exception : #21 :: Invalid ROI dimensions
	Invalid ROI dimensions
	Image Exception : #63 :: No image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????
	Aborted (core dumped)
	rm: cannot remove '/scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/thr_zstat????.nii.gz': No such file or directory
	Image Exception : #63 :: No image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr
	terminate called after throwing an instance of 'std::runtime_error'
	  what():  No image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr
	Aborted (core dumped)
	Traceback (most recent call last):
	  File "/opt/ICA-AROMA/ICA_AROMA.py", line 210, in <module>
	    aromafunc.register2MNI(fslDir, melIC, melIC_MNI, affmat, warp)
	  File "/opt/ICA-AROMA/ICA_AROMA_functions.py", line 161, in register2MNI
	    pixdim1 = float(subprocess.getoutput('%sfslinfo %s | grep pixdim1 | awk \'{print $2}\'' % (fslDir, inFile)))
	ValueError: could not convert string to float: 'Image Exception : #63 :: No image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr\nNo image files match: /scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/melodic_IC_thr'
Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 454, 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 '/scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_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 399, 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 461, in aggregate_outputs
	    raise FileNotFoundError(msg)
	FileNotFoundError: No such file or directory '/scratch/fmriprep_23_1_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma/out/denoised_func_data_nonaggr.nii.gz' for output 'nonaggr_denoised_file' of a ICA_AROMARPT interface

[maartenmennes]

Hi Chris @effigies, I just stumbled onto this. I wouldn't go as far as saying that AROMA is not maintained. I agree it isn't the nicest codebase, but thus far it has required limited changes to fit into existing pipelines and thus appear unmaintained. Issues are monitored though...

Without knowing the details, it looks like the error reported above is related to using a different MNI template than the original MNI152 one that is shipped with FSL. The incompatibility between templates is a very annoying feature of MRI research and one that I would indeed like AROMA to not rely on...

Then again I'm unfortunately not following fMRIprep close enough to know whether you in the mean time have made your own implementation of AROMA available. If not, I would be hesitant to simply remove AROMA if the only alternative is scrubbing...

[effigies]

Hi @maartenmennes. The FSL compatibility issue caused us to rethink the inclusion of AROMA, but once I realized that AROMA could be performed post-fMRIPrep without losing functionality, it became very compelling. fMRIPrep is a large and intricate enough workflow without it.

I would like to rebundle the workflow here so that users can easily get the derivatives and reports they were getting before: https://github.com/nipreps/fmripost-aroma. AROMA being a slow-moving target compared to the rest of fMRIPrep, this seems like a better fit.

I think it's about 1-2 days of work to build and test, and would make a good OHBM hackathon project.