Insights into ICA-AROMA fails and next steps

ddillon · December 22, 2021, 10:10pm

Hi everyone! This week I started playing around with ICA-AROMA and used fmriprep to re-process some old (circa 2014), non-multiband, task-related data collected on a 3T Tim Trio with a 12-channel coil. Surprisingly to me, several runs crashed because ICA-AROMA couldn’t find any signal components. I’m running fmriprep v1.1.4 and will upgrade to stop the crashing (https://github.com/nipreps/fmriprep/pull/1467), but I was surprised that the ICA had any trouble because the data from the failed runs doesn’t look bad to me. For instance, here’s a carpet plot from a run that ICA-AROMA thought had no useful signal in it:

PST_TRAIN_run-2_bold_carpetplot

As you can see, there’s not a lot of motion and nothing seems obviously amiss, and the registrations and recon-all outputs (not shown) all look fine too. I thus have two questions:

What can I do to address this? There don’t seem to be many options for tweaking ICA-AROMA, particularly as implemented in fmriprep, in order to see what could be causing these failures, but I’m totally new to AROMA and pretty new to fmriprep too, so please correct me if I’m wrong. I’m wondering if there is anything I can do so that the ICA will play nice with these data.
Any ideas for why these runs are failing? It’s hard to believe that there are no signal ICs here, because each run includes 60 trials of a task where subjects see stimuli, make a choice, press a button, and get feedback for each response. I’ve analyzed the behavior and it looks good, and a level 3 FEAT analysis on the non-ICA’d fmriprep output yields strong signals in the regions I’d expect to see (this is an RL task and we get signal in accumbens, VMPFC, etc). Perhaps I should just leave well enough alone and stick with the non-ICA’d results, but I’m curious as to why the ICA doesn’t like these data . . . I would think I’d at least see ICs that corresponded to activity in visual or motor systems, even if the subject was drowsy or inattentive or something.

Apologies for the book-length message–any feedback greatly appreciated!

Dan

Steven · December 22, 2021, 11:54pm

Hi Dan,

It would help to know:

What was your command to run fMRIPrep?
What was the error message (can you paste the outputs from the logs)?
Does this persist in the most recent fMRIPrep release?
Are your data BIDS-valid?
Are the crashes subject-specific or does it fail on everyone?

Hopefully upgrading to 21.0.0 fixes this, but if not, happy to help more.

Best,
Steven

ddillon · December 23, 2021, 5:24pm

Hi Steven. Thanks very much for the reply–I’ve added mine in turn below. Appreciate your input on this!

Dan

1. What was your command to run fMRIPrep? I’m running this in a singularity container on a cluster (via slurm), and the exact command is “sh fmriprep BIDS fmriprep_output_aroma participant --participant-label REWMEM006 --use-aroma”.

2. What was the error message (can you paste the outputs from the logs)? The error message indicates that ICA-AROMA failed because no signal components were extracted for PST_train run 2 (subjects are doing the probabilistic selection task, aka PST). The logs are long but I’ve copied what I think are the two key parts below:

First this . . .
> [Node] Finished “fmriprep_wf.single_subject_REWMEM006_wf.func_preproc_ses_140127REWMEM006_task_PST_TRAIN_run_2_wf.ica_aroma_wf.ica_aroma”.

211222-05:57:15,484 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_REWMEM006_wf.func_preproc_ses_140127REWMEM006_task_PST_TRAIN_run_2_wf.ica_aroma_wf.ica_aroma_confound_extraction” in “/net/holynfs01/srv/export/ncf_anl/share_root/anl01/REWMEM/work/fmriprep_wf/single_subject_REWMEM006_wf/func_preproc_ses_140127REWMEM006_task_PST_TRAIN_run_2_wf/ica_aroma_wf/ica_aroma_confound_extraction”.
211222-05:57:15,508 nipype.workflow INFO:
[Node] Running “ica_aroma_confound_extraction” (“fmriprep.interfaces.confounds.ICAConfounds”)
211222-05:57:15,534 nipype.interface WARNING:
No signal components were classified
211222-05:57:15,543 nipype.workflow WARNING:
[Node] Error on “fmriprep_wf.single_subject_REWMEM006_wf.func_preproc_ses_140127REWMEM006_task_PST_TRAIN_run_2_wf.ica_aroma_wf.ica_aroma_confound_extraction” (/net/holynfs01/srv/export/ncf_anl/share_root/anl01/REWMEM/work/fmriprep_wf/single_subject_REWMEM006_wf/func_preproc_ses_140127REWMEM006_task_PST_TRAIN_run_2_wf/ica_aroma_wf/ica_aroma_confound_extraction)
211222-06:12:33,828 nipype.workflow INFO:

. . . and then this, from the very end of the log:

Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 342, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py”, line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 162, in run
self._clean_queue(jobid, graph, result=result))
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 224, in _clean_queue
raise RuntimeError("".join(result[‘traceback’]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 480, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 644, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 521, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/confounds.py”, line 119, in _run_interface
raise RuntimeError(‘ICA-AROMA failed’)
RuntimeError: ICA-AROMA failed

3. Does this persist in the most recent fMRIPrep release? I’m not sure of the answer here yet, as I’m running this on a cluster and I think we only have v1.1.4 installed, which is what I used here. I’ve asked for fmriprep to be updated and when it is I can report back. I think the crashing would certainly stop as my understanding is that that specific problem was fixed, but if nothing else changes I expect that I would still get no signal components for this run and the others that crashed, which is puzzling because they seem fine to me and when I run fmriprep without ICA-AROMA the results look good.

4. Are your data BIDS-valid? Yes, I think so. They’re all in BIDS format and running fmriprep without ICA-AROMA works fine. Also, running fmriprep with ICA-AROMA works fine for 15/22 subjects I have in this dataset.

5. Are the crashes subject-specific or does it fail on everyone? As mentioned above, the crashes are subject-specific: fmriprep with ICA-AROMA works on 15/22 subjects and fails on the other 7, and I’m at a loss for what differentiates the successes from the fails. I collected the data myself on the same scanner in a short span of time, all the participants are community adults, and I don’t see any obvious differences in run quality–in fact, some of the failed runs look cleaner (less motion) than runs that succeeded.

I’ve been trying to think of things to play with in order to gain insight here, and I noticed comments on other threads indicating that global signal regression can sometimes improve ICA-AROMA fits. My understanding is that the global signal (along with CSF and WM covariates) are computed before ICA-AROMA is run. Do you know if there’s a way to ask fmriprep to regress the global signal out of the BOLD data before it’s passed to ICA-AROMA? I thought that might be worth trying, to see if it makes any difference, but I’m not a nipype ninja so am not sure how difficult this would be to do.

ddillon · February 22, 2022, 10:42pm

To tie up this old thread, I upgraded to fmriprep v 21.0.1 and the problem stopped–I can run ICA-AROMA without crashing, and what’s more there are no longer any runs without signal ICs in them. I’m not sure what (if anything) changed w.r.t the ICA-AROMA implementation from earlier to later versions of fmriprep, but it works now (which seems appropriate as the data are reasonably clean) so I’m not looking this gift horse in the mouth:)