ICA_AROMA.py: error: unrecognized arguments: -np

1

The error below is appearing in the log-files. Tried already changing AROMA versions but the option “-np” doesn’t seem to exist really…

Traceback (most recent call last):
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
    result = self._run_interface(execute=True)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
    return self._run_command(execute)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 395, in run
    runtime = self._run_interface(runtime)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 792, in _run_interface
    self.raise_exception(runtime)
  File "/gpfs/gsfs4/users/kircanskik/AP2-TAU/code/env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 724, in raise_exception
    ).format(**runtime.dictcopy())
RuntimeError: Command:
ICA_AROMA.py -tr 2.300 -np -den nonaggr -i /lscratch/46247133/s1305.wrk/fmriprep_wf/single_subject_s1305_wf/func_preproc_task_TAU_run_1_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_cut_smooth.nii.gz -m /lscratch/46247133/s1305.wrk/fmriprep_wf/single_subject_s1305_wf/func_preproc_task_TAU_run_1_wf/bold_std_trans_wf/_key_MNI152NLin6Asym/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -meldir /lscratch/46247133/s1305.wrk/fmriprep_wf/single_subject_s1305_wf/func_preproc_task_TAU_run_1_wf/ica_aroma_wf/melodic -mc /lscratch/46247133/s1305.wrk/fmriprep_wf/single_subject_s1305_wf/func_preproc_task_TAU_run_1_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /lscratch/46247133/s1305.wrk/fmriprep_wf/single_subject_s1305_wf/func_preproc_task_TAU_run_1_wf/ica_aroma_wf/ica_aroma/out
Standard output:

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

Standard error:
usage: ICA_AROMA.py [-h] -o OUTDIR [-i INFILE] [-mc MC] [-a AFFMAT] [-w WARP]
                    [-m MASK] [-f INFEAT] [-tr TR] [-den DENTYPE] [-md MELDIR]
                    [-dim DIM]
ICA_AROMA.py: error: unrecognized arguments: -np
Return code: 2
2

After 3 weeks I think it’s ok to bump… :slight_smile:
Thanks all!

3

Hi @winkler,

Thanks for your patience, I took a look and fmriprep uses a fork of ICA-AROMA.

where the option to not output classification plots (-np or “no plots”) was added.

The way forward would be to download/unpack and point to this version of ICA-AROMA if possible: https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz

Would that be a viable solution on your end?
James

4

Hi James,

Thanks for the feedback. It solved the problem! However, immediately after, it crashes for another reason. I’ll open a separate thread. Thanks!

Anderson

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