ENH: Confounds metadata

[rciric]

• Resolves Write out metadata about Global Signal regressors #1617
• Resolves Write out metadata about ICA-AROMA regressors #1618

[oesteban]

At some point this evening I thought I'm mad when found myself with AROMA's repo open and thinking about exactly that :p A couple of things discouraged me from starting right away: - First, the project seems a bit abandoned, judging by the outstanding PR proposing a 0.4.4 release. We will need a fast turnaround - The other is that we might just implement it as an interface for nipype like compcor. The current implementation has a lot of boilerplate to run normalization and MELODIC which we don't need. Maybe just picking up the classification of components would suffice.

…

On Wed, Sep 11, 2019, 18:04 Chris Markiewicz ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In fmriprep/workflows/bold/confounds.py <#1708 (comment)>: > @@ -687,6 +690,13 @@ def _getusans_func(image, thresh): ica_aroma_confound_extraction = pe.Node(ICAConfounds(err_on_aroma_warn=err_on_aroma_warn), name='ica_aroma_confound_extraction') + ica_aroma_metadata_fmt = pe.Node( + TSV2JSON(index_column='IC', output=None, enforce_case=True, + additional_metadata={'Method': { + 'Name': 'ICA-AROMA', + 'Version': '0.3-beta'}}), Would it make sense just to help package ICA-AROMA, make sure it has __version__, and put it on PyPI? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1708>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAESDRXJEER4Q3NQE436YV3QJGISDANCNFSM4IFN3O4A> .

[effigies]

Maybe a good candidate for repackaging as a niflow (so we don't have to worry about perceived authorship, as we would if we just packaged up AROMA and pushed it without @maartenmennes' blessing)? Is there anything besides version numbering that we actually need to update in the short term? If not, we can target a hackathon where there are two or three of us who are familiar with nipype and AROMA to just get the thing done.

As for determining the version dynamically, perhaps we can do a diff between releases and see if we can find a characteristic string or object that can be used as an indicator of the version.

[oesteban]

Just to note: this PR is still failing (https://circleci.com/gh/poldracklab/fmriprep/9634). It doesn't look like a big deal.

Node: fmriprep_wf.single_subject_01_wf.func_preproc_task_mixedgamblestask_run_02_wf.ica_aroma_wf.ica_aroma_metadata_fmt
Working directory: /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma_metadata_fmt

Node inputs:

additional_metadata = {'Method': {'Name': 'ICA-AROMA', 'Version': '0.4.4-beta'}}
drop_columns = None
enforce_case = True
in_file = /scratch/fmriprep_wf/single_subject_01_wf/func_preproc_task_mixedgamblestask_run_02_wf/ica_aroma_wf/ica_aroma_confound_extraction/classification_overview.tsv
index_column = IC
output = None

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/legacymultiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 564, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 649, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 376, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/utils.py", line 822, in _run_interface
    enforce_case=self.inputs.enforce_case
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/utils.py", line 879, in _tsv2json
    tsv_data[k] = v
  File "/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/frame.py", line 3119, in __setitem__
    self._set_item(key, value)
  File "/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/frame.py", line 3194, in _set_item
    value = self._sanitize_column(key, value)
  File "/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/frame.py", line 3391, in _sanitize_column
    value = _sanitize_index(value, self.index, copy=False)
  File "/usr/local/miniconda/lib/python3.7/site-packages/pandas/core/series.py", line 4001, in _sanitize_index
    raise ValueError('Length of values does not match length of ' 'index')
ValueError: Length of values does not match length of index