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ENH: Revise confounds in confounds-correlation plots #2252

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Merged
merged 4 commits into from
Sep 4, 2020
Merged

ENH: Revise confounds in confounds-correlation plots #2252

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263f182
chore(dep): pin niworkflows ~= 1.2.8
oesteban Sep 3, 2020
3fe059f
enh: revise confounds in confounds-correlation plots
oesteban Sep 3, 2020
1895b6d
fix: use ``high_variance_masks`` from tCompCor
oesteban Sep 3, 2020
2287eac
fix: drop ``std_dvars`` as their correlation with ``dvars`` is 1.0 al…
oesteban Sep 3, 2020
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20 changes: 16 additions & 4 deletions fmriprep/workflows/bold/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -249,8 +249,10 @@ def init_bold_confs_wf(
acompcor.inputs.repetition_time = metadata['RepetitionTime']

# Global and segment regressors
signals_class_labels = ["csf", "white_matter", "global_signal"]
mrg_lbl = pe.Node(niu.Merge(3), name='merge_rois', run_without_submitting=True)
signals_class_labels = [
"csf", "white_matter", "global_signal", "csf_wm", "tcompcor",
]
mrg_lbl = pe.Node(niu.Merge(5), name='merge_rois', run_without_submitting=True)
signals = pe.Node(SignalExtraction(class_labels=signals_class_labels),
name="signals", mem_gb=mem_gb)

Expand Down Expand Up @@ -320,7 +322,7 @@ def init_bold_confs_wf(

# Generate reportlet (Confound correlation)
conf_corr_plot = pe.Node(
ConfoundsCorrelationPlot(reference_column='global_signal', max_dim=70),
ConfoundsCorrelationPlot(reference_column='global_signal', max_dim=20),
name='conf_corr_plot')
ds_report_conf_corr = pe.Node(
DerivativesDataSink(desc='confoundcorr', datatype="figures", dismiss_entities=("echo",)),
Expand All @@ -333,6 +335,13 @@ def _pick_csf(files):
def _pick_wm(files):
return files[1] # after smriprep#189, this is BIDS-compliant.

def _select_cols(table):
import pandas as pd
return [
col for col in pd.read_table(table, nrows=2).columns
if not col.startswith(("a_comp_cor_", "t_comp_cor_", "std_dvars"))
]

workflow.connect([
# Massage ROIs (in T1w space)
(inputnode, acc_tpm, [('t1w_tpms', 'in_files')]),
Expand Down Expand Up @@ -387,6 +396,8 @@ def _pick_wm(files):
(wm_tfm, wm_msk, [('output_image', 'roi_file')]),
(wm_msk, mrg_lbl, [('out', 'in2')]),
(inputnode, mrg_lbl, [('bold_mask', 'in3')]),
(acc_msk, mrg_lbl, [('out', 'in4')]),
(tcompcor, mrg_lbl, [('high_variance_masks', 'in5')]),
(mrg_lbl, signals, [('out', 'label_files')]),

# Collate computed confounds together
Expand Down Expand Up @@ -428,7 +439,8 @@ def _pick_wm(files):
(acompcor, mrg_cc_metadata, [('metadata_file', 'in2')]),
(mrg_cc_metadata, compcor_plot, [('out', 'metadata_files')]),
(compcor_plot, ds_report_compcor, [('out_file', 'in_file')]),
(concat, conf_corr_plot, [('confounds_file', 'confounds_file')]),
(concat, conf_corr_plot, [('confounds_file', 'confounds_file'),
(('confounds_file', _select_cols), 'columns')]),
(conf_corr_plot, ds_report_conf_corr, [('out_file', 'in_file')]),
])

Expand Down
2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -27,7 +27,7 @@ install_requires =
nipype >= 1.4
nitime
nitransforms >= 20.0.0rc3,<20.2
niworkflows ~= 1.2.5
niworkflows ~= 1.2.8
numpy
pandas
psutil >= 5.4
Expand Down