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FIX: Restrict carpet plot crown mask to BOLD coverage #3642

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Merged
effigies merged 1 commit into from
May 13, 2026
Merged

FIX: Restrict carpet plot crown mask to BOLD coverage #3642

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28 changes: 25 additions & 3 deletions fmriprep/workflows/bold/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -262,6 +262,9 @@ def init_bold_confs_wf(
# Create the crown mask
dilated_mask = pe.Node(BinaryDilation(), name='dilated_mask')
subtract_mask = pe.Node(BinarySubtraction(), name='subtract_mask')
crown_clip = pe.Node(
niu.Function(function=_clip_mask_to_coverage), name='crown_clip', mem_gb=mem_gb
)

# DVARS
dvars = pe.Node(
Expand Down Expand Up @@ -536,7 +539,9 @@ def _select_cols(table):
(union_mask, dilated_mask, [('out', 'in_mask')]),
(union_mask, subtract_mask, [('out', 'in_subtract')]),
(dilated_mask, subtract_mask, [('out_mask', 'in_base')]),
(subtract_mask, outputnode, [('out_mask', 'crown_mask')]),
(subtract_mask, crown_clip, [('out_mask', 'mask')]),
(inputnode, crown_clip, [('bold', 'bold')]),
(crown_clip, outputnode, [('out', 'crown_mask')]),
# aCompCor
(inputnode, acompcor, [('bold', 'realigned_file'),
('skip_vols', 'ignore_initial_volumes')]),
Expand All @@ -555,7 +560,7 @@ def _select_cols(table):
# crownCompCor
(inputnode, crowncompcor, [('bold', 'realigned_file'),
('skip_vols', 'ignore_initial_volumes')]),
(subtract_mask, crowncompcor, [('out_mask', 'mask_files')]),
(crown_clip, crowncompcor, [('out', 'mask_files')]),

# tCompCor
(inputnode, tcompcor, [('bold', 'realigned_file'),
Expand Down Expand Up @@ -606,7 +611,7 @@ def _select_cols(table):
('bold_mask', 'in_mask')]),
(tcompcor, mrg_compcor, [('high_variance_masks', 'in1')]),
(acc_msk_bin, mrg_compcor, [(('out_file', _last), 'in2')]),
(subtract_mask, mrg_compcor, [('out_mask', 'in3')]),
(crown_clip, mrg_compcor, [('out', 'in3')]),
(mrg_compcor, rois_plot, [('out', 'in_rois')]),
(rois_plot, ds_report_bold_rois, [('out_report', 'in_file')]),
(tcompcor, mrg_cc_metadata, [('metadata_file', 'in1')]),
Expand Down Expand Up @@ -786,6 +791,23 @@ def _binary_union(mask1, mask2):
return str(out_name)


def _clip_mask_to_coverage(mask, bold):
"""Restrict mask to voxels where the BOLD time series carries variance."""
from pathlib import Path

import nibabel as nb
import numpy as np

img = nb.load(mask)
mskarr = np.asanyarray(img.dataobj, dtype=int) > 0
has_signal = nb.load(bold).get_fdata().var(axis=-1) > 0
out = img.__class__(mskarr & has_signal, img.affine, img.header)
out.set_data_dtype('uint8')
out_name = Path('crown_mask_clipped.nii.gz').absolute()
out.to_filename(out_name)
return str(out_name)


def _carpet_parcellation(segmentation, crown_mask, acompcor_mask, nifti=False):
"""Generate the union of two masks."""
from pathlib import Path
Expand Down
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