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FIX: Ensure correct WM and CSF masks are picked in confounds workflow #2128

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May 21, 2020
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FIX: Ensure correct WM and CSF masks are picked in confounds workflow #2128

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7 changes: 4 additions & 3 deletions fmriprep/workflows/bold/confounds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,8 @@ def init_bold_confs_wf(
name='outputnode')

# Get masks ready in T1w space
acc_tpm = pe.Node(AddTPMs(indices=[0, 2]), name='tpms_add_csf_wm') # acc stands for aCompCor
acc_tpm = pe.Node(AddTPMs(indices=[1, 2]), # BIDS convention (WM=1, CSF=2)
name='acc_tpm') # acc stands for aCompCor
csf_roi = pe.Node(TPM2ROI(erode_mm=0, mask_erode_mm=30), name='csf_roi')
wm_roi = pe.Node(TPM2ROI(
erode_prop=0.6, mask_erode_prop=0.6**3), # 0.6 = radius; 0.6^3 = volume
Expand Down Expand Up @@ -327,10 +328,10 @@ def init_bold_confs_wf(
mem_gb=DEFAULT_MEMORY_MIN_GB)

def _pick_csf(files):
return files[0]
return files[2] # after smriprep#189, this is BIDS-compliant.

def _pick_wm(files):
return files[-1]
return files[1] # after smriprep#189, this is BIDS-compliant.

workflow.connect([
# Massage ROIs (in T1w space)
Expand Down