From dc9fe2ca1b6ba90540274bb7219dbbba3fa605a8 Mon Sep 17 00:00:00 2001 From: oesteban Date: Tue, 19 May 2020 09:13:55 -0700 Subject: [PATCH] fix: Ensure correct WM and CSF masks are picked in confounds workflow Depends: poldracklab/smriprep#189. --- fmriprep/workflows/bold/confounds.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/confounds.py b/fmriprep/workflows/bold/confounds.py index 9452b4880..ca9fe9178 100644 --- a/fmriprep/workflows/bold/confounds.py +++ b/fmriprep/workflows/bold/confounds.py @@ -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 @@ -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)