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PIN: nipreps/niworkflows#485 #2108

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PIN: nipreps/niworkflows#485 #2108

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ff3ae2a
fix(pin): update templateflow >= 0.6.0 / follow my branch
oesteban Apr 30, 2020
0c98ce1
enh: use new ``brainmask_thresh`` argument, set it to a high value
oesteban Jun 3, 2020
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2 changes: 1 addition & 1 deletion fmriprep/workflows/bold/base.py
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Expand Up @@ -294,7 +294,7 @@ def init_func_preproc_wf(bold_file):
])

# Generate a tentative boldref
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads, brainmask_thresh=0.85)
bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
if sbref_file is not None:
workflow.connect([
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2 changes: 1 addition & 1 deletion fmriprep/workflows/bold/registration.py
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Expand Up @@ -325,7 +325,7 @@ def init_bold_t1_trans_wf(freesurfer, mem_gb, omp_nthreads, multiecho=False, use
merge = pe.Node(Merge(compress=use_compression), name='merge', mem_gb=mem_gb)

# Generate a reference on the target T1w space
gen_final_ref = init_bold_reference_wf(omp_nthreads, pre_mask=True)
gen_final_ref = init_bold_reference_wf(omp_nthreads, pre_mask=True, brainmask_thresh=0.85)

if not multiecho:
# Merge transforms placing the head motion correction last
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4 changes: 2 additions & 2 deletions fmriprep/workflows/bold/resampling.py
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Expand Up @@ -352,7 +352,7 @@ def init_bold_std_trans_wf(

# Generate a reference on the target standard space
gen_final_ref = init_bold_reference_wf(
omp_nthreads=omp_nthreads, pre_mask=True)
omp_nthreads=omp_nthreads, pre_mask=True, brainmask_thresh=0.85)

workflow.connect([
(iterablesource, split_target, [('std_target', 'in_target')]),
Expand Down Expand Up @@ -526,7 +526,7 @@ def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,
mem_gb=mem_gb * 3)

# Generate a new BOLD reference
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads, brainmask_thresh=0.85)
bold_reference_wf.__desc__ = None # Unset description to avoid second appearance

workflow.connect([
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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 ~= 1.2.3
niworkflows @ git+https://github.com/oesteban/niworkflows.git@294a8679d0a1eb3a7536429b7c794fa902f01703
numpy
pandas
psutil >= 5.4
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