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out_fields = [
'anat2std_xfm',
'standardized',
'std2anat_xfm',
'std_dseg',
'std_mask',
'std_tpms',
'template',
'template_spec',
]
poutputnode = pe.Node(niu.IdentityInterface(fields=out_fields), name='poutputnode')
split_desc = pe.Node(TemplateDesc(), run_without_submitting=True, name='split_desc')
tf_select = pe.Node(TemplateFlowSelect(resolution=1 + debug),
name='tf_select', run_without_submitting=True)
# With the improvements from poldracklab/niworkflows#342 this truncation is now necessary
trunc_mov = pe.Node(ImageMath(operation='TruncateImageIntensity', op2='0.01 0.999 256'),
name='trunc_mov')
registration = pe.Node(RobustMNINormalization(
float=True, flavor=['precise', 'testing'][debug],
), name='registration', n_procs=omp_nthreads, mem_gb=2)
# Resample T1w-space inputs
tpl_moving = pe.Node(ApplyTransforms(
dimension=3, default_value=0, float=True,
interpolation='LanczosWindowedSinc'), name='tpl_moving')
std_mask = pe.Node(ApplyTransforms(interpolation='MultiLabel'), name='std_mask')
dismiss_entities=("session",)),
name='ds_t1w_dseg_mask_report', run_without_submitting=True)
workflow.connect([
(inputnode, t1w_conform_check, [('t1w_conform_report', 'in_file')]),
(t1w_conform_check, ds_t1w_conform_report, [('out', 'in_file')]),
(inputnode, ds_t1w_conform_report, [('source_file', 'source_file')]),
(inputnode, ds_t1w_dseg_mask_report, [('source_file', 'source_file')]),
(inputnode, seg_rpt, [('t1w_preproc', 'in_file'),
('t1w_mask', 'in_mask'),
('t1w_dseg', 'in_rois')]),
(seg_rpt, ds_t1w_dseg_mask_report, [('out_report', 'in_file')]),
])
# Generate reportlets showing spatial normalization
tf_select = pe.Node(TemplateFlowSelect(resolution=1),
name='tf_select', run_without_submitting=True)
norm_msk = pe.Node(niu.Function(
function=_rpt_masks, output_names=['before', 'after'],
input_names=['mask_file', 'before', 'after', 'after_mask']),
name='norm_msk')
norm_rpt = pe.Node(SimpleBeforeAfter(), name='norm_rpt', mem_gb=0.1)
norm_rpt.inputs.after_label = 'Participant' # after
ds_std_t1w_report = pe.Node(
DerivativesDataSink(base_directory=output_dir, suffix='T1w', datatype="figures",
dismiss_entities=("session",)),
name='ds_std_t1w_report', run_without_submitting=True)
workflow.connect([
(inputnode, tf_select, [('template', 'template')]),
(inputnode, norm_rpt, [('template', 'before_label')]),