diff --git a/fmriprep/workflows/bold/fit.py b/fmriprep/workflows/bold/fit.py index 9c3acc4ac..0b938966b 100644 --- a/fmriprep/workflows/bold/fit.py +++ b/fmriprep/workflows/bold/fit.py @@ -229,8 +229,10 @@ def init_bold_fit_wf( # fmt:off workflow.connect([ (hmcref_buffer, outputnode, [("boldref", "hmc_boldref")]), - (regref_buffer, outputnode, [("boldref", "coreg_boldref"), - ("boldmask", "bold_mask")]), + (regref_buffer, outputnode, [ + ("boldref", "coreg_boldref"), + ("boldmask", "bold_mask"), + ]), (fmapreg_buffer, outputnode, [("boldref2fmap_xfm", "boldref2fmap_xfm")]), (hmc_buffer, outputnode, [("hmc_xforms", "motion_xfm")]), (inputnode, func_fit_reports_wf, [ @@ -556,6 +558,7 @@ def init_bold_native_wf( fields=[ # BOLD fit "boldref", + "bold_mask", "motion_xfm", "fmapreg_xfm", "dummy_scans", diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py index d83f71a3e..b893abf50 100644 --- a/fmriprep/workflows/bold/outputs.py +++ b/fmriprep/workflows/bold/outputs.py @@ -588,7 +588,7 @@ def init_ds_bold_native_wf( workflow.connect(inputnode, 'source_files', raw_sources, 'in_files') if bold_output: - ds_bold_native = pe.Node( + ds_bold = pe.Node( DerivativesDataSink( base_directory=output_dir, desc='preproc', @@ -598,19 +598,19 @@ def init_ds_bold_native_wf( dismiss_entities=("echo",), **timing_parameters, ), - name='ds_bold_native', + name='ds_bold', run_without_submitting=True, mem_gb=DEFAULT_MEMORY_MIN_GB, ) workflow.connect([ - (inputnode, ds_bold_native, [ + (inputnode, ds_bold, [ ('source_files', 'source_file'), - ('bold_native', 'in_file'), + ('bold', 'in_file'), ]), ]) # fmt:skip if bold_output or echo_output: - ds_bold_mask_native = pe.Node( + ds_bold_mask = pe.Node( DerivativesDataSink( base_directory=output_dir, desc='brain', @@ -618,16 +618,16 @@ def init_ds_bold_native_wf( compress=True, dismiss_entities=("echo",), ), - name='ds_bold_mask_native', + name='ds_bold_mask', run_without_submitting=True, mem_gb=DEFAULT_MEMORY_MIN_GB, ) workflow.connect([ - (inputnode, ds_bold_mask_native, [ + (inputnode, ds_bold_mask, [ ('source_files', 'source_file'), - ('bold_mask_native', 'in_file'), + ('bold_mask', 'in_file'), ]), - (raw_sources, ds_bold_mask_native, [('out', 'RawSources')]), + (raw_sources, ds_bold_mask, [('out', 'RawSources')]), ]) # fmt:skip if bold_output and multiecho: @@ -676,7 +676,7 @@ def init_ds_bold_native_wf( workflow.connect([ (inputnode, ds_bold_echos, [ ('source_files', 'source_file'), - ('bold_echos_native', 'in_file'), + ('bold_echos', 'in_file'), ]), ]) # fmt:skip