diff --git a/nibabies/workflows/bold/outputs.py b/nibabies/workflows/bold/outputs.py index 03f58562..befeaa24 100644 --- a/nibabies/workflows/bold/outputs.py +++ b/nibabies/workflows/bold/outputs.py @@ -68,10 +68,10 @@ def prepare_timing_parameters(metadata: dict): When SliceTiming is available and used, then ``SliceTimingCorrected`` is ``True`` and the ``StartTime`` indicates a series offset. - >>> with mock.patch("fmriprep.config.workflow.ignore", []): + >>> with mock.patch("nibabies.config.workflow.ignore", []): ... prepare_timing_parameters(dict(RepetitionTime=2, SliceTiming=[0.0, 0.2, 0.4, 0.6])) {'RepetitionTime': 2, 'SliceTimingCorrected': True, 'DelayTime': 1.2, 'StartTime': 0.3} - >>> with mock.patch("fmriprep.config.workflow.ignore", []): + >>> with mock.patch("nibabies.config.workflow.ignore", []): ... prepare_timing_parameters( ... dict(VolumeTiming=[0.0, 1.0, 2.0, 5.0, 6.0, 7.0], ... SliceTiming=[0.0, 0.2, 0.4, 0.6, 0.8])) #doctest: +NORMALIZE_WHITESPACE @@ -81,10 +81,10 @@ def prepare_timing_parameters(metadata: dict): When SliceTiming is available and not used, then ``SliceTimingCorrected`` is ``False`` and TA is indicated with ``DelayTime`` or ``AcquisitionDuration``. - >>> with mock.patch("fmriprep.config.workflow.ignore", ["slicetiming"]): + >>> with mock.patch("nibabies.config.workflow.ignore", ["slicetiming"]): ... prepare_timing_parameters(dict(RepetitionTime=2, SliceTiming=[0.0, 0.2, 0.4, 0.6])) {'RepetitionTime': 2, 'SliceTimingCorrected': False, 'DelayTime': 1.2} - >>> with mock.patch("fmriprep.config.workflow.ignore", ["slicetiming"]): + >>> with mock.patch("nibabies.config.workflow.ignore", ["slicetiming"]): ... prepare_timing_parameters( ... dict(VolumeTiming=[0.0, 1.0, 2.0, 5.0, 6.0, 7.0], ... SliceTiming=[0.0, 0.2, 0.4, 0.6, 0.8])) #doctest: +NORMALIZE_WHITESPACE @@ -93,10 +93,10 @@ def prepare_timing_parameters(metadata: dict): If SliceTiming metadata is present but empty, then treat it as missing: - >>> with mock.patch("fmriprep.config.workflow.ignore", []): + >>> with mock.patch("nibabies.config.workflow.ignore", []): ... prepare_timing_parameters(dict(RepetitionTime=2, SliceTiming=[])) {'RepetitionTime': 2, 'SliceTimingCorrected': False} - >>> with mock.patch("fmriprep.config.workflow.ignore", []): + >>> with mock.patch("nibabies.config.workflow.ignore", []): ... prepare_timing_parameters(dict(RepetitionTime=2, SliceTiming=[0.0])) {'RepetitionTime': 2, 'SliceTimingCorrected': False} """ @@ -427,7 +427,7 @@ def init_ds_boldref_wf( BIDSURI( numinputs=1, dataset_links=config.execution.dataset_links, - out_dir=str(config.execution.fmriprep_dir.absolute()), + out_dir=str(config.execution.output_dir.absolute()), ), name='sources', ) @@ -476,7 +476,7 @@ def init_ds_registration_wf( BIDSURI( numinputs=1, dataset_links=config.execution.dataset_links, - out_dir=str(config.execution.fmriprep_dir.absolute()), + out_dir=str(config.execution.output_dir.absolute()), ), name='sources', ) @@ -525,7 +525,7 @@ def init_ds_hmc_wf( BIDSURI( numinputs=1, dataset_links=config.execution.dataset_links, - out_dir=str(config.execution.fmriprep_dir.absolute()), + out_dir=str(config.execution.output_dir.absolute()), ), name='sources', ) @@ -591,7 +591,7 @@ def init_ds_bold_native_wf( BIDSURI( numinputs=3, dataset_links=config.execution.dataset_links, - out_dir=str(config.execution.fmriprep_dir.absolute()), + out_dir=str(config.execution.output_dir.absolute()), ), name='sources', ) @@ -740,7 +740,7 @@ def init_ds_volumes_wf( BIDSURI( numinputs=6, dataset_links=config.execution.dataset_links, - out_dir=str(config.execution.fmriprep_dir.absolute()), + out_dir=str(config.execution.output_dir.absolute()), ), name='sources', ) @@ -902,7 +902,7 @@ def init_bold_preproc_report_wf( :graph2use: orig :simple_form: yes - from fmriprep.workflows.bold.resampling import init_bold_preproc_report_wf + from nibabies.workflows.bold.resampling import init_bold_preproc_report_wf wf = init_bold_preproc_report_wf(mem_gb=1, reportlets_dir='.') Parameters