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@tsalo
tsalo committed Oct 11, 2023
1 parent 36128c2 commit dd4f805
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Showing 4 changed files with 123 additions and 96 deletions.
1 change: 1 addition & 0 deletions xcp_d/workflows/bold.py
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Original file line number Diff line number Diff line change
Expand Up @@ -531,6 +531,7 @@ def init_postprocess_nifti_wf(
(inputnode, postproc_derivatives_wf, [
("fmriprep_confounds_file", "inputnode.fmriprep_confounds_file"),
("atlas_names", "inputnode.atlas_names"),
("atlas_files", "inputnode.atlas_files"),
]),
(prepare_confounds_wf, postproc_derivatives_wf, [
("outputnode.confounds_file", "inputnode.confounds_file"),
Expand Down
1 change: 1 addition & 0 deletions xcp_d/workflows/cifti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -500,6 +500,7 @@ def init_postprocess_cifti_wf(
(inputnode, postproc_derivatives_wf, [
("fmriprep_confounds_file", "inputnode.fmriprep_confounds_file"),
("atlas_names", "inputnode.atlas_names"),
("atlas_files", "inputnode.atlas_files"),
]),
(denoise_bold_wf, postproc_derivatives_wf, [
("outputnode.interpolated_filtered_bold", "inputnode.interpolated_filtered_bold"),
Expand Down
137 changes: 57 additions & 80 deletions xcp_d/workflows/concatenation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -133,19 +133,16 @@ def init_concatenate_data_wf(
CleanNameSource(),
name="clean_name_source",
)

# fmt:off
workflow.connect([(inputnode, clean_name_source, [("name_source", "name_source")])])
# fmt:on

filter_out_failed_runs = pe.Node(
filter_runs = pe.Node(
FilterOutFailedRuns(),
name="filter_out_failed_runs",
name="filter_runs",
)

# fmt:off
workflow.connect([
(inputnode, filter_out_failed_runs, [
(inputnode, filter_runs, [
("preprocessed_bold", "preprocessed_bold"),
("fmriprep_confounds_file", "fmriprep_confounds_file"),
("filtered_motion", "filtered_motion"),
Expand All @@ -170,7 +167,7 @@ def init_concatenate_data_wf(

# fmt:off
workflow.connect([
(filter_out_failed_runs, concatenate_inputs, [
(filter_runs, concatenate_inputs, [
("preprocessed_bold", "preprocessed_bold"),
("fmriprep_confounds_file", "fmriprep_confounds_file"),
("filtered_motion", "filtered_motion"),
Expand Down Expand Up @@ -206,7 +203,7 @@ def init_concatenate_data_wf(
("anat_brainmask", "inputnode.anat_brainmask"),
]),
(clean_name_source, qc_report_wf, [("name_source", "inputnode.name_source")]),
(filter_out_failed_runs, qc_report_wf, [
(filter_runs, qc_report_wf, [
# nifti-only inputs
(("bold_mask", _select_first), "inputnode.bold_mask"),
(("boldref", _select_first), "inputnode.boldref"),
Expand All @@ -225,6 +222,18 @@ def init_concatenate_data_wf(
])
# fmt:on

filtered_motion_src = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="filtered_motion_src",
run_without_submitting=True,
mem_gb=1,
)
workflow.connect([(filter_runs, filtered_motion_src, [("filtered_motion", "in1")])])

ds_filtered_motion = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
Expand All @@ -242,25 +251,21 @@ def init_concatenate_data_wf(
workflow.connect([
(clean_name_source, ds_filtered_motion, [("name_source", "source_file")]),
(concatenate_inputs, ds_filtered_motion, [("filtered_motion", "in_file")]),
(filtered_motion_src, ds_filtered_motion, [("bids_uris", "Sources")]),
])
# fmt:on

filtered_motion_sources = pe.Node(
temporal_mask_src = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="filtered_motion_sources",
name="temporal_mask_src",
run_without_submitting=True,
mem_gb=1,
)
# fmt:off
workflow.connect([
(filter_out_failed_runs, filtered_motion_sources, [("filtered_motion", "in1")]),
(filtered_motion_sources, ds_filtered_motion, [("bids_uris", "Sources")]),
])
# fmt:on
workflow.connect([(filter_runs, temporal_mask_src, [("temporal_mask", "in1")])])

ds_temporal_mask = pe.Node(
DerivativesDataSink(
Expand All @@ -278,25 +283,22 @@ def init_concatenate_data_wf(
workflow.connect([
(clean_name_source, ds_temporal_mask, [("name_source", "source_file")]),
(concatenate_inputs, ds_temporal_mask, [("temporal_mask", "in_file")]),
(temporal_mask_src, ds_temporal_mask, [("bids_uris", "Sources")]),
])
# fmt:on

temporal_mask_sources = pe.Node(
timeseries_src = pe.MapNode(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="temporal_mask_sources",
name="timeseries_src",
run_without_submitting=True,
mem_gb=1,
iterfield=["in1"],
)
# fmt:off
workflow.connect([
(filter_out_failed_runs, temporal_mask_sources, [("temporal_mask", "in1")]),
(temporal_mask_sources, ds_temporal_mask, [("bids_uris", "Sources")]),
])
# fmt:on
workflow.connect([(filter_runs, timeseries_src, [("timeseries", "in1")])])

ds_timeseries = pe.MapNode(
DerivativesDataSink(
Expand All @@ -316,24 +318,24 @@ def init_concatenate_data_wf(
(inputnode, ds_timeseries, [("atlas_names", "atlas")]),
(clean_name_source, ds_timeseries, [("name_source", "source_file")]),
(concatenate_inputs, ds_timeseries, [("timeseries", "in_file")]),
(timeseries_src, ds_timeseries, [("bids_uris", "Sources")]),
])
# fmt:on

timeseries_sources = pe.MapNode(
censored_filtered_bold_src = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="timeseries_sources",
name="censored_filtered_bold_src",
run_without_submitting=True,
mem_gb=1,
iterfield=["in1"],
)

# fmt:off
workflow.connect([
(filter_out_failed_runs, timeseries_sources, [("timeseries", "in1")]),
(timeseries_sources, ds_timeseries, [("bids_uris", "Sources")]),
(filter_runs, censored_filtered_bold_src, [("censored_denoised_bold", "in1")]),
])
# fmt:on

Expand All @@ -351,6 +353,19 @@ def init_concatenate_data_wf(
mem_gb=2,
)

timeseries_ciftis_src = pe.MapNode(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="timeseries_ciftis_src",
run_without_submitting=True,
mem_gb=1,
iterfield=["in1"],
)
workflow.connect([(filter_runs, timeseries_ciftis_src, [("timeseries_ciftis", "in1")])])

ds_timeseries_cifti_files = pe.MapNode(
DerivativesDataSink(
base_directory=output_dir,
Expand All @@ -371,24 +386,7 @@ def init_concatenate_data_wf(
(clean_name_source, ds_timeseries_cifti_files, [("name_source", "source_file")]),
(inputnode, ds_timeseries_cifti_files, [("atlas_names", "atlas")]),
(concatenate_inputs, ds_timeseries_cifti_files, [("timeseries_ciftis", "in_file")]),
])
# fmt:on

timeseries_ciftis_sources = pe.MapNode(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="timeseries_ciftis_sources",
run_without_submitting=True,
mem_gb=1,
iterfield=["in1"],
)
# fmt:off
workflow.connect([
(filter_out_failed_runs, timeseries_ciftis_sources, [("timeseries_ciftis", "in1")]),
(timeseries_ciftis_sources, ds_timeseries_cifti_files, [("bids_uris", "Sources")]),
(timeseries_ciftis_src, ds_timeseries_cifti_files, [("bids_uris", "Sources")]),
])
# fmt:on

Expand Down Expand Up @@ -432,6 +430,7 @@ def init_concatenate_data_wf(
run_without_submitting=True,
mem_gb=2,
)

if smoothing:
ds_smoothed_denoised_bold = pe.Node(
DerivativesDataSink(
Expand Down Expand Up @@ -462,25 +461,7 @@ def init_concatenate_data_wf(
workflow.connect([
(clean_name_source, ds_censored_filtered_bold, [("name_source", "source_file")]),
(concatenate_inputs, ds_censored_filtered_bold, [("censored_denoised_bold", "in_file")]),
])
# fmt:on

censored_filtered_bold_sources = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="censored_filtered_bold_sources",
run_without_submitting=True,
mem_gb=1,
)
# fmt:off
workflow.connect([
(filter_out_failed_runs, censored_filtered_bold_sources, [
("censored_denoised_bold", "in1"),
]),
(censored_filtered_bold_sources, ds_censored_filtered_bold, [("bids_uris", "Sources")]),
(censored_filtered_bold_src, ds_censored_filtered_bold, [("bids_uris", "Sources")]),
])
# fmt:on

Expand All @@ -494,24 +475,21 @@ def init_concatenate_data_wf(
])
# fmt:on

smoothed_denoised_bold_sources = pe.Node(
smoothed_denoised_bold_src = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="smoothed_denoised_bold_sources",
name="smoothed_denoised_bold_src",
run_without_submitting=True,
mem_gb=1,
)

# fmt:off
workflow.connect([
(filter_out_failed_runs, smoothed_denoised_bold_sources, [
("smoothed_denoised_bold", "in1"),
]),
(smoothed_denoised_bold_sources, ds_smoothed_denoised_bold, [
("bids_uris", "Sources"),
]),
(filter_runs, smoothed_denoised_bold_src, [("smoothed_denoised_bold", "in1")]),
(smoothed_denoised_bold_src, ds_smoothed_denoised_bold, [("bids_uris", "Sources")]),
])
# fmt:on

Expand All @@ -525,22 +503,21 @@ def init_concatenate_data_wf(
])
# fmt:on

interpolated_filtered_bold_sources = pe.Node(
interpolated_filtered_bold_src = pe.Node(
InferBIDSURIs(
numinputs=1,
dataset_name="xcp_d",
dataset_path=os.path.join(output_dir, "xcp_d"),
),
name="interpolated_filtered_bold_sources",
name="interpolated_filtered_bold_src",
run_without_submitting=True,
mem_gb=1,
)

# fmt:off
workflow.connect([
(filter_out_failed_runs, interpolated_filtered_bold_sources, [
("interpolated_filtered_bold", "in1"),
]),
(interpolated_filtered_bold_sources, ds_interpolated_filtered_bold, [
(filter_runs, interpolated_filtered_bold_src, [("interpolated_filtered_bold", "in1")]),
(interpolated_filtered_bold_src, ds_interpolated_filtered_bold, [
("bids_uris", "Sources"),
]),
])
Expand Down
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