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Give this a try.
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@tsalo
tsalo committed Oct 13, 2023
1 parent ad93edf commit 544a093
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Showing 2 changed files with 38 additions and 61 deletions.
4 changes: 0 additions & 4 deletions xcp_d/data/xcp_d_bids_config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,6 @@
{
"name": "measure",
"pattern": "(?:^|_)measure-([a-zA-Z0-9]+)"
},
{
"name": "Sources",
"pattern": "ignore-(this)"
}
],
"default_path_patterns": [
Expand Down
95 changes: 38 additions & 57 deletions xcp_d/workflows/outputs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -377,15 +377,29 @@ def init_postproc_derivatives_wf(
])
# fmt:on

def _make_dictionary(**kwargs):
return dict(kwargs)

make_dict = pe.MapNode(
niu.Function(
function=_make_dictionary,
input_names=["Sources"],
output_names=["metadata"],
),
run_without_submitting=True,
mem_gb=1,
name="make_dict",
iterfields=["Sources"],
)
workflow.connect([(merge_parcellated_src, make_dict, [("out", "Sources")])])

ds_temporal_mask = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=["atlas", "den", "res", "space", "cohort", "desc"],
suffix="outliers",
extension=".tsv",
source_file=name_source,
# Metadata
Sources=None,
),
name="ds_temporal_mask",
run_without_submitting=True,
Expand All @@ -411,8 +425,6 @@ def init_postproc_derivatives_wf(
desc="filtered" if motion_filter_type else None,
suffix="motion",
extension=".tsv",
# Metadata
Sources=None,
),
name="ds_filtered_motion",
run_without_submitting=True,
Expand All @@ -439,8 +451,6 @@ def init_postproc_derivatives_wf(
datatype="func",
suffix="design",
extension=".tsv",
# Metadata
Sources=None,
),
name="ds_confounds",
run_without_submitting=False,
Expand All @@ -460,14 +470,11 @@ def init_postproc_derivatives_wf(
cohort=cohort,
suffix="coverage",
extension=".tsv",
# Metadata
Sources=None,
DummyMetadata="TEST",
),
name="ds_coverage_files",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file", "Sources"],
iterfield=["atlas", "in_file", "meta_dict"],
)
ds_timeseries = pe.MapNode(
DerivativesDataSink(
Expand All @@ -477,13 +484,11 @@ def init_postproc_derivatives_wf(
cohort=cohort,
suffix="timeseries",
extension=".tsv",
# Metadata
Sources=None,
),
name="ds_timeseries",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file", "Sources"],
iterfield=["atlas", "in_file", "meta_dict"],
)
ds_correlations = pe.MapNode(
DerivativesDataSink(
Expand All @@ -494,13 +499,11 @@ def init_postproc_derivatives_wf(
measure="pearsoncorrelation",
suffix="conmat",
extension=".tsv",
# Metadata
Sources=None,
),
name="ds_correlations",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file", "Sources"],
iterfield=["atlas", "in_file", "meta_dict"],
)

for i_exact_scan, exact_scan in enumerate(exact_scans):
Expand All @@ -525,8 +528,6 @@ def init_postproc_derivatives_wf(
desc=f"{exact_scan}volumes",
suffix="conmat",
extension=".tsv",
# Metadata
Sources=None,
),
name=f"ds_correlations_exact_{i_exact_scan}",
run_without_submitting=True,
Expand All @@ -549,12 +550,13 @@ def init_postproc_derivatives_wf(
suffix="reho",
extension=".tsv",
# Metadata
Sources=None,
SoftwareFilters=software_filters,
Neighborhood="vertices",
),
name="ds_parcellated_reho",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file", "Sources"],
iterfield=["atlas", "in_file", "meta_dict"],
)

# fmt:off
Expand All @@ -563,23 +565,23 @@ def init_postproc_derivatives_wf(
("coverage", "in_file"),
("atlas_names", "atlas"),
]),
(merge_parcellated_src, ds_coverage_files, [("out", "Sources")]),
(make_dict, ds_coverage_files, [("metadata", "meta_dict")]),
(inputnode, ds_timeseries, [
("timeseries", "in_file"),
("atlas_names", "atlas"),
]),
(merge_parcellated_src, ds_timeseries, [("out", "Sources")]),
(make_dict, ds_timeseries, [("metadata", "meta_dict")]),
(ds_timeseries, outputnode, [("out_file", "timeseries")]),
(inputnode, ds_correlations, [
("correlations", "in_file"),
("atlas_names", "atlas"),
]),
(merge_parcellated_src, ds_correlations, [("out", "Sources")]),
(make_dict, ds_correlations, [("metadata", "meta_dict")]),
(inputnode, ds_parcellated_reho, [
("parcellated_reho", "in_file"),
("atlas_names", "atlas"),
]),
(merge_parcellated_src, ds_parcellated_reho, [("out", "Sources")]),
(make_dict, ds_parcellated_reho, [("metadata", "meta_dict")]),
])
# fmt:on

Expand All @@ -592,13 +594,11 @@ def init_postproc_derivatives_wf(
cohort=cohort,
suffix="alff",
extension=".tsv",
# Metadata
Sources=None,
),
name="ds_parcellated_alff",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file", "Sources"],
iterfield=["atlas", "in_file", "meta_dict"],
)

# fmt:off
Expand All @@ -607,7 +607,7 @@ def init_postproc_derivatives_wf(
("parcellated_alff", "in_file"),
("atlas_names", "atlas"),
]),
(merge_parcellated_src, ds_parcellated_alff, [("out", "Sources")]),
(make_dict, ds_parcellated_alff, [("metadata", "meta_dict")]),
])
# fmt:on

Expand All @@ -616,15 +616,14 @@ def init_postproc_derivatives_wf(
ds_denoised_bold = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
meta_dict=cleaned_data_dictionary,
source_file=name_source,
cohort=cohort,
desc="denoised",
extension=".nii.gz",
compression=True,
# Metadata
meta_dict=cleaned_data_dictionary,
SoftwareFilters=software_filters,
Sources=None,
),
name="ds_denoised_bold",
run_without_submitting=True,
Expand All @@ -635,14 +634,13 @@ def init_postproc_derivatives_wf(
ds_interpolated_denoised_bold = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
meta_dict=cleaned_data_dictionary,
source_file=name_source,
desc="interpolated",
extension=".nii.gz",
compression=True,
# Metadata
meta_dict=cleaned_data_dictionary,
SoftwareFilters=software_filters,
Sources=None,
),
name="ds_interpolated_denoised_bold",
run_without_submitting=True,
Expand All @@ -658,8 +656,6 @@ def init_postproc_derivatives_wf(
desc="linc",
suffix="qc",
extension=".csv",
# Metadata
Sources=None,
),
name="ds_qc_file",
run_without_submitting=True,
Expand All @@ -678,7 +674,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
Neighborhood="vertices",
Sources=None,
),
name="ds_reho",
run_without_submitting=True,
Expand All @@ -697,7 +692,6 @@ def init_postproc_derivatives_wf(
compression=True,
# Metadata
SoftwareFilters=software_filters,
Sources=None,
),
name="ds_alff",
run_without_submitting=True,
Expand All @@ -717,7 +711,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
FWHM=smoothing,
Sources=None,
),
name="ds_smoothed_bold",
run_without_submitting=True,
Expand All @@ -737,7 +730,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
FWHM=smoothing,
Sources=None,
),
name="ds_smoothed_alff",
run_without_submitting=True,
Expand All @@ -749,16 +741,15 @@ def init_postproc_derivatives_wf(
ds_denoised_bold = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
meta_dict=cleaned_data_dictionary,
source_file=name_source,
dismiss_entities=["den"],
cohort=cohort,
desc="denoised",
den="91k",
extension=".dtseries.nii",
# Metadata
meta_dict=cleaned_data_dictionary,
SoftwareFilters=software_filters,
Sources=None,
),
name="ds_denoised_bold",
run_without_submitting=True,
Expand All @@ -769,14 +760,13 @@ def init_postproc_derivatives_wf(
ds_interpolated_denoised_bold = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
meta_dict=cleaned_data_dictionary,
source_file=name_source,
dismiss_entities=["den"],
desc="interpolated",
den="91k",
extension=".dtseries.nii",
# Metadata
Sources=None,
meta_dict=cleaned_data_dictionary,
),
name="ds_interpolated_denoised_bold",
run_without_submitting=True,
Expand All @@ -793,8 +783,6 @@ def init_postproc_derivatives_wf(
desc="linc",
suffix="qc",
extension=".csv",
# Metadata
Sources=None,
),
name="ds_qc_file",
run_without_submitting=True,
Expand All @@ -810,13 +798,11 @@ def init_postproc_derivatives_wf(
cohort=cohort,
suffix="coverage",
extension=".pscalar.nii",
# Metadata
Sources=None,
),
name="ds_coverage_cifti_files",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file"],
iterfield=["atlas", "in_file", "meta_dict"],
)
ds_timeseries_cifti_files = pe.MapNode(
DerivativesDataSink(
Expand All @@ -828,13 +814,11 @@ def init_postproc_derivatives_wf(
den="91k",
suffix="timeseries",
extension=".ptseries.nii",
# Metadata
Sources=None,
),
name="ds_timeseries_cifti_files",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file"],
iterfield=["atlas", "in_file", "meta_dict"],
)
ds_correlation_cifti_files = pe.MapNode(
DerivativesDataSink(
Expand All @@ -847,13 +831,11 @@ def init_postproc_derivatives_wf(
measure="pearsoncorrelation",
suffix="conmat",
extension=".pconn.nii",
# Metadata
Sources=None,
),
name="ds_correlation_cifti_files",
run_without_submitting=True,
mem_gb=1,
iterfield=["atlas", "in_file"],
iterfield=["atlas", "in_file", "meta_dict"],
)

# fmt:off
Expand All @@ -862,15 +844,18 @@ def init_postproc_derivatives_wf(
("coverage_ciftis", "in_file"),
("atlas_names", "atlas"),
]),
(make_dict, ds_coverage_cifti_files, [("metadata", "meta_dict")]),
(inputnode, ds_timeseries_cifti_files, [
("timeseries_ciftis", "in_file"),
("atlas_names", "atlas"),
]),
(make_dict, ds_timeseries_cifti_files, [("metadata", "meta_dict")]),
(ds_timeseries_cifti_files, outputnode, [("out_file", "timeseries_ciftis")]),
(inputnode, ds_correlation_cifti_files, [
("correlation_ciftis", "in_file"),
("atlas_names", "atlas"),
]),
(make_dict, ds_correlation_cifti_files, [("metadata", "meta_dict")]),
])
# fmt:on

Expand All @@ -887,7 +872,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
Neighborhood="vertices",
Sources=None,
),
name="ds_reho",
run_without_submitting=True,
Expand All @@ -907,7 +891,6 @@ def init_postproc_derivatives_wf(
extension=".dscalar.nii",
# Metadata
SoftwareFilters=software_filters,
Sources=None,
),
name="ds_alff",
run_without_submitting=True,
Expand All @@ -929,7 +912,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
FWHM=smoothing,
Sources=None,
),
name="ds_smoothed_bold",
run_without_submitting=True,
Expand All @@ -951,7 +933,6 @@ def init_postproc_derivatives_wf(
# Metadata
SoftwareFilters=software_filters,
FWHM=smoothing,
Sources=None,
),
name="ds_smoothed_alff",
run_without_submitting=True,
Expand Down

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