diff --git a/AFQ/api/group.py b/AFQ/api/group.py index 6ba04a303..565e34f69 100644 --- a/AFQ/api/group.py +++ b/AFQ/api/group.py @@ -185,8 +185,8 @@ def __init__(self, pipeline_description = { "Name": bids_description["Name"], "BIDSVersion": bids_description["BIDSVersion"], - "PipelineDescription": {"Name": "pyAFQ", - "Version": pyafq_version}} + "GeneratedBy": {"Name": "pyAFQ", + "Version": pyafq_version}} pl_desc_file = op.join(self.afq_path, 'dataset_description.json') diff --git a/AFQ/data/fetch.py b/AFQ/data/fetch.py index a90785d3b..7de056cd0 100644 --- a/AFQ/data/fetch.py +++ b/AFQ/data/fetch.py @@ -763,7 +763,7 @@ def organize_cfin_data(path=None): to_bids_description( dmriprep_folder, **{"Name": "CFIN", - "PipelineDescription": {"Name": "dipy"}}) + "GeneratedBy": {"Name": "dipy"}}) def organize_stanford_data(path=None, clear_previous_afq=False): @@ -851,10 +851,10 @@ def organize_stanford_data(path=None, clear_previous_afq=False): # And descriptions of the pipelines in the derivatives: to_bids_description(dmriprep_folder, **{"Name": "Stanford HARDI", - "PipelineDescription": {"Name": "vistasoft"}}) + "GeneratedBy": {"Name": "vistasoft"}}) to_bids_description(freesurfer_folder, **{"Name": "Stanford HARDI", - "PipelineDescription": {"Name": "freesurfer"}}) + "GeneratedBy": {"Name": "freesurfer"}}) fetch_hcp_atlas_16_bundles = _make_reusable_fetcher( @@ -1462,6 +1462,6 @@ def fetch_hcp(subjects, to_bids_description(base_dir, **{"Name": study, "Acknowledgements": hcp_acknowledgements, - "PipelineDescription": {'Name': 'dmriprep'}}) + "GeneratedBy": {'Name': 'dmriprep'}}) return data_files, op.join(my_path, study) diff --git a/AFQ/tests/test_api.py b/AFQ/tests/test_api.py index 62ecdb003..655ff2995 100644 --- a/AFQ/tests/test_api.py +++ b/AFQ/tests/test_api.py @@ -114,7 +114,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True): afd.to_bids_description( dmriprep_dir, **{"Name": "Dummy", - "PipelineDescription": {"Name": "synthetic"}}) + "GeneratedBy": {"Name": "synthetic"}}) for subject in subjects: for session in sessions: @@ -140,7 +140,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True): afd.to_bids_description( dmriprep_dir, **{"Name": "Dummy", - "PipelineDescription": {"Name": "synthetic"}}) + "GeneratedBy": {"Name": "synthetic"}}) for d in range(n_subjects): subject = subjects[d] @@ -163,7 +163,7 @@ def create_dummy_bids_path(n_subjects, n_sessions, share_sessions=True): afd.to_bids_description( dmriprep_dir, **{"Name": "Dummy", - "PipelineDescription": {"Name": "synthetic"}}) + "GeneratedBy": {"Name": "synthetic"}}) for subject in subjects: for modality in ['anat', 'dwi']: @@ -205,7 +205,7 @@ def test_AFQ_missing_files(): "otherDeriv"), **{ "Name": "Missing", - "PipelineDescription": {"Name": "otherDeriv"}}) + "GeneratedBy": {"Name": "otherDeriv"}}) touch(op.join(subses_folder, "sub-01_ses-01_dwi.nii.gz")) with pytest.raises( @@ -218,7 +218,7 @@ def test_AFQ_missing_files(): afd.to_bids_description( op.join(bids_path, "missingPipe"), **{ "Name": "Missing", - "PipelineDescription": {"Name": "missingPipe"}}) + "GeneratedBy": {"Name": "missingPipe"}}) with pytest.raises( ValueError, match="No non-json files recognized by pyBIDS" diff --git a/examples/plot_bids_layout.py b/examples/plot_bids_layout.py index c174fb454..0a1efa605 100644 --- a/examples/plot_bids_layout.py +++ b/examples/plot_bids_layout.py @@ -107,7 +107,7 @@ afd.to_bids_description( tractography_path, **{"Name": "my_tractography", - "PipelineDescription": {"Name": "my_tractography"}}) + "GeneratedBy": {"Name": "my_tractography"}}) ###########################################################################