diff --git a/bids_prov/afni/afni_parser.py b/bids_prov/afni/afni_parser.py index ab4119e0d..552541a14 100644 --- a/bids_prov/afni/afni_parser.py +++ b/bids_prov/afni/afni_parser.py @@ -130,8 +130,8 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False): inputs, outputs, cmd_args_remain = get_entities(cmd_s[1:], df) - # if "used" in df: - # arg = df["used"] + # if "Used" in df: + # arg = df["Used"] # entities, args_consumed_list = get_entities(cmd_s, arg) # renamed_entities = [clean_label_suffix( # os.path.split(ent)[1]) for ent in entities] @@ -139,8 +139,8 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False): # for arg in args_consumed_list: # cmd_args_remain.remove(arg) - # if "generatedBy" in df: - # arg = df["generatedBy"] + # if "GeneratedBy" in df: + # arg = df["GeneratedBy"] # entities, args_consumed_list = get_entities(cmd_s, arg) # renamed_entities = [clean_label_suffix( # os.path.split(ent)[1]) for ent in entities] @@ -362,7 +362,7 @@ def fusion_activities(activities, label): return { "@id": f"urn:{get_id()}", "Label": label, - "AssociatedWith": activities[0]["associatedWith"], + "AssociatedWith": activities[0]["AssociatedWith"], "Command": command, "Used": used_entities, } @@ -411,8 +411,8 @@ def get_extern_entities_from_activities(graph, activities, id_fusion_activity): generated_entities.append(ent) # for ent in used_ents: - # if "generatedBy" in ent: - # ent["generatedBy"] = id_fusion_activity + # if "GeneratedBy" in ent: + # ent["GeneratedBy"] = id_fusion_activity for ent in generated_entities: if "GeneratedBy" in ent: diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py index d1277a74c..9c017ecdd 100644 --- a/bids_prov/fsl/fsl_parser.py +++ b/bids_prov/fsl/fsl_parser.py @@ -143,7 +143,7 @@ def readlines(filename: str) -> Mapping[str, List[str]]: def _get_kwarg(serie, with_value=True): """ - Get the named arguments (kwarg) from a column ("used", "generatedBy", "parameters_value" or "parameters_no_value" ) of the dataframe coming frome in description_functions.json + Get the named arguments (kwarg) from a column ("Used", "GeneratedBy", "parameters_value" or "parameters_no_value" ) of the dataframe coming frome in description_functions.json Parameters ---------- @@ -201,7 +201,7 @@ def _get_kwarg(serie, with_value=True): def _get_arg(serie, arg_rest): """ - Get the ordinal arguments from a column ("used", "generatedBy") of the dataframe coming from in description_functions.json. _get_arg shoud be used when all named arguments are removed from the initial command. + Get the ordinal arguments from a column ("Used", "GeneratedBy") of the dataframe coming from in description_functions.json. _get_arg shoud be used when all named arguments are removed from the initial command. Parameters ---------- @@ -306,11 +306,11 @@ def get_entities(cmd_s, parameters): ------- >>> df = { - "name": "command", - "used": [0, "-a"], - "generatedBy": [-1, "-b"] + "name": "Command", + "Used": [0, "-a"], + "GeneratedBy": [-1, "-b"] } - >>> cmd_s = ["command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] + >>> cmd_s = ["Command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] >>> inputs, outputs, parameters = get_entities(cmd_s[1:], df) >>> (["kwarg_0", "arg_0"], ["kwarg_1", "arg_1"], []) diff --git a/bids_prov/spm/spm_parser.py b/bids_prov/spm/spm_parser.py index 351a785ad..aa4e9ec03 100644 --- a/bids_prov/spm/spm_parser.py +++ b/bids_prov/spm/spm_parser.py @@ -47,7 +47,7 @@ def get_input_entity(right: str) -> List[dict]: Returns ------- dict[str, str] - else with key "@id", "label", "prov" + else with key "@id", "Label", "prov" """ @@ -62,8 +62,8 @@ def get_input_entity(right: str) -> List[dict]: entity_label_short = "_".join(file_location.split("/")[-2:]) # Sub01_con_0001.nii entity = { "@id": "urn:" + get_id(), - "label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"), - "prov:atLocation": file_location + "Label": label_mapping(entity_label_short, "spm/spm_activity_labels.json"), + "AtLocation": file_location } entities.append(entity) @@ -159,7 +159,7 @@ def get_entities_from_ext_config(conf_dic: dict, activity_name: str, activity_id Returns ------- list[dict] - each element is an entity dict with key "@id", "label", "prov:atLocation", "wasGeneratedBy" + each element is an entity dict with key "@id", "Label", "AtLocation", "wasGeneratedBy" """ output_entities = list() @@ -200,7 +200,7 @@ def find_closest_activity(activities: list, right: str) -> dict: dep_number = re.search(r"{(\d+)}", right) # retrieve name of the output_entity closest_activity = None for act in activities: - if act["label"].endswith(dep_number.group(1)): + if act["Label"].endswith(dep_number.group(1)): closest_activity = act break @@ -221,14 +221,14 @@ def find_output_id_from_closest(closest_activity: dict, records: dict) -> str: """ for entity in records["Entities"]: if "GeneratedBy" in entity: - if entity["GeneratedBy"] == closest_activity["@id"]: # entity["label"] == parts[-1] + if entity["GeneratedBy"] == closest_activity["@id"]: # entity["Label"] == parts[-1] output_id = entity["@id"] break else: output_id = "urn:" + get_id() # output_id = next( # (entity["@id"] for entity in records["prov:Entity"] - # if parts[-1] == entity["label"] and entity["generatedBy"] == closest_activity["@id"] + # if parts[-1] == entity["Label"] and entity["GeneratedBy"] == closest_activity["@id"] # ), "urn:" + get_id() # ) # find entity id generated by closest activity, if None new get_id @@ -365,7 +365,7 @@ def get_records(task_groups: dict, agent_id: str, verbose=False) -> dict: output_entity = { # output for closest activity but input for current one "@id": output_id, "Label": out_label, # label_mapping(parts[-1], "spm/spm_labels.json"), - # "prov:atLocation": TODO + # "AtLocation": TODO "GeneratedBy": closest_activity["@id"], } output_entities.append(output_entity) diff --git a/bids_prov/tests/samples_test/batch_example_spm.jsonld b/bids_prov/tests/samples_test/batch_example_spm.jsonld index ed1277551..bcd72cd0b 100644 --- a/bids_prov/tests/samples_test/batch_example_spm.jsonld +++ b/bids_prov/tests/samples_test/batch_example_spm.jsonld @@ -2,67 +2,67 @@ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json", "BIDSProvVersion": "dev", "@id": "http://example.org/ds00000X", - "records": { - "prov:Agent": [ + "Records": { + "Activities": [ { "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "RRID": "RRID:SCR_007037", "@type": "prov:SoftwareAgent", - "label": "SPM", - "version": "SPM12r7224" + "Label": "SPM", + "Version": "SPM12r7224" } ], - "prov:Activity": [ + "Activities": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:4a800646-417a-4105-bc31-99944567ceb1" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};", - "parameters": { + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};", + "Parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}" } }, { "@id": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:df7142dc-af29-46f8-b774-4cca4d909eb2" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};", - "parameters": { + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};", + "Parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}" } }, { "@id": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" }, { "@id": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" }, { "@id": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07", - "label": "Realign", - "used": [ + "Label": "Realign", + "Used": [ "urn:467c0714-a9fb-4797-aa59-c1698d242349" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';", "parameters": { "eoptions.quality": "0.9", "eoptions.sep": "4", @@ -80,13 +80,13 @@ }, { "@id": "urn:11e760a5-a6d5-430a-82b7-075d2a3a0c78", - "label": "Coregister", - "used": [ + "Label": "Coregister", + "Used": [ "urn:071d1481-5649-48e9-9846-6a921f7ea79c", "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];", "parameters": { "other": "{''}", "eoptions.cost_fun": "'nmi'", @@ -97,12 +97,12 @@ }, { "@id": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", - "label": "Segment", - "used": [ + "Label": "Segment", + "Used": [ "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];", "parameters": { "channel.biasreg": "0.001", "channel.biasfwhm": "60", @@ -142,13 +142,13 @@ }, { "@id": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:071d1481-5649-48e9-9846-6a921f7ea79c" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -158,13 +158,13 @@ }, { "@id": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -174,12 +174,12 @@ }, { "@id": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86", - "label": "Smooth", - "used": [ + "Label": "Smooth", + "Used": [ "urn:ac189004-8387-4e75-bc93-a36cdff27e9f" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';", "parameters": { "fwhm": "[6, 6, 6]", "dtype": "0", @@ -189,13 +189,13 @@ }, { "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3", - "label": "Stat Design", - "used": [ + "Label": "Stat Design", + "Used": [ "urn:4804ef24-cc59-44d0-bc17-d84637db2982", "urn:1f05f4d1-1a38-4927-812e-cd08801f772d" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';", "parameters": { "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'}", "timing.units": "'secs'", @@ -217,12 +217,12 @@ }, { "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a", - "label": "Estimate stat.", - "used": [ + "Label": "Estimate stat.", + "Used": [ "urn:29663157-072a-468b-9e47-921f47d9e875" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;", "parameters": { "write_residuals": "0", "method.Classical": "1" @@ -230,12 +230,12 @@ }, { "@id": "urn:afaaa713-1d26-4313-a970-3feebd8700eb", - "label": "Estimate contrast", - "used": [ + "Label": "Estimate contrast", + "Used": [ "urn:6cd92a40-17cd-479a-9600-66c386988190" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;", "parameters": { "consess{1}.tcon.name": "'tone counting vs baseline'", "consess{1}.tcon.weights": "[1, 0]", @@ -248,12 +248,12 @@ }, { "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260", - "label": "Threshold", - "used": [ + "Label": "Threshold", + "Used": [ "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.contrasts = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.mtype = 0;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.contrasts = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.mtype = 0;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;", "parameters": { "conspec.titlestr": "''", "conspec.contrasts": "1", @@ -273,95 +273,95 @@ "prov:Entity": [ { "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz", + "Label": "func_sub-01_task-tonecounting_bold.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz", "digest": { "sha256": "fb2cf448c0c65ac4dd070fadddb9f8f5dd784be41b59c7c1049646bd651f706b" } }, { "@id": "urn:df7142dc-af29-46f8-b774-4cca4d909eb2", - "label": "anat_sub-01_T1w.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz", + "Label": "anat_sub-01_T1w.nii.gz", + "AtLocation": 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}, { "@id": "urn:071d1481-5649-48e9-9846-6a921f7ea79c", - "label": "meanfunc_sub-01_task-tonecounting_bold.nii", - "generatedBy": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07" + "Label": "meanfunc_sub-01_task-tonecounting_bold.nii", + "GeneratedBy": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07" }, { "@id": "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0", - "label": "anat_sub-01_T1w.nii", - "generatedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" + "Label": "anat_sub-01_T1w.nii", + "GeneratedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" }, { "@id": "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", - "label": "segment1", - "prov:atLocation": "c1anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", + "Label": "segment1", + "AtLocation": "c1anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", "digest": { "sha256": "7931047dca66b97c916267a25cf55b95011813ec3d36f0160a6eda561be2c8be" } }, { "@id": "urn:a40f9ca3-df62-492c-982a-3add9b872a76", - "label": "segment2", - "prov:atLocation": "c2anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", + "Label": "segment2", + "AtLocation": "c2anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", "digest": { "sha256": "4c1823ee4716970114afc99ad01a1839d442765a038f0f2403dda6b70926a533" } }, { "@id": "urn:ac189004-8387-4e75-bc93-a36cdff27e9f", - "label": "wsegment1", - "generatedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" + "Label": "wsegment1", + "GeneratedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" }, { "@id": "urn:1f05f4d1-1a38-4927-812e-cd08801f772d", - "label": "ONSETS_sub-01-MultiCond.mat", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat", + "Label": "ONSETS_sub-01-MultiCond.mat", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat", "digest": { "sha256": 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a/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld b/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld index 2c7b623bf..1e47043a5 100644 --- a/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld +++ b/bids_prov/tests/samples_test/batch_example_spm_ref.jsonld @@ -8,56 +8,56 @@ "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "RRID": "RRID:SCR_007037", "@type": "prov:SoftwareAgent", - "label": "SPM", + "Label": "SPM", "version": "SPM12r7224" } ], "prov:Activity": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:4a800646-417a-4105-bc31-99944567ceb1" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}" } }, { "@id": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:df7142dc-af29-46f8-b774-4cca4d909eb2" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}" } }, { "@id": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" }, { "@id": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" }, { "@id": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07", - "label": "Realign", - "used": [ + "Label": "Realign", + "Used": [ "urn:467c0714-a9fb-4797-aa59-c1698d242349" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "eoptions.quality": "0.9", "eoptions.sep": "4", @@ -75,12 +75,12 @@ }, { "@id": "urn:11e760a5-a6d5-430a-82b7-075d2a3a0c78", - "label": "Coregister", - "used": [ + "Label": "Coregister", + "Used": [ "urn:071d1481-5649-48e9-9846-6a921f7ea79c", "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "other": "{''}", "eoptions.cost_fun": "'nmi'", @@ -91,11 +91,11 @@ }, { "@id": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", - "label": "Segment", - "used": [ + "Label": "Segment", + "Used": [ "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "channel.biasreg": "0.001", "channel.biasfwhm": "60", @@ -135,12 +135,12 @@ }, { "@id": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:071d1481-5649-48e9-9846-6a921f7ea79c" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -150,12 +150,12 @@ }, { "@id": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -165,11 +165,11 @@ }, { "@id": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86", - "label": "Smooth", - "used": [ + "Label": "Smooth", + "Used": [ "urn:ac189004-8387-4e75-bc93-a36cdff27e9f" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "fwhm": "[6, 6, 6]", "dtype": "0", @@ -179,12 +179,12 @@ }, { "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3", - "label": "Stat Design", - "used": [ + "Label": "Stat Design", + "Used": [ "urn:4804ef24-cc59-44d0-bc17-d84637db2982", "urn:1f05f4d1-1a38-4927-812e-cd08801f772d" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'}", "timing.units": "'secs'", @@ -206,11 +206,11 @@ }, { "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a", - "label": "Estimate stat.", - "used": [ + "Label": "Estimate stat.", + "Used": [ "urn:29663157-072a-468b-9e47-921f47d9e875" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "write_residuals": "0", "method.Classical": "1" @@ -218,11 +218,11 @@ }, { "@id": "urn:afaaa713-1d26-4313-a970-3feebd8700eb", - "label": "Estimate contrast", - "used": [ + "Label": "Estimate contrast", + "Used": [ "urn:6cd92a40-17cd-479a-9600-66c386988190" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "consess{1}.tcon.name": "'tone counting vs baseline'", "consess{1}.tcon.weights": "[1, 0]", @@ -235,11 +235,11 @@ }, { "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260", - "label": "Threshold", - "used": [ + "Label": "Threshold", + "Used": [ "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "conspec.titlestr": "''", "conspec.contrasts": "1", @@ -259,80 +259,80 @@ "prov:Entity": [ { "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz" + "Label": "func_sub-01_task-tonecounting_bold.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz" }, { "@id": "urn:df7142dc-af29-46f8-b774-4cca4d909eb2", - "label": "anat_sub-01_T1w.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz" + "Label": "anat_sub-01_T1w.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz" }, { "@id": "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "generatedBy": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1" + "Label": "func_sub-01_task-tonecounting_bold.nii.gz", + "GeneratedBy": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1" }, { "@id": "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21", - "label": "anat_sub-01_T1w.nii.gz", - "generatedBy": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f" + "Label": "anat_sub-01_T1w.nii.gz", + "GeneratedBy": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f" }, { "@id": "urn:467c0714-a9fb-4797-aa59-c1698d242349", - "label": "func_sub-01_task-tonecounting_bold.nii", - "generatedBy": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762" + "Label": "func_sub-01_task-tonecounting_bold.nii", + "GeneratedBy": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762" }, { "@id": "urn:071d1481-5649-48e9-9846-6a921f7ea79c", - "label": "meanfunc_sub-01_task-tonecounting_bold.nii", - "generatedBy": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07" + "Label": "meanfunc_sub-01_task-tonecounting_bold.nii", + "GeneratedBy": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07" }, { "@id": "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0", - "label": "anat_sub-01_T1w.nii", - "generatedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" + "Label": "anat_sub-01_T1w.nii", + "GeneratedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" }, { "@id": "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", - "label": "segment1", - "prov:atLocation": "c1anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" + "Label": "segment1", + "AtLocation": "c1anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" }, { "@id": "urn:a40f9ca3-df62-492c-982a-3add9b872a76", - "label": "segment2", - "prov:atLocation": "c2anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" + "Label": "segment2", + "AtLocation": "c2anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" }, { "@id": "urn:ac189004-8387-4e75-bc93-a36cdff27e9f", - "label": "wsegment1", - "generatedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" + "Label": "wsegment1", + "GeneratedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" }, { "@id": "urn:1f05f4d1-1a38-4927-812e-cd08801f772d", - "label": "ONSETS_sub-01-MultiCond.mat", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat" + "Label": "ONSETS_sub-01-MultiCond.mat", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat" }, { "@id": "urn:4804ef24-cc59-44d0-bc17-d84637db2982", - "label": "swsegment1", - "generatedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" + "Label": "swsegment1", + "GeneratedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" }, { "@id": "urn:29663157-072a-468b-9e47-921f47d9e875", - "label": "SPM.mat", - "generatedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" + "Label": "SPM.mat", + "GeneratedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" }, { "@id": "urn:6cd92a40-17cd-479a-9600-66c386988190", - "label": "SPM.mat", - "generatedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" + "Label": "SPM.mat", + "GeneratedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" }, { "@id": "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6", - "label": "SPM.mat", - "generatedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" + "Label": "SPM.mat", + "GeneratedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" } ] } diff --git a/bids_prov/tests/samples_test/partial_conjunction.jsonld b/bids_prov/tests/samples_test/partial_conjunction.jsonld index 8723d5bc8..0b9b5278e 100644 --- a/bids_prov/tests/samples_test/partial_conjunction.jsonld +++ b/bids_prov/tests/samples_test/partial_conjunction.jsonld @@ -8,61 +8,61 @@ "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "RRID": "RRID:SCR_007037", "@type": "prov:SoftwareAgent", - "label": "SPM", + "Label": "SPM", "version": "SPM12r7224" } ], "prov:Activity": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:4a800646-417a-4105-bc31-99944567ceb1" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}" } }, { "@id": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:df7142dc-af29-46f8-b774-4cca4d909eb2" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}" } }, { "@id": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" }, { "@id": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));" }, { "@id": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07", - "label": "Realign", - "used": [ + "Label": "Realign", + "Used": [ "urn:467c0714-a9fb-4797-aa59-c1698d242349" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';", "parameters": { "eoptions.quality": "0.9", "eoptions.sep": "4", @@ -80,13 +80,13 @@ }, { "@id": "urn:11e760a5-a6d5-430a-82b7-075d2a3a0c78", - "label": "Coregister", - "used": [ + "Label": "Coregister", + "Used": [ "urn:071d1481-5649-48e9-9846-6a921f7ea79c", "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];", "parameters": { "other": "{''}", "eoptions.cost_fun": "'nmi'", @@ -97,12 +97,12 @@ }, { "@id": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", - "label": "Segment", - "used": [ + "Label": "Segment", + "Used": [ "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];", "parameters": { "channel.biasreg": "0.001", "channel.biasfwhm": "60", @@ -142,13 +142,13 @@ }, { "@id": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:071d1481-5649-48e9-9846-6a921f7ea79c" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -158,13 +158,13 @@ }, { "@id": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -174,12 +174,12 @@ }, { "@id": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86", - "label": "Smooth", - "used": [ + "Label": "Smooth", + "Used": [ "urn:ac189004-8387-4e75-bc93-a36cdff27e9f" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';", "parameters": { "fwhm": "[6, 6, 6]", "dtype": "0", @@ -189,13 +189,13 @@ }, { "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3", - "label": "Stat Design", - "used": [ + "Label": "Stat Design", + "Used": [ "urn:4804ef24-cc59-44d0-bc17-d84637db2982", "urn:1f05f4d1-1a38-4927-812e-cd08801f772d" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';", "parameters": { "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'}", "timing.units": "'secs'", @@ -217,12 +217,12 @@ }, { "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a", - "label": "Estimate stat.", - "used": [ + "Label": "Estimate stat.", + "Used": [ "urn:29663157-072a-468b-9e47-921f47d9e875" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;", "parameters": { "write_residuals": "0", "method.Classical": "1" @@ -230,12 +230,12 @@ }, { "@id": "urn:afaaa713-1d26-4313-a970-3feebd8700eb", - "label": "Estimate contrast", - "used": [ + "Label": "Estimate contrast", + "Used": [ "urn:6cd92a40-17cd-479a-9600-66c386988190" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;", "parameters": { "consess{1}.tcon.name": "'tone counting vs baseline'", "consess{1}.tcon.weights": "[1, 0]", @@ -248,12 +248,12 @@ }, { "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260", - "label": "Threshold", - "used": [ + "Label": "Threshold", + "Used": [ "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;", "parameters": { "conspec.titlestr": "''", "conspec.contrasts": "[1, 2]", @@ -271,95 +271,95 @@ "prov:Entity": [ { "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz", + "Label": "func_sub-01_task-tonecounting_bold.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz", "digest": { "sha256": "fb2cf448c0c65ac4dd070fadddb9f8f5dd784be41b59c7c1049646bd651f706b" } }, { "@id": "urn:df7142dc-af29-46f8-b774-4cca4d909eb2", - "label": "anat_sub-01_T1w.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz", + "Label": "anat_sub-01_T1w.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz", "digest": { "sha256": "6c8218922a9c951808b41435d1c0915fae003c74acd598385cc25d00f8463e3a" } }, { 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"c2anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", "digest": { "sha256": "4c1823ee4716970114afc99ad01a1839d442765a038f0f2403dda6b70926a533" } }, { "@id": "urn:ac189004-8387-4e75-bc93-a36cdff27e9f", - "label": "wsegment1", - "generatedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" + "Label": "wsegment1", + "GeneratedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" }, { "@id": "urn:1f05f4d1-1a38-4927-812e-cd08801f772d", - "label": "ONSETS_sub-01-MultiCond.mat", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat", + "Label": "ONSETS_sub-01-MultiCond.mat", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat", "digest": { "sha256": "11d27033ca8efe522163b6f908853ee9cee7b9be9398e2035992610588d39cb8" } }, { "@id": "urn:4804ef24-cc59-44d0-bc17-d84637db2982", - "label": "swsegment1", - "generatedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" + "Label": "swsegment1", + "GeneratedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" }, { "@id": "urn:29663157-072a-468b-9e47-921f47d9e875", - "label": "SPM.mat", - "generatedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" + "Label": "SPM.mat", + "GeneratedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" }, { "@id": "urn:6cd92a40-17cd-479a-9600-66c386988190", - "label": "SPM.mat", - "generatedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" + "Label": "SPM.mat", + "GeneratedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" }, { "@id": "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6", - "label": "SPM.mat", - "generatedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" + "Label": "SPM.mat", + "GeneratedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" } ] } diff --git a/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld b/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld index 624af79fa..a23d83f18 100644 --- a/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld +++ b/bids_prov/tests/samples_test/partial_conjunction_ref.jsonld @@ -8,56 +8,56 @@ "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "RRID": "RRID:SCR_007037", "@type": "prov:SoftwareAgent", - "label": "SPM", + "Label": "SPM", "version": "SPM12r7224" } ], "prov:Activity": [ { "@id": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:4a800646-417a-4105-bc31-99944567ceb1" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}" } }, { "@id": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f", - "label": "Move file", - "used": [ + "Label": "Move file", + "Used": [ "urn:df7142dc-af29-46f8-b774-4cca4d909eb2" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}" } }, { "@id": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" }, { "@id": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7", - "label": "Gunzip", - "used": [ + "Label": "Gunzip", + "Used": [ "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75" }, { "@id": "urn:293a9acc-2652-48ff-842a-2f9da1b4ba07", - "label": "Realign", - "used": [ + "Label": "Realign", + "Used": [ "urn:467c0714-a9fb-4797-aa59-c1698d242349" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "eoptions.quality": "0.9", "eoptions.sep": "4", @@ -75,12 +75,12 @@ }, { "@id": "urn:11e760a5-a6d5-430a-82b7-075d2a3a0c78", - "label": "Coregister", - "used": [ + "Label": "Coregister", + "Used": [ "urn:071d1481-5649-48e9-9846-6a921f7ea79c", "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "other": "{''}", "eoptions.cost_fun": "'nmi'", @@ -91,11 +91,11 @@ }, { "@id": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63", - "label": "Segment", - "used": [ + "Label": "Segment", + "Used": [ "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "channel.biasreg": "0.001", "channel.biasfwhm": "60", @@ -135,12 +135,12 @@ }, { "@id": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:071d1481-5649-48e9-9846-6a921f7ea79c" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -150,12 +150,12 @@ }, { "@id": "urn:5d3ffd11-a23c-4698-a32d-c48296ce3859", - "label": "Normalize", - "used": [ + "Label": "Normalize", + "Used": [ "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "woptions.bb": "[-78, -112, -70, 78, 76, 85]", "woptions.vox": "[2, 2, 2]", @@ -165,11 +165,11 @@ }, { "@id": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86", - "label": "Smooth", - "used": [ + "Label": "Smooth", + "Used": [ "urn:ac189004-8387-4e75-bc93-a36cdff27e9f" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "fwhm": "[6, 6, 6]", "dtype": "0", @@ -179,12 +179,12 @@ }, { "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3", - "label": "Stat Design", - "used": [ + "Label": "Stat Design", + "Used": [ "urn:4804ef24-cc59-44d0-bc17-d84637db2982", "urn:1f05f4d1-1a38-4927-812e-cd08801f772d" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'}", "timing.units": "'secs'", @@ -206,11 +206,11 @@ }, { "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a", - "label": "Estimate stat.", - "used": [ + "Label": "Estimate stat.", + "Used": [ "urn:29663157-072a-468b-9e47-921f47d9e875" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "write_residuals": "0", "method.Classical": "1" @@ -218,11 +218,11 @@ }, { "@id": "urn:afaaa713-1d26-4313-a970-3feebd8700eb", - "label": "Estimate contrast", - "used": [ + "Label": "Estimate contrast", + "Used": [ "urn:6cd92a40-17cd-479a-9600-66c386988190" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "consess{1}.tcon.name": "'tone counting vs baseline'", "consess{1}.tcon.weights": "[1, 0]", @@ -235,11 +235,11 @@ }, { "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260", - "label": "Threshold", - "used": [ + "Label": "Threshold", + "Used": [ "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6" ], - "associatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", + "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", "parameters": { "conspec.titlestr": "''", "conspec.contrasts": "[1, 2]", @@ -257,80 +257,80 @@ "prov:Entity": [ { "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1", - "label": "func_sub-01_task-tonecounting_bold.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz" + "Label": "func_sub-01_task-tonecounting_bold.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz" }, { "@id": "urn:df7142dc-af29-46f8-b774-4cca4d909eb2", - "label": "anat_sub-01_T1w.nii.gz", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz" + "Label": "anat_sub-01_T1w.nii.gz", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz" }, { "@id": "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a", - "label": 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"urn:293a9acc-2652-48ff-842a-2f9da1b4ba07" }, { "@id": "urn:daa4ed3c-3454-4ae4-8628-7225154d1eb0", - "label": "anat_sub-01_T1w.nii", - "generatedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" + "Label": "anat_sub-01_T1w.nii", + "GeneratedBy": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7" }, { "@id": "urn:e57b37e7-704b-4d09-af2e-ab42fd8cfe33", - "label": "segment1", - "prov:atLocation": "c1anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" + "Label": "segment1", + "AtLocation": "c1anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" }, { "@id": "urn:a40f9ca3-df62-492c-982a-3add9b872a76", - "label": "segment2", - "prov:atLocation": "c2anat_sub-01_T1w.nii", - "generatedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" + "Label": "segment2", + "AtLocation": "c2anat_sub-01_T1w.nii", + "GeneratedBy": "urn:95522f9a-6757-4c02-a1c2-df96fa5e2d63" }, { "@id": "urn:ac189004-8387-4e75-bc93-a36cdff27e9f", - "label": "wsegment1", - "generatedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" + "Label": "wsegment1", + "GeneratedBy": "urn:942af46d-1c8d-4358-a2db-0c01afd798c2" }, { "@id": "urn:1f05f4d1-1a38-4927-812e-cd08801f772d", - "label": "ONSETS_sub-01-MultiCond.mat", - "prov:atLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat" + "Label": "ONSETS_sub-01-MultiCond.mat", + "AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat" }, { "@id": "urn:4804ef24-cc59-44d0-bc17-d84637db2982", - "label": "swsegment1", - "generatedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" + "Label": "swsegment1", + "GeneratedBy": "urn:bf3ba33a-183c-44e2-9d66-a3582e62fe86" }, { "@id": "urn:29663157-072a-468b-9e47-921f47d9e875", - "label": "SPM.mat", - "generatedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" + "Label": "SPM.mat", + "GeneratedBy": "urn:9fc62455-73dd-4732-8555-2a83319f69e3" }, { "@id": "urn:6cd92a40-17cd-479a-9600-66c386988190", - "label": "SPM.mat", - "generatedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" + "Label": "SPM.mat", + "GeneratedBy": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a" }, { "@id": "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6", - "label": "SPM.mat", - "generatedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" + "Label": "SPM.mat", + "GeneratedBy": "urn:afaaa713-1d26-4313-a970-3feebd8700eb" } ] } diff --git a/bids_prov/tests/test_fsl_parser.py b/bids_prov/tests/test_fsl_parser.py index 4bff838bc..c59c5ec6b 100644 --- a/bids_prov/tests/test_fsl_parser.py +++ b/bids_prov/tests/test_fsl_parser.py @@ -78,21 +78,21 @@ def test_readlines(): def test_get_entities(): # positionnal argument df = { - "name": "command", - "used": [0], - "generatedBy": [1] + "name": "Command", + "Used": [0], + "GeneratedBy": [1] } - cmd_s = ["command", "arg_0", "arg_1"] + cmd_s = ["Command", "arg_0", "arg_1"] expected_results = (['arg_0'], ['arg_1'], []) assert get_entities(cmd_s[1:], df) == expected_results # inputs, outputs : arg and kwarg df = { - "name": "command", - "used": [0, "-a"], - "generatedBy": [1, "-b"] + "name": "Command", + "Used": [0, "-a"], + "GeneratedBy": [1, "-b"] } - cmd_s = ["command", "arg_0", "arg_1", "-a", "kwarg_0", "-b", "kwarg_1"] + cmd_s = ["Command", "arg_0", "arg_1", "-a", "kwarg_0", "-b", "kwarg_1"] inputs, outputs, parameters = get_entities(cmd_s[1:], df) expected_inputs = ["kwarg_0", "arg_0"] expected_outputs = ["kwarg_1", "arg_1"] @@ -103,11 +103,11 @@ def test_get_entities(): # inputs, outputs : shuffle arg and kwarg df = { - "name": "command", - "used": [0, "-a"], - "generatedBy": [1, "-b"] + "name": "Command", + "Used": [0, "-a"], + "GeneratedBy": [1, "-b"] } - cmd_s = ["command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] + cmd_s = ["Command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] inputs, outputs, parameters = get_entities(cmd_s[1:], df) expected_inputs = ["kwarg_0", "arg_0"] expected_outputs = ["kwarg_1", "arg_1"] @@ -118,11 +118,11 @@ def test_get_entities(): # inputs, outputs : arg -1 and kwarg df = { - "name": "command", - "used": [0, "-a"], - "generatedBy": [-1, "-b"] + "name": "Command", + "Used": [0, "-a"], + "GeneratedBy": [-1, "-b"] } - cmd_s = ["command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] + cmd_s = ["Command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1"] inputs, outputs, parameters = get_entities(cmd_s[1:], df) expected_inputs = ["kwarg_0", "arg_0"] expected_outputs = ["kwarg_1", "arg_1"] @@ -133,11 +133,11 @@ def test_get_entities(): # inputs, outputs : arg "0:-1" and kwarg df = { - "name": "command", - "used": ["0:-1", "-a"], - "generatedBy": [-1, "-b"] + "name": "Command", + "Used": ["0:-1", "-a"], + "GeneratedBy": [-1, "-b"] } - cmd_s = ["command", "-a", "kwarg_0", "arg_0", + cmd_s = ["Command", "-a", "kwarg_0", "arg_0", "arg_1", "-b", "kwarg_1", "arg_2"] inputs, outputs, parameters = get_entities(cmd_s[1:], df) expected_inputs = ["kwarg_0", "arg_0", "arg_1"] @@ -149,9 +149,9 @@ def test_get_entities(): # inputs, outputs : arg and kwarg dict df = { - "name": "command", - "used": ["0:-1", "-a"], - "generatedBy": [-1, "-b", { + "name": "Command", + "Used": ["0:-1", "-a"], + "GeneratedBy": [-1, "-b", { "name": "-c", "index": ["0:2"] }, @@ -161,7 +161,7 @@ def test_get_entities(): },] } cmd_s = [ - "command", + "Command", "-a", "kwarg_0", "arg_0", "arg_1", @@ -182,9 +182,9 @@ def test_get_entities(): # inputs, outputs, parameters : arg and kwarg, parameters df = { - "name": "command", - "used": [0, "-a"], - "generatedBy": [-1, "-b"], + "name": "Command", + "Used": [0, "-a"], + "GeneratedBy": [-1, "-b"], "parameters_value": ["-c", { "name": "-d", @@ -193,7 +193,7 @@ def test_get_entities(): "parameters_no_value": ["-e", "-f"] } cmd_s = [ - "command", + "Command", "-a", "kwarg_0", "arg_0", "arg_1", @@ -213,9 +213,9 @@ def test_get_entities(): # inputs, outputs : arg and kwarg dict and nargs df = { - "name": "command", - "used": ["0:-1", "-a"], - "generatedBy": [-1, "-b", { + "name": "Command", + "Used": ["0:-1", "-a"], + "GeneratedBy": [-1, "-b", { "name": "-c", "index": ["0:2"], "nargs": 3, @@ -227,7 +227,7 @@ def test_get_entities(): },] } cmd_s = [ - "command", + "Command", "-a", "kwarg_0", "arg_0", "arg_1", @@ -250,7 +250,7 @@ def test_get_entities(): def test_get_entities_rm(): df = { "name": "rm", - "used": ["0:"] + "Used": ["0:"] } cmd = "/bin/rm -f sl?.png highres2standard2.png" cmd_s = cmd.split(" ") @@ -268,8 +268,8 @@ def test_get_entities_rm(): def test_get_entities_mv(): df = { "name": "mv", - "used": ["0:-1"], - "generatedBy": [-1] + "Used": ["0:-1"], + "GeneratedBy": [-1] } cmd = "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms " \ "prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms " \ diff --git a/bids_prov/tests/test_spm_parser.py b/bids_prov/tests/test_spm_parser.py index 34aedfdb3..a98696399 100644 --- a/bids_prov/tests/test_spm_parser.py +++ b/bids_prov/tests/test_spm_parser.py @@ -89,8 +89,8 @@ def test_get_input_entity(): # entity label : sub-01_task-tonecounting_bold.nii.gz entities = [{ "@id": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75", - "label": "func_sub-01_task-tonecounting_bold_trunctest.nii.gz", - "prov:atLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz" + "Label": "func_sub-01_task-tonecounting_bold_trunctest.nii.gz", + "AtLocation": "ds011/sub-01/func/sub-01_task-tonecounting_bold_trunctest.nii.gz" }] init_random_state() right_entity = get_input_entity(right)[0] diff --git a/bids_prov/tests/test_utils.py b/bids_prov/tests/test_utils.py index 1386ba631..75ae36eec 100644 --- a/bids_prov/tests/test_utils.py +++ b/bids_prov/tests/test_utils.py @@ -32,13 +32,13 @@ def test_get_default_graph(): # Test the default arguments graph, agent_id = get_default_graph(label) assert graph["@context"] == CONTEXT_URL - assert graph["records"]["prov:Agent"][0]["label"] == label + assert graph["records"]["prov:Agent"][0]["Label"] == label assert agent_id is not None # Test custom arguments graph, agent_id = get_default_graph(label, context_url, spm_ver) assert graph["@context"] == context_url - assert graph["records"]["prov:Agent"][0]["label"] == label + assert graph["records"]["prov:Agent"][0]["Label"] == label assert graph["records"]["prov:Agent"][0]["version"] == spm_ver assert agent_id is not None diff --git a/bids_prov/utils.py b/bids_prov/utils.py index 923391261..3abad2b34 100644 --- a/bids_prov/utils.py +++ b/bids_prov/utils.py @@ -25,7 +25,7 @@ def get_default_graph(label: str, context_url: str = CONTEXT_URL, soft_ver: str "@id": "urn:" + agent_id, "RRID": "RRID:SCR_007037", "@type": "prov:SoftwareAgent", - "label": label, + "Label": label, "version": soft_ver } ], @@ -74,7 +74,7 @@ def get_sha256(file_path: str): def compute_sha_256_entity(entities: dict): """ - This method calculates the sha256 of all entities if they contain the key "prov:atLocation". + This method calculates the sha256 of all entities if they contain the key "AtLocation". If the file does not exist, then it is generated. Parameters @@ -88,12 +88,12 @@ def compute_sha_256_entity(entities: dict): """ directory = 'bids_prov/file_generation' for entity in entities: - if "prov:atLocation" in entity: - if len(entity["prov:atLocation"]) > 0: - if entity["prov:atLocation"][0] == "/": - relative_path = os.path.abspath(directory + entity["prov:atLocation"]) + if "AtLocation" in entity: + if len(entity["AtLocation"]) > 0: + if entity["AtLocation"][0] == "/": + relative_path = os.path.abspath(directory + entity["AtLocation"]) else: - relative_path = os.path.abspath(directory + "/" + entity["prov:atLocation"]) + relative_path = os.path.abspath(directory + "/" + entity["AtLocation"]) # Temporary process. If the file does not exist then it is created to have a digest value file_directory = os.path.dirname(relative_path)