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First version of heudiconv prov example
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‎.gitmodules‎

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[submodule "examples/heudiconv/examples/heudiconv/sourcedata/hirni-demo"]
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path = examples/heudiconv/examples/heudiconv/sourcedata/hirni-demo
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url = https://github.com/psychoinformatics-de/hirni-demo.git

‎examples/heudiconv/.bidsignore‎

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.duecredit.p

‎examples/heudiconv/CHANGES‎

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0.0.1 Initial data acquired
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TODOs:
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- verify and possibly extend information in participants.tsv (see for example http://datasets.datalad.org/?dir=/openfmri/ds000208)
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- fill out dataset_description.json, README, sourcedata/README (if present)
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- provide _events.tsv file for each _bold.nii.gz with onsets of events (see '8.5 Task events' of BIDS specification)

‎examples/heudiconv/README‎

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TODO: Provide description for the dataset -- basic details about the study, possibly pointing to pre-registration (if public or embargoed)

‎examples/heudiconv/code/merge_prov.py‎

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#!/usr/bin/python
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# coding: utf-8
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""" Merge available prov JSON files into one JSON-LD graph """
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import json
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from pathlib import Path
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# List of available prov files
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prov_soft_files = [
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'prov/prov-heudiconv_soft.prov.json'
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]
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prov_env_files = [
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'prov/prov-heudiconv_env.prov.json'
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]
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prov_act_files = [
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'prov/prov-heudiconv_act.prov.json'
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]
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prov_ent_files = [
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'prov/prov-heudiconv_ent.prov.json'
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]
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sidecar_files = [
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'sub-None/func/sub-None_task-oneback_run-01_bold.json',
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'sub-None/anat/sub-None_run-1_T1w.json'
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]
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# Base jsonld
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base_provenance = {
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"Records": {
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"Software": [],
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"Activities": [],
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"Entities": []
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}
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}
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# Add context and version
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with open('prov/prov-heudiconv_base.prov.json', encoding = 'utf-8') as file:
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base_provenance.update(json.load(file))
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# Parse Software
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for prov_file in prov_soft_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Software'].append(value)
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# Parse Environments
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for prov_file in prov_env_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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# /!\ Workaround: environments are added in the Entities list because
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# the Environments term is not defined in the BIDS Prov context yet
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base_provenance['Records']['Entities'].append(value)
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# Parse Activities
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for prov_file in prov_act_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Activities'].append(value)
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# Parse Entities
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for prov_file in prov_ent_files:
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with open(prov_file, encoding = 'utf-8') as file:
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data = json.load(file)
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for key, value in data.items():
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value['Id'] = key
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base_provenance['Records']['Entities'].append(value)
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# Parse Sidecar files
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for sidecar_file in sidecar_files:
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# Identify data file(s) associated with the sidecar
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sidecar_filename = Path(sidecar_file)
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data_files = Path('').glob(f'{sidecar_filename.with_suffix("")}.*')
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data_files = [str(f) for f in list(data_files) if str(sidecar_filename) not in str(f)]
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# Write provenance
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with open(sidecar_file, encoding = 'utf-8') as file:
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data = json.load(file)
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if 'GeneratedBy' in data:
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activity_id = data['GeneratedBy']
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for data_file in data_files:
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base_provenance['Records']['Entities'].append({
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"Id": f"bids::{data_file}",
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"GeneratedBy": activity_id
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})
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# Write jsonld
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with open('prov/merged/prov-heudiconv.prov.jsonld', 'w', encoding = 'utf-8') as file:
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file.write(json.dumps(base_provenance, indent = 2))

‎examples/heudiconv/examples/heudiconv/sourcedata/hirni-demo‎

Submodule hirni-demo added at f5aa766

‎examples/heudiconv/prov/merged/prov-heudiconv.prov.jsonld‎

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{
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"Records": {
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"Software": [
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{
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"Label": "Heudiconv",
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"Version": "v1.3.2",
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"Id": "bids::prov/heudiconv-a9x5yd3j"
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}
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],
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"Activities": [
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{
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"Label": "Conversion",
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"Command": "heudiconv --files sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/*.dcm -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq1 -c dcm2niix -b --minmeta --overwrite",
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"AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
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"Used": [
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"bids::prov/fedora-1cu6r6ou",
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"bids::sourcedata/hirni-demo/acq1/studyspec.json",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"bids::sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py"
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],
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"Id": "bids::prov/conversion-00f3a18f"
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},
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{
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"Label": "Conversion",
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"Command": "heudiconv --files sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms/* -o . -f sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py -s 01 -ss acq2 -c dcm2niix -b --minmeta --overwrite",
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"AssociatedWith": "bids::prov/heudiconv-a9x5yd3j",
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"Used": [
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"bids::prov/fedora-pgrzf567",
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"bids::sourcedata/hirni-demo/acq2/studyspec.json",
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"bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms",
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"bids::sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py"
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],
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"Id": "bids::prov/conversion-5a66f5be"
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}
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],
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"Entities": [
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{
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64",
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"EnvVars": {
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"HIRNI_STUDY_SPEC": "sourcedata/hirni-demo/acq1/studyspec.json"
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},
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"Id": "bids::prov/fedora-1cu6r6ou"
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},
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{
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"Label": "Fedora release 36 (Thirty Six)",
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"OperatingSystem": "GNU/Linux 6.2.15-100.fc36.x86_64",
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"EnvVars": {
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"HIRNI_STUDY_SPEC": "sourcedata/hirni-demo/acq2/studyspec.json"
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},
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"Id": "bids::prov/fedora-pgrzf567"
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},
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{
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"Label": "heuristics",
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"Id": "bids::sourcedata/hirni-demo/code/hirni-toolbox/converters/heudiconv/hirni_heuristic.py"
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},
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{
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"Label": "studyspec",
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"Id": "bids::sourcedata/hirni-demo/acq1/studyspec.json"
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},
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{
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"Label": "studyspec",
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"Id": "bids::sourcedata/hirni-demo/acq2/studyspec.json"
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},
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{
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"Label": "dicoms",
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
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},
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{
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"Label": "dicoms",
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"Id": "bids::sourcedata/hirni-demo/acq2/dicoms/example-dicom-functional-master/dicoms"
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},
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{
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"Label": "CHANGES",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::CHANGES"
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},
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{
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"Label": "README",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::README"
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},
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{
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"Label": "dataset_description.json",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::dataset_description.json"
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},
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{
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"Label": "participants.json",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::participants.json"
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},
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{
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"Label": "participants.tsv",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::participants.tsv"
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},
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{
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"Label": "scans.json",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::scans.json"
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},
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{
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"Label": "task-oneback_bold.json",
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"GeneratedBy": [
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"bids::prov/conversion-00f3a18f",
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"bids::prov/conversion-5a66f5be"
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],
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"Id": "bids::task-oneback_bold.json"
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},
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{
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"Id": "bids::sub-None/func/sub-None_task-oneback_run-01_bold.nii.gz",
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"GeneratedBy": "bids::prov/conversion-5a66f5be"
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},
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{
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"Id": "bids::sub-None/anat/sub-None_run-1_T1w.nii.gz",
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"GeneratedBy": "bids::prov/conversion-00f3a18f"
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}
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]
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},
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"@context": "https://purl.org/nidash/bidsprov/context.json",
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"BIDSProvVersion": "0.0.1"
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}

‎examples/heudiconv/prov/merged/prov-heudiconv.prov.png‎

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‎examples/heudiconv/sourcedata/README‎

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TODO: Provide description about source data, e.g.
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Directory below contains DICOMS compressed into tarballs per each sequence, replicating directory hierarchy of the BIDS dataset itself.

‎examples/heudiconv/sourcedata/hirni-demo‎

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Subproject commit f5aa766d900037d97c82329e7dfc94ee80086b92

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