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First provenance traces of anat preprocessing
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‎examples/fmriprep/derivatives/fmriprep/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-fmriprep_soft.prov.json'
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]
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prov_env_files = [
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'prov/prov-fmriprep_env.prov.json'
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]
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prov_act_files = [
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'sub-001/anat/sub-001_prov-fmriprep_act.prov.json'
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]
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prov_ent_files = [
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'prov/prov-fmriprep_ent.prov.json',
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'sub-001/anat/sub-001_prov-fmriprep_ent.prov.json'
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]
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sidecar_files = [
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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-fmriprep_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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print("Parsing soft files")
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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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print("Parsing env files")
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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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print("Parsing act files")
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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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print("Parsing ent files")
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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-fmriprep.prov.jsonld', 'w', encoding = 'utf-8') as file:
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file.write(json.dumps(base_provenance, indent = 2))

‎examples/fmriprep/derivatives/fmriprep/prov/merged/prov-fmriprep.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": "fmriprep",
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"Version": "v1.1.6",
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"AltIdentifier": "RRID:SCR_016216",
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"Id": "bids::prov/fmriprep-ughfyb4k"
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},
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{
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"Label": "ANTs",
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"Version": "2.2.0",
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"AltIdentifier": "RRID:SCR_004757",
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"Id": "urn:ants-bagzrxi0"
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},
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{
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"Label": "FreeSurfer",
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"Version": "6.0.1",
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"AltIdentifier": "RRID:SCR_001847",
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"Id": "urn:freesurfer-bqv4h9k2"
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},
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{
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"Label": "FSL",
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"Version": "5.0.9",
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"AltIdentifier": "RRID:SCR_002823",
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"Id": "urn:fsl-e1oq534p"
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}
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],
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"Activities": [
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{
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"Label": "Correction for intensity non-uniformity (INU)",
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"Command": "N4BiasFieldCorrection",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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],
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"Used": [
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{
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"Id": "bids:ds001734:sub-001/anat/sub-001_T1w.nii.gz",
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"Type": "Entity",
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"Label": "sub-001_T1w.nii.gz"
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}
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],
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"Id": "bids::prov/inu-correction-ue9qstw1"
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},
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{
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"Label": "Skull stripping",
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"Command": "antsBrainExtraction.sh",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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],
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"Used": [
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"https://github.com/brainspaces/OASIS/blob/master/OASIS-2x2x2.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz"
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],
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"Id": "bids::prov/skull-stripping-ics87cwt"
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},
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{
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"Label": "Brain surface reconstruction",
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"Command": "recon-all",
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"AssociatedWith": [
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"urn:freesurfer-bqv4h9k2",
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"bids::prov/fmriprep-ughfyb4k"
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],
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"Used": [],
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"Id": "bids::prov/brain-surface-reconstruction-uac8ysmu"
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},
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{
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"Label": "Spatial normalization to the ICBM 152",
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"Command": "antsRegistration",
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"AssociatedWith": [
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"urn:ants-bagzrxi0",
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"bids::prov/fmriprep-ughfyb4k"
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],
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"Used": [
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"http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_brainmask.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-CSF_probtissue.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-GM_probtissue.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-WM_probtissue.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_dtissue.nii.gz",
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"bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz"
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],
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"Id": "bids::prov/spatial-normalisation-uuwz1aep"
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},
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{
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"Label": "Brain tissue segmentation",
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"Command": "feat",
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"AssociatedWith": [
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"urn:fsl-e1oq534p",
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"bids::prov/fmriprep-ughfyb4k"
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],
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"Used": [],
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"Id": "bids::prov/brain-segmentation-egbeiwg9"
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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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"Id": "bids::prov/fedora-6qmhtq53"
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},
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{
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"Label": "poldracklab/fmriprep:1.1.4",
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"Id": "bids::prov/fmriprep-container-hzlji7es"
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},
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{
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"Label": "OASIS template",
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"Id": "https://github.com/brainspaces/OASIS/blob/master/OASIS-2x2x2.nii.gz"
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},
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{
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"Label": "ICBM 152 Nonlinear Asymmetrical template version 2009c",
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"Id": "http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip"
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},
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{
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"Label": "T1w-brainmask.nii.gz",
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"GeneratedBy": "bids::prov/skull-stripping-ics87cwt",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_brainmask.nii.gz"
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},
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{
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"Label": "T1w_class-CSF_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/brain-segmentation-egbeiwg9",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-CSF_probtissue.nii.gz"
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},
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{
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"Label": "T1w_class-GM_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/brain-segmentation-egbeiwg9",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-GM_probtissue.nii.gz"
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},
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{
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"Label": "T1w_class-WM_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/brain-segmentation-egbeiwg9",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_class-WM_probtissue.nii.gz"
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},
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{
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"Label": "T1w_dtissue.nii.gz",
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"GeneratedBy": "bids::prov/brain-segmentation-egbeiwg9",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_dtissue.nii.gz"
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},
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{
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"Label": "T1w_inflated.L.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_inflated.L.surf.gii"
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},
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{
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"Label": "T1w_inflated.R.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_inflated.R.surf.gii"
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},
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{
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"Label": "T1w_label-aparcaseg_roi.nii.gz",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_label-aparcaseg_roi.nii.gz"
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},
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{
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"Label": "T1w_label-aseg_roi.nii.gz",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_label-aseg_roi.nii.gz"
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},
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{
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"Label": "T1w_midthickness.L.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_midthickness.L.surf.gii"
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},
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{
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"Label": "T1w_midthickness.R.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_midthickness.R.surf.gii"
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},
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{
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"Label": "T1w_pial.L.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_pial.L.surf.gii"
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},
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{
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"Label": "T1w_pial.R.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_pial.R.surf.gii"
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},
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{
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"Label": "T1w_preproc.nii.gz",
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"GeneratedBy": "bids::prov/inu-correction-ue9qstw1",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_preproc.nii.gz"
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},
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{
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"Label": "T1w_smoothwm.L.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_smoothwm.L.surf.gii"
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},
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{
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"Label": "T1w_smoothwm.R.surf.gii",
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"GeneratedBy": "bids::prov/brain-surface-reconstruction-uac8ysmu",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_smoothwm.R.surf.gii"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_brainmask.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_dtissue.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
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},
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{
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"Label": "T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-MNI152NLin2009cAsym_target-T1w_warp.h5"
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},
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{
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"Label": "T1w_space-orig_target-T1w_affine.txt",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_space-orig_target-T1w_affine.txt"
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},
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{
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"Label": "T1w_target-fsnative_affine.txt",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_target-fsnative_affine.txt"
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},
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{
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"Label": "T1w_target-MNI152NLin2009cAsym_warp.h5",
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"GeneratedBy": "bids::prov/spatial-normalisation-uuwz1aep",
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"Id": "bids:ds001734:derivatives/fmriprep/sub-001/anat/sub-001_T1w_target-MNI152NLin2009cAsym_warp.h5"
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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/fmriprep/derivatives/fmriprep/prov/merged/prov-fmriprep.prov.png‎

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‎examples/fmriprep/prov/prov-fmriprep_base.prov.json‎ renamed to ‎examples/fmriprep/derivatives/fmriprep/prov/prov-fmriprep_base.prov.json‎

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‎examples/fmriprep/derivatives/fmriprep/prov/prov-fmriprep_ent.prov.json‎

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{
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"https://github.com/brainspaces/OASIS/blob/master/OASIS-2x2x2.nii.gz": {
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"Label": "OASIS template"
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},
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"http://www.bic.mni.mcgill.ca/~vfonov/icbm/2009/mni_icbm152_nlin_sym_09c_nifti.zip": {
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"Label": "ICBM 152 Nonlinear Asymmetrical template version 2009c"
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}
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}

‎examples/fmriprep/derivatives/fmriprep/prov/prov-fmriprep_env.prov.json‎

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{
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"bids::prov/fedora-6qmhtq53": {
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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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},
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"bids::prov/fmriprep-container-hzlji7es": {
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"Label": "poldracklab/fmriprep:1.1.4"
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}
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}

‎examples/fmriprep/derivatives/fmriprep/prov/prov-fmriprep_soft.prov.json‎

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{
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"bids::prov/fmriprep-ughfyb4k": {
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"Label": "fmriprep",
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"Version": "v1.1.6",
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"AltIdentifier": "RRID:SCR_016216"
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},
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"urn:ants-bagzrxi0": {
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"Label": "ANTs",
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"Version": "2.2.0",
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"AltIdentifier": "RRID:SCR_004757"
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},
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"urn:freesurfer-bqv4h9k2": {
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"Label": "FreeSurfer",
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"Version": "6.0.1",
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"AltIdentifier": "RRID:SCR_001847"
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},
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"urn:fsl-e1oq534p": {
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"Label": "FSL",
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"Version": "5.0.9",
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"AltIdentifier": "RRID:SCR_002823"
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}
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}

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