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‎.gitignore‎

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venv3.11/
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.idea/*
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.pytest_cache/*
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build/*
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*.egg-info

‎.gitmodules‎

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path = examples/fmriprep/ds001734
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url = [email protected]:OpenNeuroDatasets/ds001734.git
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datalad-id = ca05bc10-29a0-11e9-9a7b-0242ac13000d
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[submodule "examples/heudiconv/sourcedata/hirni-demo"]
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path = examples/heudiconv/sourcedata/hirni-demo
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url = https://github.com/psychoinformatics-de/hirni-demo.git

‎README.md‎

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@@ -34,6 +34,8 @@ Camille Maumet ([@cmaumet](https://github.com/cmaumet)) and Satrajit Ghosh ([@sa
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- Cyril Regan ([@cyril-data](https://github.com/cyril-data))<a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=cyril-data" title="Code">💻</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/pulls?q=is%3Apr+reviewed-by%3Acyril-data" title="Reviewed Pull Requests">👀</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=cyril-data" title="Documentation">📖</a>
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<a href="https://github.com/bids-standard/BEP028_BIDSprov/issues?q=author%3Acyril-data" title="Bug reports">🐛</a>
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- Boris Clénet ([@bclenet](https://github.com/bclenet))<a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=bclenet" title="Code">💻</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/commits?author=bclenet" title="Documentation">📖</a><a href="https://github.com/bids-standard/BEP028_BIDSprov/issues?q=author%3Abclenet" title="Bug reports">🐛</a>
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This project follows the
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[all-contributors](https://github.com/all-contributors/all-contributors)
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specification. Contributions of any kind welcome!
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[New features (to be included)](new_features.md)
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## Run parsers on the SPM, FSL and AFNI data
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## Using the code
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### Visualize your BIDSprov data
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To visualize your BIDSprov data, perform the following steps :
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1. [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the code inside a `BEP028_BIDSprov` directory, and cd into this directory :
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```shell
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git clone [email protected]:bids-standard/BEP028_BIDSprov.git
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cd BEP028_BIDSprov
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```
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3. install the `bids_prov` python package :
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```shell
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pip install .
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```
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4. you should be able to launch the visualizer on your .jsonld files with the command `bids_prov_visualizer`
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```shell
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bids_prov_visualizer --input_file graph.jsonld --output_file graph.png
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bids_prov -h
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usage: bids_prov_visualizer [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]
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options:
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-h, --help show this help message and exit
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--input_file INPUT_FILE
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input BIDSprov data as a .jsonld file
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--output_file OUTPUT_FILE
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output .png file showing BIDSprov graph
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```
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### Run parsers on the SPM, FSL and AFNI data
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To obtain data in **bids-prov format**, you can use the developed parsers.
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* [Tutorial](https://github.com/bids-standard/BEP028_BIDSprov/blob/master/bids_prov/README.md)

‎bep028spec.md‎

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```
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Contexts are created at the BIDS organization level, and only if necessary extended by a dataset. Thus most dataset creators will be able to reuse existing contexts. For terms, many of these are already in BIDS, with additional ones being curated by the NIDM-terms grant. Additional, terms can and should be re-used from schema.org, bioschemas, and other ontologies and vocabularies whenever possible.
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Contexts are created at the BIDS organization level, and only if necessary extended by a dataset. Thus most dataset creators will be able to reuse existing contexts. For terms, many of these are already in BIDS, with additional ones being curated by the NIDM-terms grant. Additional, terms can and should be reused from schema.org, bioschemas, and other ontologies and vocabularies whenever possible.
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<!-- Footnotes themselves at the bottom. -->

‎bids_prov/visualize.py‎

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viz_jsonld11(jsonld11, output_file)
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if __name__ == "__main__":
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def entry_point():
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""" A command line tool for the visualize module """
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parser = argparse.ArgumentParser()
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parser.add_argument("--input_file", type=str, default="res.jsonld", help="data jsonld file ")
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parser.add_argument("--output_file", type=str, default="res.png", help="output dir where results are written")
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parser.add_argument("--input_file", type=str, help="input BIDSprov data as a .jsonld file ", required=True)
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parser.add_argument("--output_file", type=str, default="output_graph.png", help="output .png file showing BIDSprov graph")
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opt = parser.parse_args()
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main(opt.input_file, output_file=opt.output_file, omit_details=True)
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# >> python -m bids_prov.visualize --input_file ./res_temp.jsonld --output_file res.png
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if __name__ == "__main__":
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entry_point()

‎examples/dcm2niix_1/README.md‎

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# BIDS Prov example #1 for `dcm2niix`
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This example aims at showing provenance traces from a DICOM to Nifti conversion, performed by `dcm2niix` on a Linux-based (Fedora) operating system.
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## Overview
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We use the single file `prov/dcm2niix.prov.jsonld` to store all provenance traces relative to the conversion steps.
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After conversion, and adding provenance traces, the resulting directory tree looks like this:
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```
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prov/
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└── dcm2niix.prov.jsonld
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sourcedata/
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sub-02/
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└── anat
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├── sub-02_T1w.json
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└── sub-02_T1w.nii
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```
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Note that the `sourcedata/` directory contains the source dataset described in the [section hereafter](#source-dataset).
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## Provenance visualization
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We are able to visualize these provenance files using the following commands (current directory is `examples/dcm2niix_1/`):
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```shell
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pip install bids-prov==0.1.0
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bids_prov_visualizer --input_file prov/dcm2niix.prov.jsonld --output_file prov/dcm2niix.prov.png
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```
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![](/examples/dcm2niix_1/prov/dcm2niix.prov.png)
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## Source dataset
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We get raw data from https://github.com/psychoinformatics-de/hirni-demo.git, a demo datalad dataset containing dicoms.
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```shell
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# Get example dicom(s) in a sourcedata/ directory
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mkdir sourcedata
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cd sourcedata
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datalad install --recursive https://github.com/psychoinformatics-de/hirni-demo.git
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cd acq1
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datalad get ./*
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cd ..
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ls -1
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acq1
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acq2
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code
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dataset_description.json
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README
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studyspec.json
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cd ..
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```
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Note that we will only convert the anatomical data available in this dataset (`acq1/` directory).
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## Perform the conversions
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Install `dcm2niix`.
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```shell
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sudo yum install dcm2niix
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```
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With this setup we are ready to convert dicoms to nifti files using `dcm2niix`.
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```shell
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dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/acq1/dicoms/example-dicom-structural-master/dicoms/
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```
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## Limitations
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### `Used` key for activities
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Although the BIDS-Prov spec mentions:
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> Used : OPTIONAL. UUID. Identifier of an entity used by this activity (the corresponding Entity must be defined with its own Entity record).
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We represented used entities in a list to link all the dicom files of a directory to the corresponding conversion activity.
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### `Environments` not defined in the context
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We cannot use an `Environments` list because the current context (commit ce0eb77) does not define the `Environments` term. Therefore, we defined the `urn:fedora-b7hmkmqd` environments as an `Entity`.
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### High number of dicom files
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Listing all the DICOM files used by the dcm2niix conversion steps would lower readability of the JSON-LD provenance files. Therefore we only listed the following directories as `Entities`:
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```
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bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms
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```
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although it is not allowed by the current version of the BIDS Prov specification to have directories as `Entities`.

‎examples/dcm2niix_1/prov/dcm2niix.prov.jsonld‎

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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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"Records": {
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"Software": [
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{
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"Id": "urn:dcm2niix-xce5m9z3",
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"Label": "dcm2niix",
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"Version": "v1.0.20220720"
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}
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],
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"Activities": [
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{
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"Id": "urn:conversion-00f3a18f",
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"Label": "Conversion",
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"Command": "dcm2niix -o . -f sub-%i/anat/sub-%i_T1w sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms/",
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"AssociatedWith": "urn:dcm2niix-xce5m9z3",
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"Used": [
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"urn:fedora-b7hmkmqd",
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"bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms"
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]
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}
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],
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"Entities": [
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{
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"Id": "bids::sourcedata/hirni-demo/acq1/dicoms/example-dicom-structural-master/dicoms",
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"Label": "dicoms"
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},
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{
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"Id": "bids::sub-02/anat/sub-02_ses-20130717141500_T1w.nii",
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"Label": "sub-02_T1w.nii",
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"GeneratedBy": "urn:conversion-00f3a18f"
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},
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{
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"Id": "bids::sub-02/anat/sub-02_ses-20130717141500_T1w.json",
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"Label": "sub-02_T1w.json",
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"GeneratedBy": "urn:conversion-00f3a18f"
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},
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{
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"Id": "urn:fedora-b7hmkmqd",
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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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]
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}
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}

‎examples/dcm2niix_1/prov/dcm2niix.prov.png‎

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‎examples/dcm2niix_1/sourcedata/hirni-demo‎

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Subproject commit f5aa766d900037d97c82329e7dfc94ee80086b92

‎examples/dcm2niix_1/sub-02/anat/sub-02_T1w.json‎

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{
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"Modality": "MR",
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"ManufacturersModelName": "nifti2dicom",
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"SoftwareVersions": "0.4.11",
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"SeriesDescription": "anat-T1w",
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"ProtocolName": "anat-T1w",
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"ImageType": ["DERIVED", "SECONDARY"],
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"RawImage": false,
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"SeriesNumber": 401,
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"AcquisitionTime": "13:25:18.000000",
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"AcquisitionNumber": 1,
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"SliceThickness": 0.666667,
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"SpacingBetweenSlices": 0.666667,
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"ImageOrientationPatientDICOM": [
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0.999032,
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-0.0217884,
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0.0382096,
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0.0265195,
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0.991414,
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-0.128044 ],
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20220720"
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}

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