https://github.com/repronim/stuff2nidm
Repo for the process of adding "stuff" (ie the results of fmriprep, etc. processing) to the NIDM graph.
https://github.com/repronim/stuff2nidm
Last synced: 5 months ago
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Repo for the process of adding "stuff" (ie the results of fmriprep, etc. processing) to the NIDM graph.
- Host: GitHub
- URL: https://github.com/repronim/stuff2nidm
- Owner: ReproNim
- License: mit
- Created: 2025-04-08T19:52:10.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-07-02T09:33:44.000Z (12 months ago)
- Last Synced: 2025-07-02T10:41:58.128Z (12 months ago)
- Language: Python
- Homepage:
- Size: 695 KB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# "stuff"2NIDM
Repo for the process of adding the results of any processing (for example, fmriprep) to the NIDM graph.
These examples are designed to be specific examples of a generic [csv2NIDM](https://github.com/incf-nidash/PyNIDM?tab=readme-ov-file#csv-file-to-nidm-conversion) problem.
In general, the goal is to:
* Run an analysis tool (such as fmriprep),
* Represent the results of the tool in a CSV file (example [here](CSVs/fmriprep/ABIDE_fmriprep_results_v2.csv))
* Generate (or fetch) a dictionary for the results as a CSV file (example [here](CSVs/fmriprep/fmriprep_data_dictionary_v3.csv))
* Generate a tool description file (as a CSV file) that captures the details of the analysis
(example [here](CSVs/fmriprep/fmriprep_software_metadata.csv))
* Use the above 3 CSV files as input to *pynidm* to generate either a standalone NIDM representation of the results
of the analysis tool, or append the tool results to the NIDM representation of the dataset that the tool was applied to.
## Examples
### fmriprep
We show a worked example for ***fmriprep*** [here](docs/fmriprep.md)
### mriqc
We show a worked example for ***mriqc*** [here](docs/mriqc.md)