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bclenet committed Oct 4, 2024
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Expand Up @@ -87,28 +87,33 @@ Mature building blocks of NIDM:
### Visualize your BIDSprov data

To visualize your BIDSprov data, perform the following steps :
1. [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the code inside a `BEP028_BIDSprov` directory ;
2. in a terminal, change the current directory
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 :

`cd BEP028_BIDSprov`
```shell
git clone git@github.com:bids-standard/BEP028_BIDSprov.git
cd BEP028_BIDSprov
```

3. install the `bids_prov` python package :

`pip install .`
```shell
pip install .
```

4. you should be able to launch the visualizer on your .jsonld files with the command `bids_prov_visualizer`

`bids_prov_visualizer --input_file graph.jsonld --output_file graph`
```shell
bids_prov_visualizer --input_file graph.jsonld --output_file graph.png

```
usage: bids_prov_visualizer [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]
options:
-h, --help show this help message and exit
--input_file INPUT_FILE
input BIDSprov data as a .jsonld file
--output_file OUTPUT_FILE
output .png file showing BIDSprov graph
bids_prov -h
usage: bids_prov_visualizer [-h] --input_file INPUT_FILE [--output_file OUTPUT_FILE]

options:
-h, --help show this help message and exit
--input_file INPUT_FILE
input BIDSprov data as a .jsonld file
--output_file OUTPUT_FILE
output .png file showing BIDSprov graph
```

### Run parsers on the SPM, FSL and AFNI data
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