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Merge branch '#2137-anonymise-patient-id-2' of github.com:jcomedoutea…
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…u/shanoir_downloader into #2137-anonymise-patient-id-2

# Conflicts:
#	shanoir_downloader_check.py
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jcomedouteau committed Jul 19, 2024
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Expand Up @@ -52,7 +52,11 @@ The dictionary in the json file must have four keys :
-> "bidsDir" : str, BIDS subdirectory sequence name (eg : "anat", "func" or "dwi", ...)
-> "bidsName" : str, BIDS sequence name (eg: "t1w-mprage", "t2-hr", "cusp66-ap-b0", ...)
```
An example is provided in the file `s2b_example_config.json`

An example is provided in the file `s2b_example_config.json`.

To download longitudinal data, a key `session` and a new entry `bidsSession` in `data_to_bids` dictionaries should be defined in the JSON configuration files. Of note, only one session can be downloaded at once. Then, the key `session` is just a string, not a list as for subjects.


### Example usage

Expand Down Expand Up @@ -100,4 +104,4 @@ You can either use the `.env` file or run `export shanoir_password=XXX` (`set sh
To anonymize the dicoms, download or clone the latest version of [DicomAnonymizer](https://github.com/KitwareMedical/dicom-anonymizer/) (for example in this repository) and install it :
- install wheel with `pip install wheel`
- in the `dicom-anonymizer` folder, package the source files with `python ./setup.py bdist_wheel`
- install `dicom-anonymizer` with `pip install ./dist/dicom_anonymizer-1.0.9-py2.py3-none-any.whl` (the version number might be higher)
- install `dicom-anonymizer` with `pip install ./dist/dicom_anonymizer-1.0.9-py2.py3-none-any.whl` (the version number might be higher)

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