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BIDSonym

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Description

A BIDS app for de-identification of neuroimaging data. Gathers all T1w images from a BIDS dataset and applies one of several popular de-identification algorithms. BIDSonym currently supports:

Pydeface

MRI deface

Quickshear

mridefacer

alternate text

Using BIDSonym ensures that you can make collected neuroimaging data available for others without violating subjects' privacy or anonymity (depending on the regulations of the country you're in).

Usage

This App has the following command line arguments:

usage: run.py [-h]

[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]

[--deid {pydeface,mri_deface,quickshear}]

[--del_nodeface {del,no_del}]

[--check_meta]

[--del_meta META_DATA_FIELD [META_DATA_FIELD ...]]

bids_dir {participant,group}

a BIDS app for de-identification of neuroimaging data

positional arguments:
bids_dir The directory with the input dataset formatted
according to the BIDS standard.
output_dir The directory where the not de-identified raw files should be stored,
in case you decide to keep them.
{participant,group} Level of the analysis that will be performed. Multiple
participant level analyses can be run independently (in parallel) using the same output_dir.
optional arguments:
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
The label(s) of the participant(s) that should be analyzed. The label corresponds to sub-<participant_label> from the BIDS spec (so it does not include "sub-"). If this parameter is not provided all subjects should be analyzed. Multiple participants can be specified with a space separated list.
--deid {pydeface,mri_deface,quickshear}
Approach to use for de-identifictation.
--del_nodeface {del,no_del}
Overwrite and delete original data or copy original data to different folder.
--del_meta META_DATA_FIELD [META_DATA_FIELD ...]
Indicate if and which information from the .json meta-data files should be deleted. If so, the original .json files will be copied to sourcedata/ .

Run it in participant level mode (for one participant):

docker run -i --rm \
            -v /Users/peer/ds005:/bids_dataset \
            peerherholz/bidsonym \
            /bids_dataset \
            participant --deid pydeface --del_nodeface no_del --del_meta 'InstitutionAddress' \
            --participant_label 01

Run it in group level mode (for all participants):

docker run -i --rm \
           -v /Users/peer/ds005:/bids_dataset \
           peerherholz/bidsonym \
           /bids_dataset  group --deid pydeface --del_nodeface no_del --del_meta 'InstitutionAddress'

Installation

Following the BIDS apps standard it is recommend to install and use BIDSonym in its Docker or Singularity form. To get the BIDSonym Docker image, you need to install docker and within the terminal of your choice type:

docker pull peerherholz/bidsonym

To get its Singularity version, you need to _install singularity and within the terminal of your choice type:

singularity pull docker://peerherholz/bidsonym

Documentation

A documentation is currently in the works and will be available soon. Sorry for any inconvenience this might cause.

How to report errors

Running into any bugs 🐞? Check out the open issues to see if we're already working on it. If not, open up a new issue and we will check it out when we can!

How to contribute

Thank you for considering contributing to our project! Before getting involved, please review our Code of Conduct. Next, you can review open issues that we are looking for help with. If you submit a new pull request please be as detailed as possible in your comments. Please also have a look at our contribution guidelines.

Acknowledgements

If you intend to or already used BIDSonym, we would be very happy if you cite this github repo, till we have "something" out there!

Support

This work was supported in part by funding provided by Brain Canada, in partnership with Health Canada, for the Canadian Open Neuroscience Platform initiative.

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