Metadata-Version: 1.2
Name: bidsonym
Version: 0.0.4
Summary: A BIDSapp for deidentification of neuroimaging data.
Home-page: https://github.com/peerherholz/bidsonym
Author: Peer Herholz
Author-email: herholz.peer@gmail.com
License: BSD (3-clause)
Description: ===============================
        BIDSonym
        ===============================
        
        .. image:: https://img.shields.io/travis/PeerHerholz/BIDSonym.svg
                :target: https://travis-ci.org/PeerHerholz/BIDSonym
        
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            :alt: Hits
            :target: http://hits.dwyl.io/PeerHerholz/BIDSonym
        
        .. image:: https://img.shields.io/docker/cloud/automated/peerherholz/bidsonym
            :alt: Dockerbuild
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        .. image:: https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg
            :alt: SingularityHub
            :target: https://singularity-hub.org/collections/4645
        
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            :alt: License
            :target: https://opensource.org/licenses/BSD-3-Clause
        
        .. image:: https://upload.wikimedia.org/wikipedia/commons/7/74/Zotero_logo.svg
            :alt: Zotero
            :target: https://www.zotero.org/groups/2362367/bidsonym
        
        .. image:: https://img.shields.io/badge/Supported%20by-%20CONP%2FPCNO-red
            :alt: support_conp
            :target: https://conp.ca/
        
        Description
        ===========
        A `BIDS <https://bids-specification.readthedocs.io/en/stable/>`_ `App <https://bids-apps.neuroimaging.io/>`_ for the de-identification of neuroimaging data. ``BIDSonym`` gathers all T1w images from a BIDS dataset and applies one of several popular de-identification algorithms. It currently supports:
        
        `MRI deface <https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface>`_, `Pydeface <https://github.com/poldracklab/pydeface>`_, `Quickshear <https://github.com/nipy/quickshear>`_ and `mridefacer <https://github.com/mih/mridefacer>`_.
        
        .. image:: https://raw.githubusercontent.com/PeerHerholz/BIDSonym/master/img/bidsonym_example.png
           :alt: alternate text
        
        Additionally, the user can choose to evaluate the sidecar JSON files regarding potentially sensitive information,
        like for example participant names and define a list of fields which information should be deleted.
        
        **Using BIDSonym can help 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).**
        
        .. intro-marker
        
        Usage
        =====
        
        .. usage-marker
        
        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}]
        
        [--deface_t2w]
        
        [--check_meta]
        
        [--del_meta META_DATA_FIELD [META_DATA_FIELD ...]]
        
        [--brainextraction {bet,nobrainer}]
        
        [--bet_frac BET_FRAC]
        
        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.
          --deface_t2w \
                    Deface T2w images by using defaced T1w image as deface-mask.
          --check_meta META_DATA_FIELD [META_DATA_FIELD ...]  
                    Indicate which information from the image and
                    :code:`.json` meta-data files should be check for potentially problematic information. 
                    Indicate strings that should be searched for.
                    The results will be saved to :code:`sourcedata/`.
          --del_meta META_DATA_FIELD [META_DATA_FIELD ...]
        			Indicate (via strings) if and which information from the :code:`.json` meta-data
        			files should be deleted. If so, the original :code:`.json` files
        			will be copied to :code:`sourcedata/`.
          --brainextraction {BET, no_brainer}
        			What algorithm should be used for pre-defacing brain extraction
        			(outputs will be used in quality control).
          --bet_frac [BET_FRAC]
        			In case BET is used for pre-defacing brain extraction, provide a Frac value.
          --skip_bids_validation \
                    Assume the input dataset is BIDS compliant and skip the validation (default: False).
          -v \
            BIDS-App version.
        
        
        Run it in participant level mode (for one participant):
        
        .. code-block::
        
        	docker run -i --rm \
        		    -v /Users/peer/ds005:/bids_dataset \
        	            peerherholz/bidsonym \
        		    /bids_dataset \
        		    participant --deid pydeface --del_meta 'InstitutionAddress' \
        		    --participant_label 01
        		    --brainextraction bet --bet_frac 0.5
        
        
        Run it in group level mode (for all participants):
        
        .. code-block::
        
        	docker run -i --rm \
        		   -v /Users/peer/ds005:/bids_dataset \
        		   peerherholz/bidsonym \
        		   /bids_dataset  group --deid pydeface --del_meta 'InstitutionAddress' \
        		   --brainextraction bet --bet_frac 0.5
        
        .. usage-marker-end
        
        
        Installation
        ============
        Following the `BIDS apps standard <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005209>`_ 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 <https://docs.docker.com/install/>`_ and within the terminal of your choice type:
        
        :code:`docker pull peerherholz/bidsonym`
        
        To get its Singularity version, you need to `install singularity <https://singularity.lbl.gov/all-releases>`_ and within the terminal of your choice type:
        
        :code:`singularity pull PeerHerholz/BIDSonym`
        
        Documentation
        =============
        BIDSonym's documentation can be found `here <https://peerherholz.github.io/BIDSonym/>`_.
        
        
        How to report errors
        ====================
        Running into any bugs :beetle:? Check out the `open issues <https://github.com/PeerHerholz/BIDSonym/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 <https://github.com/PeerHerholz/BIDSonym/blob/master/CODE_OF_CONDUCT.rst>`_. Next, you can review `open issues <https://github.com/PeerHerholz/BIDSonym/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 <https://github.com/PeerHerholz/BIDSonym/blob/master/CONTRIBUTING.rst>`_.
        
        Acknowledgements
        ================
        Please acknowledge this work by mentioning explicitly the name of this software
        (*BIDSonym*) and the version, along with a link to the `GitHub repository
        <https://github.com/peerherholz/bidsonym>`_ or the Zenodo reference.
        For more details, please see `citation <https://peerherholz.github.io/BIDSonym/citing.html>`_.
        
        Support
        =======
        This work is supported in part by funding provided by `Brain Canada <https://braincanada.ca/>`_, in partnership with `Health Canada <https://www.canada.ca/en/health-canada.html>`_, for the `Canadian Open Neuroscience Platform initiative <https://conp.ca/>`_.
        
        .. image:: https://conp.ca/wp-content/uploads/elementor/thumbs/logo-2-o5e91uhlc138896v1b03o2dg8nwvxyv3pssdrkjv5a.png
            :alt: logo_conp
            :target: https://conp.ca/
        
        Furthermore, the project is supported by [Repronim](https://www.repronim.org/) under NIH-NIBIB P41 EB019936. 
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
