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bidsonym-0.0.4
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مشاهده بیشترتوضیحات
A BIDSapp for deidentification of neuroimaging data.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bidsonym-0.0.4 |
| نام | bidsonym |
| نسخه کتابخانه | 0.0.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Peer Herholz |
| ایمیل نویسنده | herholz.peer@gmail.com |
| آدرس صفحه اصلی | https://github.com/peerherholz/bidsonym |
| آدرس اینترنتی | https://pypi.org/project/bidsonym/ |
| مجوز | BSD (3-clause) |
===============================
BIDSonym
===============================
.. image:: https://img.shields.io/travis/PeerHerholz/BIDSonym.svg
:target: https://travis-ci.org/PeerHerholz/BIDSonym
.. image:: https://img.shields.io/github/issues-pr/PeerHerholz/BIDSonym.svg
:alt: PRs
:target: https://github.com/PeerHerholz/BIDSonym/pulls/
.. image:: https://img.shields.io/github/contributors/PeerHerholz/BIDSonym.svg
:alt: Contributors
:target: https://GitHub.com/PeerHerholz/BIDSonym/graphs/contributors/
.. image:: https://github-basic-badges.herokuapp.com/commits/PeerHerholz/BIDSonym.svg
:alt: Commits
:target: https://github.com/PeerHerholz/BIDSonym/commits/master
.. image:: http://hits.dwyl.io/PeerHerholz/BIDSonym.svg
:alt: Hits
:target: http://hits.dwyl.io/PeerHerholz/BIDSonym
.. image:: https://img.shields.io/docker/cloud/automated/peerherholz/bidsonym
:alt: Dockerbuild
:target: https://cloud.docker.com/u/peerherholz/repository/docker/peerherholz/bidsonym
.. image:: https://img.shields.io/docker/pulls/peerherholz/bidsonym
:alt: Dockerpulls
:target: https://cloud.docker.com/u/peerherholz/repository/docker/peerherholz/bidsonym
.. image:: https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg
:alt: SingularityHub
:target: https://singularity-hub.org/collections/4645
.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
: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.
نیازمندی
| مقدار | نام |
|---|---|
| - | argparse |
| - | pandas |
| - | nibabel |
| - | nipype |
| - | nilearn |
| - | duecredit |
| - | pybids |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl bidsonym-0.0.4:
pip install bidsonym-0.0.4.whl
نصب پکیج tar.gz bidsonym-0.0.4:
pip install bidsonym-0.0.4.tar.gz