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Made intro independent of "DICOM" as we are moving to other modalities. Added a snapshot of the landing page and reorganized some of the information under "usage"
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francopestilli authored Nov 1, 2023
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# ezBIDS

The secure, cloud-based service via a browser interface for the semi-automated mapping of entire MRI scanning sessions (DICOM files) to the Brain Imaging Data Structure ([BIDS](https://bids.neuroimaging.io/)) standard.
The secure, cloud-based service for the semi-automated mapping of entire sessions of neuroimaging data to the Brain Imaging Data Structure ([BIDS](https://bids.neuroimaging.io/)) standard.

[![This video is a tutorial for ezBIDS](https://img.youtube.com/vi/mY3_bmt_e80/0.jpg)](https://www.youtube.com/watch?v=mY3_bmt_e80&t=0)
<img width="1450" alt="Screenshot 2023-11-01 at 11 50 48 AM" src="https://github.com/brainlife/ezbids/assets/2119795/2c054297-1503-4ebb-8718-336012c80b48">

### About

This is the developmental repository for a semi-supervised DICOM to [BIDS](https://bids.neuroimaging.io/) conversion web service. ezBIDS allows users to upload to a secure server a directory containing DICOMs (or [dcm2niix](https://github.com/rordenlab/dcm2niix) output) files from an MRI scanner to be converted to BIDS.
This is the development repository for a semi-supervised neuroimaging data files to [BIDS](https://bids.neuroimaging.io/) conversion web service. The web service is hosted securely at [brainlife.io/ezbods](https://brainlife.io/ezbids). Documentation and Tutorials will

Unlike other DICOM to BIDS converters, ezBIDS eliminates the need for the command line and heuristic/configuration setup.
Unlike other BIDS converters, ezBIDS eliminates the need for code, and command line interfaces and automatically generates heuristic and configuration files (called ezBIDS Templates).

[dcm2niix](https://github.com/rordenlab/dcm2niix) is used to transform the DICOM files into a directory structure of [NIfTI](https://nifti.nimh.nih.gov/) files. After that, an inferential process analyzes the directory structure and sidecars generated by dcm2niix to *infer* as much information as possible about the data. A browser user interface then presents the users with a *first guess* about the mapping of the directory structure to the BIDS format. Finally, users provided with the opportunity to verify the *first guess* and modify the information provided as needed so as to best match the final BIDS structure.
An inferential process analyzes the directory structure and sidecars of the data uploaded to provide an *educated guess* about the data types and content. A web-browser user interface presents the users with a *first guess* mapping of the uploaded data files into a BIDS structure. Finally, users provided with the opportunity to verify the *first guess* and modify the information provided as needed so as to best match the final BIDS structure.

Data from all major scanner vendors can be directly uploaded to ezBIDS.
Data from all major scanner vendors can be directly uploaded to ezBIDS. ezBIDS provides options for the defacing of anatomical acquisitions.

The BIDS output can be downloaded back to the user's computer, or uploaded to open repositories such as
[brainlife.io](https://brainlife.io/), or in the future, [OpenNeuro](https://openneuro.org/).

### Usage
To access the ezBIDS web service, please visit https://brainlife.io/ezbids (Chrome or Firefox browser preferred).

A video demonstration of how to use ezBIDS can be found [here](https://www.youtube.com/watch?v=mY3_bmt_e80).

Users do not need to organize their uploaded data in any specific manner, so long as the data is non-anonymized. The uploaded data can contain any number of sub-folders, and users and may compress (e.g. zip, tar) their upload directory if users so choose. ezBIDS permits two types of data uploads:

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Should users feel the need to anonymize their data before uploading, we strongly recommend that subjects (and sessions) be organized into subject (and session) folders, with explicit labeling of the subject (and session) IDs (e.g. */MRI_data/sub-01/ses-01/DICOMS*). Failure to do so for non-anonymized data will result in additional work.

ezBIDS provides options for the defacing of anatomical acquisitions.

The BIDS output can be downloaded back to the user's computer, or uploaded to open repositories such as
[brainlife.io](https://brainlife.io/), or in the future, [OpenNeuro](https://openneuro.org/).

A video demonstration of how to use ezBIDS can be found [here](https://www.youtube.com/watch?v=mY3_bmt_e80)


### Usage
To access the ezBIDS web service, please visit https://brainlife.io/ezbids (Chrome or Firefox browser preferred).

### Backend Workflow
*(optional reading, if interested in the backend API workflow)*

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