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@@ -6,34 +6,35 @@ The secure, cloud-based service for the semi-automated mapping of entire session | |
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| ### About | ||
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| 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/ezbids](https://brainlife.io/ezbids). | ||
| This is the repository for a semi-supervised web-service for converting neuroimaging data files to [BIDS](https://bids.neuroimaging.io/). The web service is securely hosted at [brainlife.io/ezbids](https://brainlife.io/ezbids). For additional details on security feaures, please see [here](https://brainlife.io/docs/using_ezBIDS/#faq). | ||
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| Unlike other BIDS converters, ezBIDS eliminates the need for code, and command line interfaces and automatically generates heuristic and configuration files (called ezBIDS Templates). | ||
| Unlike other BIDS converters, ezBIDS eliminates the need for coding and command line interfaces (CLI), doing the bulk of the work behind the scenes to save users time. Importantly, ezBIDS does not require an organizational structure for uploaded data. | ||
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| An inferential process analyzes the directory structure and sidecars of the data uploaded to provide a *first 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. | ||
| A series of inferenial heuritics analyze the uploaded data to provide a *first guess* BIDS structure, which is presented to users through the web-browser user interface. Users verify the *first guess* and modify the information provided as needed so as to best match the final BIDS structure. | ||
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| Data from all major scanner vendors can be directly uploaded to ezBIDS. ezBIDS provides options for the defacing of anatomical acquisitions. | ||
| Data from all major scanner vendors are accepted by ezBIDS. ezBIDS enables pseudo-anonymization by providing options for the defacing of anatomical sequences, and removes all identifying metadata information (e.g. `PatientName`) before final conversion to BIDS. | ||
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| 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.org](https://openneuro.org/). | ||
| The BIDS output can then be downloaded back to the user's computer, or uploaded to open repositories such as | ||
| [brainlife.io](https://brainlife.io/) or [OpenNeuro.org](https://openneuro.org/). | ||
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| Helpful links: | ||
| 1. [ezBIDS website](https://brainlife.io/ezbids) (Chrome or Firefox browser preferred) | ||
| 2. [ezBIDS tutorial](https://brainlife.io/docs/tutorial/ezBIDS/) | ||
| 3. [ezBIDS tutorial video](https://www.youtube.com/embed/L8rWA8qgnpo) | ||
| 4. [ezBIDS user documentation](https://brainlife.io/docs/using_ezBIDS/) | ||
| 1. [ezBIDS website](https://brainlife.io/ezbids) (Chrome or Firefox browsers preferred) | ||
| 2. [ezBIDS user documentation](https://brainlife.io/docs/using_ezBIDS/) | ||
| 3. [ezBIDS tutorial](https://brainlife.io/docs/tutorial/ezBIDS/) | ||
| 4. [ezBIDS tutorial video](https://www.youtube.com/embed/L8rWA8qgnpo) | ||
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| ### Usage | ||
| To access the ezBIDS web service, please visit https://brainlife.io/ezbids | ||
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| 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: | ||
| To access the ezBIDS web service, please visit https://brainlife.io/ezbids. If you do not have a brainlife.io account, you will be prompted to create one for authentication purposes. | ||
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| 1. **DICOM files** - Only DICOMs should be included in the upload. No specific organizational structure is required. | ||
| 2. **dcm2niix generated output (i.e. NIfTI, json, bval, and bvec) files** - Only these files (no DICOMs) should be included in the upload. We strongly recommend that the dcm2niix output not be anonymized (i.e. include _-ba n_ in the dcm2niix command), in which case, no specific organizational structure is required. | ||
| Users do not need to organize their uploaded data in any specific manner, and users may choose to compress (e.g. zip, tar) their uploaded data. | ||
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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. | ||
| Should users feel the need to anonymize data before uploading, we strongly recommend that subjects (and sessions, if applicable) be organized into subject (and session) folders, with explicit labeling of the preferred subjects (and sessions) IDs (e.g. `MRI_data/sub-01/ses-01/DICOMS`). Failure to do so for non-anonymized data may result in an inaccurate *first guess* and require additional edits in the web browser. | ||
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| If users wish to install ezBIDS locally, to ensure that data do not leave their institution site, please see [here](https://brainlife.io/docs/using_ezBIDS/#installing-ezbids-locally). | ||
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| ### Authors | ||
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| - [Daniel Levitas]([email protected])* | ||
| - [Soichi Hayashi]([email protected])* | ||
| - [Sophia Vinci-Booher]([email protected]) | ||
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| - [Anthony Galassi]([email protected]) | ||
| - [Guiomar Niso]([email protected]) | ||
| - [Franco Pestilli]([email protected]) | ||
| * Both authors contributed equally to this work | ||
| * _Both authors contributed equally to this project_ | ||
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| ### Funding Acknowledgement | ||
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| brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your code and publications. Copy and past the following lines into your repository when using this code. | ||
| brainlife.io is publicly funded, and for the sustainability of the project it is helpful to acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your code and publications. Copy and past the following lines into your repository when using this code. | ||
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| [](https://nsf.gov/awardsearch/showAward?AWD_ID=1734853) | ||
| [](https://nsf.gov/awardsearch/showAward?AWD_ID=1636893) | ||
| [](https://nsf.gov/awardsearch/showAward?AWD_ID=1916518) | ||
| [](https://nsf.gov/awardsearch/showAward?AWD_ID=1912270) | ||
| [](https://grantome.com/grant/NIH/R01-EB029272-01) | ||
| [![NIH-NIMH-R01MH126699]](https://img.shields.io/badge/NIH_NIMH-R01MH126699-green.svg)](https://grantome.com/grant/NIH/R01-EB029272) | ||
| [](https://grantome.com/grant/NIH/R01-EB029272) | ||
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| ### Citations | ||
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