Behavior and Neuroimaging Core User Manual
  • About
  • Infrastructure Overview
  • XNAT
    • Getting Started
    • Accessing XNAT
    • BIDS Ready Protocols
    • New XNAT projects
    • Uploading Data
    • Downloading Data
  • Demo Dataset
    • Introduction
    • How to access it
    • Protocol Information
    • Basic analysis example: checks task
  • XNAT to BIDS
    • Getting Started
    • XNAT2BIDS Software
    • Exporting to BIDS using Oscar
      • Oscar Utility Script
        • Running xnat2bids using default configuration
        • Running xnat2bids with a custom configuration
        • Syncing your XNAT project & Oscar data directory
        • Extra tools & features
      • Step-wise via Interact Session
    • BIDS Validation
      • Oscar
      • Docker
    • Converting non-MR data
      • Physiological data
      • EEG data
  • XNAT TO BIDS (Legacy)
    • Oscar SBATCH Scripts
  • BIDS and BIDS Containers
    • Introduction to BIDS
    • mriqc
    • fmriprep
    • BIDS to NIMH Data Archive (NDA)
  • Analysis Pipelines
    • Freesurfer
    • 🚧CONN Toolbox
    • FSL topup and eddy
    • Tractography: DSI Studio
    • Brown University MRS Data Collection and Preprocessing Protocol
    • LC Model
      • Installation
      • Example Run
      • Running LCModel on your own data
    • Quantitative Susceptibility Mapping (QSM)
  • Standalone Tools
    • Multi-session spectroscopy with voxalign
    • dicomsort: a tool to organize DICOM files
    • ironmap
    • convert enhanced multi-frame DICOMs to legacy single-frame
    • DICOM anonymization
  • MRF GUIDES
    • MRI simulator room
      • Motion Trainer: Balloon Task
      • Simulating scanner triggers
    • Stimulus display & response collection
    • Eyetracking at the scanner
    • Exporting data via scannershare
    • EEG in the scanner
    • Exporting spectroscopy RDA files
  • Community
    • MRF/BNC user community meetings
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  • Requirements
  • 1. Familiarize with BNC's Demo Dataset
  • 1. XNAT Login Information
  • 2. Image Session Identifier

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  1. XNAT to BIDS

Getting Started

PreviousBasic analysis example: checks taskNextXNAT2BIDS Software

Last updated 10 months ago

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We provide custom code and sample data to export your XNAT imaging session to BIDS format. Our process relies on few basic principles:

  • Naming of sequences in a BIDS friendly manner at the scanner as outined in the

  • DICOMS exported from XNAT using our software is converted to BIDS using

  • We rely on the specification and heuristic

  • Our code is available in the

Requirements

Before exporting, you'll need to have available, XNAT authentication and session information as well as our software.

1. Familiarize with BNC's Demo Dataset

We will use the in the following walk-through examples. It is helpful to be familiar with the general description and protocol details of the data

1. XNAT Login Information

If you have not registered to use our XNAT, please follow instructions

  • XNAT Username

  • XNAT Password

2. Image Session Identifier

In order to export an imaging session, we need to find XNAT's ID for that session. You can do so as follows:

2.1 Navigate to project of interest

2.2 Navigate to subject of interest

2.3 Navigate to MR Session

2.4. Find Accession #

BIDS Ready Protocols section.
Heudiconv
ReproIn
xnat-tools repository
BNC's Demo Dataset
here
Participants associated with a project
MR Sessions associated with a participant
Accession # for a session