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
  • Community
    • MRF/BNC user community meetings
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On this page
  • 1. Create an account using your Brown Credentials
  • 2. Work with the MRF on your scan protocol and choosing a project name
  • 3. Contact us to request a new XNAT project
  • 3. Collect your data and send to XNAT
  • 4. Check that ALL your data has been received and it is complete

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  1. XNAT

Getting Started

Getting Started with XNAT

PreviousInfrastructure OverviewNextAccessing XNAT

Last updated 9 months ago

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If this is your first time using XNAT, here is a short outline of things you'll need to do!

1. Create an account using your Brown Credentials

2. Work with the MRF on your scan protocol and choosing a project name

We will match the naming of your scan protocol and your XNAT project so that your data automatically ends up in the right place after your scan

If you will be using our XNAT to BIDS conversion tools, your sequences on the scanner should be named in a "BIDS Ready" format. The BNC is happy to work with you to figure out the appropriate naming for your sequences.

3. Contact us to request a new XNAT project

3. Collect your data and send to XNAT

At the scanner, once your scan is complete, export your data to XNAT.

If you are collecting multi-session data, follow these instructions to add a session label to your subject ID. This will allow XNAT to organize your data properly and avoid conflicts.

4. Check that ALL your data has been received and it is complete

Try your best to check the integrity of your data within a day. While it may take an hour or so for your data to appear on XNAT, it should not take longer than half a day. If you have not received your data, or anything looks strange, contact us!

Accessing XNAT
New XNAT projects
Uploading Data