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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On this page
  • Summary of tools and methods to download your data
  • 1. Download via Web UI
  • 1.1 Navigate to your MR Data Session
  • 1.2 Download ONE sequence
  • 1.3 Download ALL sequences
  • 1.4 Download with granularity
  • 2. Downloading via XNAT Desktop Client
  • 3. Download data programmatically

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  1. XNAT

Downloading Data

Details of the different options available to download your data from XNAT

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Last updated 1 year ago

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Summary of tools and methods to download your data

Method/Tool
Recommended Usage
Requirements

Download via UI

Downloading DICOM data that is not super large and when pausing, resuming is not needed.

Browser (campus network)

Download via XNAT Desktop Client

Download DICOM data with greater granularity and for large number of participants. Pausing, resumming and reporting is available

App installed. Doesn't work in OSCAR

Download via xnat-tools python package

Programmatic download. Great for batch uploads and for combining with BIDS conversion

1. Download via Web UI

This is the simplest but slowest way to download data. If you'll be downloading multiple imaging sessions, you may want to refer to other options below

1.1 Navigate to your MR Data Session

1.2 Download ONE sequence

If you only need to download one sequence, you can use the download button on the corresponding row

1.3 Download ALL sequences

You have multiple options here

1.3.1 Select ALL and use the download bulk action

Depending on the size of your data, this may take a while

1.4 Download with granularity

If you wish to have greater granularity on the types of resources downloaded you can use the menu under Actions -> Download -> Images. We will dive a little more into the options on the next section, as this is gives a great segway into talking about

2. Downloading via XNAT Desktop Client

3. Download data programmatically

Installation of xnat-tools python package. This can be done from local computer or Oscar as explained in the

The is a convenient way to upload and download data to XNAT. Unfortunately, at this time, the application doesn't work in Oscar, but if you are downloading data to your personal computer, you may want to give it a try.

The for the Desktop Client is quite detailed, so we won't repeat the steps here.

We maintain a python package that facilitates downloading your data and converting it to BIDS. The optimal way to install and run the code depends on your computation environment. The package explains different installation and execution methods for a general user.

If you do not need BIDS, you'll only need the utility. If you will be downloading and converting to BIDS, then please follow the instructions in the section.

XNAT Desktop Client
documentation
xnat-tools
documentation
xnat-dicom-export
XNAT TO BIDS
XNAT2BIDS section
MR session list for a given participant
Highlighting download button for a single sequence
Highlighting SELECT ALL and BULK DOWNLOD BUTTONS
Highlighting the Actions -> Download menu to access detailed downloading options