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
  • Uploading data from the scanner
  • Automated routing from scanner to XNAT
  • Naming for multi-session studies
  • Uploading Non-MR Data

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  1. XNAT

Uploading Data

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Last updated 7 days ago

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Uploading data from the scanner

After data collection, data can be sent to XNAT directly from the scanner. Partial data transfers will get stuck, so transfer an entire scan session at once, rather than run-by-run. If you are the operator at the console, select your dataset in the patient browser, then click Export.

Make sure all the series you want to send are checked, then select XNAT and click Export.

Automated routing from scanner to XNAT

Naming for multi-session studies

If your study involves multiple scan sessions per participant, following a specific consistent naming scheme will allow XNAT to nicely organize your data so that each scan session is nested under the the correct participant like this:

To achieve this, you need to use the Last Name and Patient ID fields in a specific way when you register your participant at the beginning of a scan. In the Last Name field, enter the subject ID you have assigned to your participant (in this demodat example, we would enter 005). In the Patient ID field, enter the same subject ID *underscore* whatever you would like to use to label your different sessions. You could do "005_sess1", "005_sess2", etc., or something that describes the different phases of your study, like "005_pretraining", "005_training", "005_posttraining".

If you scan the same participant multiple times and re-use the same Patient ID, your data will not get properly routed to your project without an XNAT administrator's help.

Uploading Non-MR Data

To upload your EEG or Physio data onto XNAT, see the instruction steps at page below.

If your XNAT project has been and named to match your protocol on the scanner, XNAT will attempt to place the data coming from the scanner in the appropriate project using information from the DICOM metadata.

created
Converting non-MR data
Individual scan sessions ("SESSION1" and "SESSION2") for participant 005
Using the Patient ID field to enable XNAT to nest multiple sessions under a single participant