SUMMARY.md

Table of contents

• 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

• 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
• Multi-session spectroscopy with voxalign

Community

• MRF/BNC user community meetings