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
    • Automated MR spectroscopy voxel placement with voxalign
      • Installation
      • Multi-session alignment
      • Center on MNI coordinate
      • Quantify voxel overlap
    • 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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  1. Standalone Tools

Automated MR spectroscopy voxel placement with voxalign

PreviousQuantitative Susceptibility Mapping (QSM)NextInstallation

Last updated 2 days ago

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We have developed a python package "" that takes much of the guesswork out of MR spectroscopy voxel placement.

  • One of voxalign's core functions is to ensure reproducible voxel placements across multiple scan sessions within the same participant. To do this, voxalign takes in the spectroscopy DICOM(s) and a T1 anatomical scan from a first MR session, and a T1 from an in-progress MR session, and provides the prescription to enter on the console to match the exact voxel position and orientation from the first session. Learn how to use voxalign for longitudinal studies like this .

Voxalign can also tell you where to position the center of your voxel if you instead have a set of MNI coordinates to target. This is useful in helping to standardize voxel placement across participants, and for choosing voxel placements in the first session of a longitudinal study. Learn how to determine your voxel position based on MNI coordinates .

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voxalign
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Scan session 1 voxel outline (dark blue) overlaid on the scan session 2 voxel
MRS voxel center position corresponding to an MNI coordinate of [-8, 38, 31]