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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  • Use voxalign on Tess (mac mini behind scanner operator) <RECOMMENDED>
  • Set up on your own computer:
  • Now that your environment is activated, you can:

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  1. Standalone Tools
  2. Automated MR spectroscopy voxel placement with voxalign

Installation

Voxalign runs on a separate computer, not the scanner console

PreviousAutomated MR spectroscopy voxel placement with voxalignNextMulti-session alignment

Last updated 2 days ago

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Voxalign is available on github at (currently set to private - contact Elizabeth at cobre-bnc@brown.edu for access)

Use voxalign on Tess (mac mini behind scanner operator) <RECOMMENDED>

*Make sure you log in as mrfuser*

A voxalign environment is already created, so all you have to do is open a terminal window and type source ~/Desktop/voxalign/bin/activate


Set up on your own computer:

I recommend installing in a python virtual environment:

  1. create an environment named voxalign: python3 -m venv voxalign

  2. activate it: source /path/to/env/voxalign/bin/activate

  3. install voxalign: pip install

You'll also need to on your computer.


Now that your environment is activated, you can:

  • Calculate a voxel prescription that exactly matches a prescription from an earlier scan session on the same participant:

  • Calculate a voxel position(s) that matches an MNI coordinate(s) of your choice:

  • Calculate the dice coefficient (a measure of overlap) to assess how well-aligned your session 1 and session 2 voxels ended up:


Use of voxalign is governed by the following license

Copyright 2025, Brown University, Providence, RI.

All Rights Reserved

Permission to use, copy, modify, and distribute this software and its documentation for any purpose other than its incorporation into a commercial product or service is hereby granted without fee, provided that the above copyright notice appear in all copies and that both that copyright notice and this permission notice appear in supporting documentation, and that the name of Brown University not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission.

BROWN UNIVERSITY DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE. IN NO EVENT SHALL BROWN UNIVERSITY BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

https://github.com/brown-bnc/voxalign
https://github.com/brown-bnc/voxalign/archive/master.zip
install FSL
run-voxalign
mni-lookup
dice-coef