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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  • Prepare in advance
  • Running voxalign

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

Multi-session alignment

For exact replication of voxel placement(s) within a single participant across multiple scan sessions

PreviousInstallationNextCenter on MNI coordinate

Last updated 11 days ago

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Prepare in advance

You can organize your data however you like, but it is helpful to collect the session 1 DICOMs in advance of the scan session and make sure that they are named and organized in a way that will make running voxalign quick and simple. For example, I like to make a new folder for each participant, with sess1 and sess2 subdirectories. You can put the T1 and spectroscopy DICOMs in the sess1 directory in advance, and the sess2 directory you'll copy the T1 DICOM into as soon as it is collected.

Running voxalign

  1. Activate the virtual environment with source /path/to/env/voxalign/bin/activate (on Tess, this will be source ~/Desktop/voxalign/bin/activate. You can tell that the environment is activated when it says (voxalign) before the command prompt.

  2. Start voxalign by typing run-voxalign.

  3. Use the voxalign file selector to select your output directory. I usually just create a folder called "output" in the participant's directory.

  4. Select your T1 and spectroscopy DICOMs. You can set up everything but the session 2 T1, which will arrive via scannershare.

  1. Click Run VoxAlign

Your new spectroscopy voxel prescriptions will be printed to the terminal, saved out in a text file, and also automatically opened in a fsleyes window.


TIPS

  • Your two T1 scans need to have the same resolution for voxalign to work properly (at the moment).

  • When you are typing your prescription in on the scanner, if the field says 'R' enter a negative number to switch it to L, and vice versa. This applies to all three directions.

  • The tools voxalign uses to convert DICOMs to NIFTIs do not play well with spaces in file paths, so - for example - running voxalign on data stored in a "Google Drive" folder will not work.

Once the session 2 T1 has been collected, and copy it to your participant/sess2 folder on Tess. Then select it in the voxalign GUI.

export it to scannershare
A simple and clear way to organize your DICOMs