PET processing in Brainstorm

Authors: Diellor Basha

This describes how to import and process PET volumes to perform multimodal analyses in Brainstorm...

Introduction

Positron Emission Tomography (PET) is a powerful imaging technique widely used in medical and scientific research to study metabolic and functional processes in the body. PET processing involves a series of computational and analytical steps to transform raw data into meaningful visualizations and quantitative insights. These steps ensure accurate reconstruction, correction, and analysis of PET scans, enabling researchers and clinicians to draw precise conclusions.

This page provides an overview of the essential methods, tools, and considerations involved in PET processing, aiming to support both newcomers and experienced users in achieving optimal results. Whether you're exploring biological pathways, assessing disease progression, or validating experimental findings, understanding the fundamentals of PET processing is key to leveraging the full potential of this versatile imaging modality.

Method Overview

pet_processing_pipeline.png

The Brainstorm extension for PET supports importing, processing, registering, visualizing, and analyzing PET data within Brainstorm. PET functionality and workflow are designed to facilitate the analysis of multimodal neuroimaging data by allowing the user to co-analyze MEG, PET and MRI-derived data. Multi-frame (4D) PET volumes are realigned during import and aggregated over time from the 4D image (i.e. mean of the n frames) to obtai a unique 3D volume for co-registration with the subject’s structural MRI. Multi-frame PET volumes are realigned using SPM’s realign and reslice functions and co-registered with SPM. The aggregated and co-registered 3D volume is masked and rescaled to obtain voxel-wise standardized uptake value ratio (SUVR) which are then projected to the cortical surface.

Import the anatomy

• Start Brainstorm

• Select the menu File > Create new protocol. Name it "XXXXXX" and select the options:
  "No, use individual anatomy",
  "No, use one channel file per acquisition run".

Reference MRI

• Go to the Anatomy view

• Right-click on the XXXXXX top node > New subject > Subject01.
  Keep the default options you defined for the protocol.

• Switch to the Anatomy view of the protocol.

• Right-click on the subject node > Import MRI.
  Set the file format: MRI: NIfTI-1 (*.nii;*.nii.gz)???.
  Select: ???????.nii

• The MRI viewer opens automatically. Click on "Click here to compute MNI normalization", option "maff8".

• Click on Save to close the MRI viewer. New node named preMRI is created.
  
  

PET volume

The MRI volume above will be used as the anatomical reference for this subject. We will now import a PET scan done on the same subject. In this dataset, PET scan corresponds to XXXX.

• Right-click on the subject node > Import PET.
  Select: ????.nii

• Choose Yes for the transformation for MRI orientation.
  

• Choose the import options for PET

  • 
    

  • Align frames: Description on what happens, method, etc
    Check this option

  • Apply smoothing: Description
    Check this option, and set FWHM to XX mm

  • Aggregate frames: Description
    Select mean

  • Register to MRI using:: Description
    Check this option, and set method to SPM

  • Reslice volume:: Description
    Check this option

Additional documentation

Related tutorials

• Import the subject anatomy

Articles

• Nolte G, Bai O, Wheaton L, Mari Z, Vorbach S, Hallett M.
  Identifying true brain interaction from EEG data using the imaginary part of coherency.
  Clinical Neurophysiology. 2004 Oct;115(10):2292–307.

Forum discussions

• Overlaying PET on cortex: https://neuroimage.usc.edu/forums/t/30241