= PET processing in Brainstorm =
''Authors: Diellor Basha''

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

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== Introduction ==
Positron Emission Tomography ([[https://en.wikipedia.org/wiki/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.

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.

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== Method Overview ==

== Import the anatomy ==
 * Start Brainstorm
 * Select the menu '''File > Create new protocol'''. Name it "'''XXXXXX'''" and select the options: <<BR>>"'''No, use individual anatomy'''",<<BR>>"'''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'''.<<BR>>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'''.<<BR>>Set the file format: '''MRI: NIfTI-1 (*.nii;*.nii.gz)???'''.<<BR>>Select: '''???????.nii'''

 * The MRI viewer opens automatically. Click on "[[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_normalization|Click here to compute MNI normalization]]", option "'''maff8'''".

 * Click on '''Save''' to close the MRI viewer. New node named '''preMRI''' is created.<<BR>><<BR>>



=== 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'''.<<BR>>Select: '''????.nii'''
 * Choose '''Yes''' for the transformation for '''MRI orientation'''.<<BR>>
 * Choose the import options for PET
  . <<BR>> {{attachment:pet_import_opts.png}}

  * '''Align frames''': Description on what happens, method, etc <<BR>> Check this option

  * '''Apply smoothing''': Description <<BR>> Check this option, and set FWHM to '''XX mm'''

  * '''Aggregate frames''': Description <<BR>> Select '''mean'''

  * '''Register to MRI using:''': Description <<BR>> Check this option, and set method to '''SPM'''

  * '''Reslice volume:''': Description <<BR>> Check this option

{{{#!wiki note

You can also decide to not perform any of these actions, and perform them once the PET volume is imported. IMAGE OF CONTEXT MENUS, for frame alignment and co-registration
}}}
== Additional documentation ==
==== Related tutorials ====
 * [[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy|Import the subject anatomy]]

==== Articles ====
 * Nolte G, Bai O, Wheaton L, Mari Z, Vorbach S, Hallett M. <<BR>> [[https://doi.org/10.1016/j.clinph.2004.04.029|Identifying true brain interaction from EEG data using the imaginary part of coherency]]. <<BR>> Clinical Neurophysiology. 2004 Oct;115(10):2292–307.

==== Forum discussions ====
 * Overlaying PET on cortex: https://neuroimage.usc.edu/forums/t/30241