1) The document discusses statistical parametric mapping (SPM) which is an fMRI analysis software package used for preprocessing, analyzing, and modeling functional neuroimaging data. 2) SPM preprocessing steps include reorientation, realignment of images to correct for head motion, normalization to standard space, and smoothing to increase the signal-to-noise ratio. 3) The document provides an overview of various neuroimaging techniques including CT, MRI, PET, fMRI, and EEG and their applications in visualizing brain structure and function.

1. STATISTICAL PARAMETRIC
MAPPING FOR NEUROIMAGING
Workshop

2. Table of Content
■ Neuroscience
■ Human Brain
■ Neuroimaging
■ What is SPM?
■ Preprocessing
■ Reorientation
■ Realignment and Unwrapping the Data
■ Normalization
■ Smoothing

3. ■ Neuroscience is the science of the brain
and the nervous system
■ Neuroscience, also known as Neural
Science, is the study of how the nervous
system develops, its structure, and what it
does.
■ Neuroscientists focus on the brain and its
impact on behavior and cognitive functions.
Neuroscience

4. Human Brain

5. Human Brain
■ An adult healthy brain has over 100 billion
neurons, each with many dendrites and an
axon.
■ Dendrites help neurons to make a connection
with other neurons and communicate with each
other. These connections we called synapses.
■ Synapses help a neuron in releasing information
in the form of a tiny burst of chemicals.
Neural Signaling Human Brain
Axon
Dendrites Axon terminals

6. Why Neuroscience is important?
Neuroscience is an interdisciplinary science that works closely with other disciplines,
such as
■ mathematics
■ computer science
■ Chemistry
■ Philosophy
■ Psychology
■ medicine.

7. Types of Brain Disorders
■ Alzheimer's Disease.
■ Dementias.
■ Brain Cancer.
■ Epilepsy and Other Seizure Disorders.
■ Mental Disorders.
■ Parkinson's and Other Movement Disorders.
■ Stroke and Transient Ischemic Attack (TIA)

8. Neuroimaging
■ Neuroimaging is a discipline that studies the structure and function of the nervous
system by means of imaging technology, and where the images of the brain can be
obtained in a non-invasive way.
■ It explores a series of mechanisms such as cognition, information processing, and
brain changes in the pathological state.

9. Neuroimaging Techniques
■ Computed Tomography (CT)
■ Magnetic Resonance Imaging (MRI)
■ Positron Emission Tomography (PET)
■ Functional Magnetic Resonance Imaging (fMRI)
■ Electroencephalography (EEG)
Provide both anatomical and functional visualizations of the nervous system, which
greatly advance modern medicine, neuroscience, and psychology.

10. Computed Tomography (CT)
■ Computed tomography (CT) is a diagnostic
imaging test used to create detailed images of
internal organs, bones, soft tissue and blood
vessels.
■ CT is fast, painless, noninvasive and accurate.
■ In emergency cases, it can reveal internal injuries
and bleeding quickly enough to help save lives.

11. Magnetic Resonance Imaging (MRI)
■ Magnetic resonance imaging (MRI) is a medical
imaging technique that uses a magnetic field and
computer-generated radio waves to create detailed
images of the organs and tissues in your body.
■ Most MRI machines are large, tube-shaped magnets.

12. Positron Emission Tomography (PET)
■ Positron emission tomography is a functional imaging technique that uses
radioactive substances known as radiotracers to visualize and measure changes in
metabolic processes, and in other physiological activities including blood flow,
regional chemical composition, and absorption.

13. Functional Magnetic Resonance Image
■ Functional magnetic resonance imaging (fMRI) measures brain functions by
detecting changes related to blood flow.
■ It demonstrates temporal and regional changes in brain metabolism.
■ If there is more oxygenated blood in one part of the brain compared to others, then
chances are that this brain area is more active.
■ This is known as the Blood-Oxygenation Level-Dependent response (otherwise
known as BOLD).

15. Electroencephalography (EEG)
■ Electroencephalography (EEG) is an electrophysiological neuroimaging
technique that measures the electrical activity generated by the human brain

16. What is SPM?
■ SPM (Statistical Parametric Mapping) is an fMRI analysis software package that is
run in Matlab.
■ In addition to fMRI analysis, SPM contains toolboxes for performing volume-based
morphometry and effective connectivity.
Matlab(https://www.mathworks.com/products/matlab.html) Commercial 
SPM(https://www.fil.ion.ucl.ac.uk/spm/software/spm12/) Free 

17. SPM(Statistical Parametric Mapping)
Realignment Smoothing
Normalisation
General linear model
Statistical parametric map (SPM)
Image time-series
Parameterestimates
Kernel Design matrix
Template
Gaussian
field theory
p <0.05
Statistical
inference
Source: www.fil.ion.ucl.ac.uk

18. Preprocessing
Think of preprocessing as cleaning up the images. When you take a photo with a camera, for
example, there are several things you can do to make the image look better:
■ Remove red eye;
■ Increase color saturation;
■ Remove shadows.
Similarly, when we preprocess fMRI data we are cleaning up the three-dimensional images
that we acquire every TR.
An fMRI volume contains not only the signal that we are interested in - changes in oxygenated
blood - but also fluctuations that we are not interested in, such as head motion, random drifts,
breathing, and heartbeats. We call these other fluctuations noise, since we want to separate
them from the signal that we are interested in. Some of these can be regressed out of the data
by modeling them (which is discussed in the chapter on modeling fitting), and others can be
reduced or removed by preprocessing.

19. Preprocessing Steps
■ Reorientation
■ Realignment and Unwrapping the Data
■ Normalization
■ Smoothing

20. Reorientation
■ The most common use for reorienting images in SPM is to roughly align structural
images with standard space prior to tissue class segmentation.
■ Go to display and set origin to 0 and reorient all images

21. Continue…
■ Then go check registration and first select a template image EPI.nii and then an
image from data.

22. Continue…

23. Continue…

24. Continue…
■ Set the parameters in left bottom window and apply to all images

25. Continue…
■ Go to check registration and check some images so that whether are they aligned
properly?

26. Realignment and Unwrapping the Data
■ The first step of preprocessing is to realign the functional images.
■ If you think of a time-series as a deck of cards, with each volume as a separate
card, realignment will put all the cards in the same orientation and make the sides
line up - similar to what you do after you shuffle a deck of cards.

27. Continue…

28. Continue…
■ Select first image then select all

29. Continue…
■ And click the run (green) button

30. Continue…
■ After realignment

32. Normalization

33. Continue…
■ Enter Templete image in image to align

34. Continue…
■ In image to write enter all realigned images

35. Continue…
■ Then click on run button

36. Smoothing

37. Continue…
■ Select all realigned and normalized images

38. Continue…
■ And click on the run button