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INTRO TO FMRI DATA:

WHAT IS FMRI DATA?

MODULE 3: WORKING WITH FMRI DATA

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SECTION OVERVIEW

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What is fMRI Data?

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Visualizing fMRI Data

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fMRI Dataset Preprocessing

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  • fMRI measures activity of the brain by tracking blood oxygenation levels in functional areas in the brain
  • Functional activity in the brain is measured by the BOLD signal

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WHAT WE KNOW...

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KEY QUESTIONS

  • What does fMRI data look like?

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  • How do we load fMRI data?

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  • What are some basic manipulations of fMRI data we can do?

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REMEMBER:

What is fMRI Data?

  • BOLD signal
  • Spatial Resolution (Voxels)
    • Gives us (X, Y, Z) coordinates
  • Temporal Resolution
    • Gives us T coordinate

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AUTHOR: HAYA HALABIEH

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  • DICOM: Digital Imaging and Communications in Medicine

fMRI Images are usually in the DICOM file format:

DICOM File Format

openneuro.org

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  • Contains coordinate definitions relating voxel index (i, j, k) to spatial location (x, y, z)
  • Standardized way to store vector-valued datasets over multi-dimensional domains
  • Doesn’t directly store fMRI data

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fMRI data can also be in the NIfTI1 or NIfTI2 format:

NIfTI File Format

BrainVoyager

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  • NiBabel package
    • Provides read/write access to common neuroimaging file formats:
      • GIFTI, NIfTI1, NIfTI2, DICOM, etc.
    • Using the package:
      • In this lesson, we’ll be looking at and manipulating an empty example NIfTI instance from the nibabel.testing package
        • Example code for loading the NIfTI data using nibabel:

Loading fMRI Data

import nibabel

from nibabel.testing import data_path

image_path = os.path.join(data_path, 'example4d.nii.gz')

img = nibabel.load(image_path)

img

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# of horizontal slices

Z-dimension

# of time points

Time

X-value of area

X-dimension

Y-value of area

Y-dimension

X

Y

Z

T

Data Format

  • Data Manipulation: Transposing data...

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  • fMRI data is from measured BOLD signals
    • Typically has 4 dimensions:
      • 3D space + time
  • fMRI data can be in many forms, usually DICOM or NIfTI
  • fMRI data can be loaded using the NiBabel package

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  • Complete Lesson 1 Google Colab Assignment
  • Lesson 2: working with experimental fMRI data

SUMMARY & WHAT’S NEXT

Summary:

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What’s next:

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QUESTIONS?

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