From the scanner to our computer

Last updated on 2024-12-21 | Edit this page

Overview

Questions

  • What are the main MRI modalities?
  • What’s the first step necessary to start working with MRI data?

Objectives

  • Understand how different MRI modalities differ and what each one represents
  • Become familiar with converting MRI data from DICOM to NIfTI

Types of MR scans

Anatomical

Sourced from https://case.edu/med/neurology/NR/MRI%20Basics.htm

  • 3D image of anatomy (i.e., shape, volume, cortical thickness, brain region)
  • can differentiate tissue types

Functional

Sourced from Wagner and Lindquist, 2015

  • tracks the blood oxygen level-dependant (BOLD) signal as an analogue of brain activity
  • 4D image (x, y, z + time)

Diffusion

Sourced from http://brainsuite.org/processing/diffusion/tractography/

  • measures diffusion of water in order to model tissue microstructure
  • 4D image (x, y, z + direction of diffusion)
  • need parameters about the strength of the diffusion “gradient” and its direction (.bval and .bvec)

Neuroimaging file formats

Common file formats:
Format Name File Extension Origin/Group
DICOM none (*) ACR/NEMA Consortium
Analyze .img/.hdr Analyze Software, Mayo Clinic
NIfTI .nii (**) Neuroimaging Informatics Technology Initiative
MINC .mnc Montreal Neurological Institute
NRRD .nrrd Gordon L. Kindlmann
MGH .mgz or .mgh Massachusetts General Hospital

(*) DICOM files typically have a .dcm file extension. (**) Some files are typically compressed and their extension may incorporate the corresponding compression tool extension (e.g. .nii.gz).

From the MRI scanner, images are initially collected in the DICOM format and can be converted to these other formats to make working with the data easier.

Let’s download some example DICOM data to see what it looks like. This data was generously shared publicly by the Princeton Handbook for Reproducible Neuroimaging.

BASH 

wget https://zenodo.org/record/3677090/files/0219191_mystudy-0219-1114.tar.gz -O ../data/0219191_mystudy-0219-1114.tar.gz
mkdir -p ../data/dicom_examples
tar -xvzf ../data/0219191_mystudy-0219-1114.tar.gz -C ../data/dicom_examples
gzip -d ../data/dicom_examples/0219191_mystudy-0219-1114/dcm/*dcm.gz
rm ../data/0219191_mystudy-0219-1114.tar.gz
dicom-to-nifti

NIfTI is one of the most ubiquitous file formats for storing neuroimaging data. If you’re interested in learning more about NIfTI images, we highly recommend this blog post about the NIfTI format. We can convert our DICOM data to NIfTI using dcm2niix.

We can learn how to run dcm2niix by taking a look at its help menu.

BASH 

dcm2niix -help

Converting DICOM to NIfTI

Convert the Princeton DICOM data to NIfTI

BASH 

mkdir -p ../data/dicom_examples/nii
dcm2niix -z y -o ../data/dicom_examples/nii ../data/dicom_examples/0219191_mystudy-0219-1114/

Key Points

  • MRI can capture anatomical (structural), functional, or diffusion features.
  • A number of file formats exist to store neuroimaging data.