The goal of brain image processing is to quantify brain features using brain images and mathematical techniques. Quantification of brain features helps researchers to have a better understanding of the brain functions and structures. This quantitation also assist physician with diagnosis of different disease. For instance, the quantization of brain structural images gives us the opportunity to compare volumes of different brain parts between subjects and image processing laboratory helps researchers through extracting quantitative features from brain images.
Magnetic resonance imaging is a technique which use strong magnetic fields and various radio waves to depict pictures of the brain. Using different pulse sequences, it’s possible to record images representing different features of the brain. Structural, functional and diffusion weighted MRI are the most well-known MRI type.
Oxygen is delivered to neurons by hemoglobin. When neural activity increases, the local demand for oxygen increases and correspondingly, the local blood flow increases. Hemoglobin has different characteristics when it is with or without oxygen. When hemoglobin is with oxygen, it has magnetic characteristic. This blood characteristic causes small changes in MR signal. Since the blood oxygen changes depending on the level of neural activity, these changes can be used for brain activity acquisition, this type of MR is known as blood oxygen level dependent(BOLD) or Functional MRI(fMRI).
Diffusion-weighted magnetic resonance imaging Is an imaging technique which use the diffusion property of water molecules to produce MR images. In contrast with water molecules in a glass of water which can diffuse to all direction (isotropic diffusion), water molecules diffusion direction in different tissues is different (anisotropic diffusion).
The measured anisotropic diffusion shows inhomogeneity in microscopic tissues. In white matter of the brain, anisotropic diffusion is due to cell membrane (myelin membrane) and axon bundles. Anisotropic diffusion can show tissue direction. In white matter, diffusion direction shows fiber directions.
There are two type of fMRI studies, the first one which is called task fMRI, tries to record brain activity during a specific task. This kind of study is usually performed under a specific cognitive task and the goal is to find brain regions that are associated with that specific cognitive task. The other kind of fMRI study, investigates brain activity during the rest, this kind of study is called rest fMRI. There are two main image processing method for analysis of fMRI images, data driven and model base methods.
As previously stated, direction of water molecules diffusion in white matter of the brain shows the direction of fiber bundles in brain. Therefore, in DWI image processing we investigate water molecules directions. The most common image processing technique for DWI images processing is DTI. In DWI image processing using DTI technique, a model called tensor is fitted to the data. Next, using the calculated tensor, parameter such as fractional anisotropy(FA), the main diffusion direction, mean diffusion can be calculated.
The brain image processing laboratory in NBML is one of the first centers that provide brain image processing services for researchers in Iran. In this lab, processing a wide range of MR images including structural, functional and diffusion weighted images is accomplish using variety of specialized softwares. Also, we offer consultancy services and advisors in this lab would be happy to answer researcher’s brain image processing questions.
|Neuroimaging tools||Web Link||Platform|
|3D slicer||http://www.slicer.org/||Windows, Linux, Mac|
|BrainVoyager||https://www.pstnet.com/software.cfm?ID=97||Windows, Linux, Mac OS X|
|Explore DTI||http://www.ExploreDTI.com||Windows, Unix, Mac|
|FreeSurfer||http://www.freesurfer.net/||Linux, Mac OS X, Windows|
|FSL||http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/||Linux, Mac OS X, Windows|
|MRIcro||http://www.mricro.com/||Windows, Linux, Mac|
|MRtrix||http://www.brain.org.au/software/||Windows, Unix, Linux,Mac OS X|
|Work Bench||http://www.humanconnectome.org/software/get-connectome-workbench||Linux, Mac OS X, Windows|
A Review on the Bioinformatics Tools for Neuroimaging, Man et al, Special Issue Neuroscience 2015
In NBML’s image processing lab, open source programs are only used for research and scientific purposes and there will be no commercial use.