National Brain Mapping Lab

Medical Image Processing Laboratory

Introducing the Image Processing Laboratory

The human brain, known as the most complex system, has inspired various sciences. So much so that in many sciences, the structure or function of the human brain has inspired the development of other sciences. Currently, the best way to identify the structure and function of the brain is to use magnetic resonance imaging (MRI). Raw MRI images do not contain specific information. For example, seeing raw fMRI images does not make sense even for a specialist, so extracting an image that can be examined in advanced MRI modalities such as fMRI and DWI requires a set of primary and secondary processing data. On the other hand, performing some of these processes requires minimal knowledge in the field of signal and image processing, which not all researchers in various sciences are professionally familiar with.

What we provide to researchers in the image processing laboratory is the knowledge and experience of brain image processing so that researchers in various sciences can focus on their field of expertise and advance their research without having to deal with complex image processing issues. Interpretable, quantitative and reliable results are provided through reliable and common analysis procedures and in a specialized manner appropriate to the needs of researchers.

Magnetic Resonance Imaging (MRI) and its features

Before starting a Neuroimaging study, it is important to have a clear understanding of MRI capabilities in order to avoid unrealistic and misleading expectations in addition to using the maximum capacity of this tool.

In general, MRI images can be divided into four categories:

  1. Structural images
  2. Functional images
  3. Magnetic Resonance Spectroscopy (MRS)
  4. Perfusion images

Each of these images is divided into several modalities that can provide the researcher with a specific contrast based on the type of data. In other words, the MRI can be compared to a camera that produces images with different settings from different phenomena or features.

The contrast in magnetic resonance imaging (which gives us the appearance of a structure) depends on how the image is acquired. By adjusting the radio frequency pulses and gradients and carefully setting their timing, you can acquire images of different tissue characteristics.

Introduction to analysis of the brain images

The purpose of the brain image processing is to quantify the characteristics of these images. This quantification helps doctors and researchers diagnose diseases as well as better understand the brain structure and mechanism. For example, quantifying the structural images of the brain allows researchers to compare the volume of different parts of the brain in different people. In the image processing section of the National Brain Mapping Laboratory, processing and preprocessing services for various MRI images are provided. Among the MRI images that have received a lot of attention in recent years are fMRI and DWI imaging, which are processed at the center, as well.

Medical Image Processing Laboratory

Figure 1 - The process of medical image recording and analysis

Beside image processing, this lab also involves with task design services using Psychtoolbox and Psychopy packages for functional images.

List of Services:


  • fMRI image preprocessing
  • Rest-fMRI image analysis using ICA
  • Task-fMRI image analysis using GLM
  • Functional connectivity and graph analysis


  • Quality Control (QC) of DWI images
  • DWI image preprocessing
  • DWI image processing using DTI methods
  • Functional connectivity and graph analysis


  • Voxel-based morphometry (VBM)
  • Deformation-based morphometry
  • Region-based morphometry
  • Surface-based morphometry
  • T1 and T2 mapping (Relaxometry)
  • Image correction and Quality Control of ¬freesurfer output


  • MRS image preprocessing
  • MRS image processing


  • ASL image preprocessing
  • Rest-ASL image processing using ICA
  • Task-based ASL image processing using GLM

Available software packages for MRI image analysis:

Neuroimaging tools Web Link Platform
3D slicer http://www.slicer.org/ Windows, Linux, Mac
AFNI http://afni.nimh.nih.gov/afni/ Unix
BrainVoyager https://www.pstnet.com/software.cfm?ID=97 Windows, Linux, Mac OSX
CAMINO http://cmic.cs.ucl.ac.uk/camino/ Java
ExploreDTI http://www.ExploreDTI.com Windows, Unix, Mac
FreeSurfer http://www.freesurfer.net/ Linux, Mac OSX, Windows
FSL http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ Linux, Mac OSX, Windows
MRIcro http://www.mricro.com/ Windows, Linux, Mac
MRIConvert http://old-lcni.uoregon.edu/~jolinda/MRIConvert/ Linux, OSX, Windows
MRtrix http://www.brain.org.au/software/ Windows, Unix, Linux,Mac OSX
SPM http://www.fl.ion.ucl.ac.uk/spm/ Matlab
Work Bench http://www.humanconnectome.org/software/get-connectome-workbench Linux, Mac OSX, Windows
ASLtbx https://cfn.upenn.edu/~zewang/ASLtbx.php Matlab
JMRUI http://www.jmrui.eu/ Windows, GNU and Linux
TARQUIN http://tarquin.sourceforge.net/ Windows, OSX and Linux
Psychtoolbox http://psychtoolbox.org/ Windows, Linux, Mac

Man, M. Y., et al. (2015). "A Review on the Bioinformatics Tools for Neuroimaging." The Malaysian journal of medical sciences : MJMS 22(Spec Issue): 9-19.

The use of open source software in the National Brain Mapping Laboratory (NBML) is purely scientific-research and no economic benefit or commercial use of these services will benefit the laboratory.

For more information, please enquire at the reception:
National Brain Mapping Lab
North Karegar Ave., After Jalal Highway, College of Engineering, Tehran, Iran
Tel : (+98) 2188225396-9
Fax : (+98) 21-86093160
Email : info@nbml.ir