Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software

The aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases.

URL: http://www.thomaskoenig.ch/Lester/ibaspm.htm

Resource ID: nlx_144301     Resource Type: Resource     Version: Latest Version


segmentation, structural mri, image, label, brain, structure, volume, visualization, atlasing, anatomical structure, probability, statistics, mean, standard deviation, atlas




Individual Brain Atlases using Statistical Parametric Mapping Software, Individual Brain Atlases using Statistical Parametric Mapping Software (IBASPM)

Additional Resource Types

Software Toolkit



Parent Organization

Original Submitter


Version Status


Submitted On

12:00am March 22, 2012

Originated From


Changes from Previous Version

  • Description was changed
  • Additional Resource Types was changed

Version 2

Created 2 months ago by Christie Wang

Version 1

Created 3 years ago by Anonymous