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.
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
* 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.
Resource Type: Resource
Version: Latest Version
segmentation, structural mri, image, label, brain, structure, volume, visualization, atlasing, anatomical structure, probability, statistics, mean, standard deviation, atlas
Additional Resource Types
Resource PubMed IDs
PMID: 20418943, PMID: 23894356
Individual Brain Atlases using Statistical Parametric Mapping Software, Individual Brain Atlases using Statistical Parametric Mapping Software (IBASPM)
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Created 3 years ago by Anonymous