Friday, July 12, 2013

logiciels pour le traitement des images IRM en neuro-imagerie; 3D

l'IRM a 30ans donc il existe une pléthore de techniques (issus de la zoologie des séquences de pulses).

Il existe bcp de logiciels de traitement des images IRM:

un des plus "complets" pour les domaines neuro-imagerie anat+fonctionnelle y compris l'animal:
fonctionne sur Mac OS et Linux

Rem: Caret et 3D Slicer peuvent importer des données générées par FreeSurfer...

-Pour le télécharger:
-pour les débutants et wiki:
-pour un overview:

Navigating the Fifth Dimension: Innovative Interface for Multidimensional Multimodality Image Navigation, 2006; doi: 10.1148/rg.261055066


medInria is a multi-platform medical image processing and visualization software. It is free and open-source. Through an intuitive user interface, medInria offers from standard to cutting-edge processing functionalities for your medical images such as 2D/3D/4D image visualization

brain visa/anatomist

BrainVISA est distribué avec une boîte à outils dédiée à la segmentation d'images IRM pondérées en T1. Le produit de la principale chaîne de traitements issue de cette boîte à outils est le suivant: une classification gris/blanc pour la morphométrie voxel par voxel, des maillages des surfaces de chaque hémiphère pour la visualisation, des maillages sphériques de la matière blanche de chaque hémisphère, un graphe des plissements corticaux, un étiquetage de ces plissements fondé sur une nomenclature des principaux sillons
You need about 1.5 Gb free disk space to install the BrainVISA pack 4.1. Yes, it's big, but it contains lots of useful things.
Here are the commands to uncompress the package:
On Linux and MacOS:
tar jxvf <brainvisa_package>.tar.bz2
On Windows: unzip the zip file using whatever unzip tool you like (windows XP has one builtin in the system).
The package consists of two main programs, anatomist and brainvisa, and a suite of utility programs. All are located in the 'bin' directory of the package. It may be dangerous in a few cases to permanently add this directory to your path, because this can create conflicts with other programs on your system (e.g. python). We suggest two possibilities.
To start a program, type the full path along with the name of the program, e.g.:

(or create symbolic links to 'anatomist' and 'brainvisa' in a directory listed in your path (maybe /home/yourlogin/bin)

Analysis of Functional NeuroImages
is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
Matlab Library
Ziad Saad and Gang Chen have developed a package of Matlab functions to read, write, and process AFNI datasets. This may be useful for those who want to carry out matlab-based computations such as Dr. Worsley's FMRISTAT or Gang Chen's 4-way ANOVA or user cuddly 3dDeconvolve.

Cortical Cartography

(March, 2012) Release of human 'Conte69 atlas' surface-based atlas See Details
Caret software for visualizing and analyzing experimental data on surfaces and volumes
The SumsDB database of published (freely available) and unpublished (private) neuroimaging data. Read more
Webcaret software for online visualization of SumsDB datasets.Read more
Atlases of human, macaque, mouse, and rat that facilitate cross-study comparisons and data mining
Neuroimaging foci. Published stereotaxic coordinates (‘foci’) are especially amenable to data mining. SumsDB currently provides free access to ~25,000 foci from ~800 studies along with tutorials. see also

en plus de ces rendus surfacique, on peut avoir besoin de maillage.
qualité maillage, un excellent programme:
3D maillages:



pour voir les données et pour voir les prétraitements des images, j'aime bien
imageJ avec 3D viewer (plug-in)

Using the 3D viewer as an ImageJ plugin

The ImageJ 3D viewer provides a plugin for ImageJ to visualize image stacks three-dimensionally. The most important features include:

Display stacks as volume renderings, iso-surfaces, orthoslices or surface plots.
Volume editing.
Landmark selection.
Rigid registration, based on manually selected landmarks.
Displaying 4D data.

Using the 3D viewer as a programming library

The viewer can not only be used as an application, but can also be utilized from other Java programs, especially ImageJ plugins, as a library. It offers a well-documented API for high-level 3D visualization.

Displaying an image stack three-dimensional is a matter of a few lines of code:
// Open image
ImagePlus imp = IJ.openImage("/path/to/image");

// Create a universe and show it
Image3DUniverse univ = new Image3DUniverse();;

// Add the image as an isosurface
Content c = univ.addVoltex(imp);
Point lists

How to create landmarks
How to show and hide landmark points.
How to save and load landmark points.
How to edit them.
Landmark-based registration

How to use landmark points for landmark-based rigid registration

How to set and apply transformations in form of matrices
How to save and load transformation matrices
How to avoid unintended object transformation by locking it
How to reset the transformation of an object.
3D Content in PDFs

How to export triangle meshes to a .u3d file or STL file import/export
How to embed the u3d file in a latex file
How to compile it into a pdf containing the 3D data
ajouter d'autres plug-in pour la segmentation de base:
Download IntSeg_3D.jar
part of his thesis
Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins.

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