Archive pour juin 2008



BrainVISA Anatomist MRIcro NeuroImage file format

BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory.

La plate-forme BrainVISA est dédiée à l’organisation et au traitement de données de neuro-imagerie (IRM, EEG, MEG, EEG …) alors que le logiciel Anatomist permet de visualiser et manipuler cet ensemble de données (changement de système de coordonnées, fusion et superposition d’objets …).

et un autre domaine publique : MRIcro.

download:

http://brainvisa.info/download.html

(2008/06/10) brainvisa/anatomist version 3.1 is available.

http://brainvisa.info/doc/brainvisa/en/help/aboutAnatomist.html

sur la multimodalité:

http://www.tsi.enst.fr/~bloch/tii_eng.html

http://www.tsi.enst.fr/~bloch/theses_3ans.html

MRIcro permet d’afficher les images issues de logiciels d’imagerie médicale cérébrale (SPM inclus), et ce afin de pouvoir les analyser plus simplement. Vous pourrez avoir accès à toutes les informations nécessaires (incluses dans les fichiers source) : dimensions, vue en coupe, vue 3D, rotation, etc. L’application dispose également d’un module de modification du contraste par région (sélectionnez la zone que vous voulez modifier), d’une option de comparaison de deux documents, etc. Un tutorial complet est disponible sur le site de l’auteur.

http://web.arizona.edu/~cnl/mricro.htm

http://www.sph.sc.edu/comd/rorden/mricro.html

pour mac: http://www.sph.sc.edu/comd/rorden/mricron/

file format converters:

DCM2NII attempts to convert images from the proprietary scanner format to the NIfTI format used by FSL, SPM5, MRIcron and many other brain imaging tools. NIfTI is a modern incarnation of the Analyze format, but includes important information like the orientation of the image. DCM2NII is a stand-alone program that is distributed with MRIcron. It is natively compiled for Windows, Linux x86, Mac OSX PPC and Mac OSX x86.

http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html

Each manufacturer has interpretted the DICOM data standard a bit differently. Therefore, you may want to test several programs to see which one is best suited for your data

  1. LONI Debabeler is a Java applet that can run on just about any computer. It can also read a number of medical imaging formats. Another nice feature is that it reorients the raw data to be approximately aligned with the nearest orthogonal orientation (i.e. coronal and sagittal scans are resliced along the axial plane).
  2. SPM5 includes a DICOM to NIfTI covnerter that works particularly well for Siemens data (requires Matlab).
  3. dicom2nifti is a Matlab script for converting DICOM to NIfTI (requires Matlab and the Matlab Image Processing Toolbox). [an alternative version is described here.]
  4. xmedcon offers limited NIfTI writing support for many image formats. It uses the niftilib tools, which look very useful.
  5. MRIconvert is a popular converter for Windows and Linux.
  6. dinifti looks useful.
  7. Here is a script that uses dicom2 and FSL to convert DICOM images to NIfTI.
  8. XMedCon includes the ability to convert between Acr/Nema 2.0, Analyze (SPM), Concorde/µPET, DICOM 3.0, CTI ECAT 6/7, NIfTI-1, InterFile3.3 and PNG or Gif87a/89a formats, as well as an elegant image viewer.
  9. r2aGUI Converts Philips PAR/REC images to NIfTI. Requires Matlab.
  10. The latest Philips Achieva research tools software can now directly produce (4D) nifti files This is a great alternative to using dcm2nii or r2agui. Kudos to Philips for directly supporting the NIfTI format.

Platforms, limitations, alternatives: MRIcro supports the Windows and Linux platforms. Here is a short list of some freeware Analyze format image viewers that are currently available for the Windows PC (for a list of Linux software, see the MRIcro for Linux web page. A more extensive list of DICOM viewers for Unix, Macintosh and PCs is available at my DICOM page):

Viewer Platforms Formats [Notes]
SPM Unix/Windows NT Analyze [requires Matlab]
Slice Overlay Unix/Windows NT Analyze [requires Matlab]
SPMwin Windows Analyze
ACTIV 2000 Windows Analyze/DICOM/GE/GIS/PAR/Siemens
Medal Windows Analyze/DICOM
etdips Windows Analyze/DICOM/TIFF
Spamalize Unix/Windows/Macintosh Analyze/GE/TIFF [requires IDL]
AMIDE Unix/Windows Analyze/DICOM/ECAT6/Interfile
XMedCon Unix/Windows Analyze/DICOM/ECAT6/Interfile
ezDICOM Windows Analyze/ECAT/Interfile/Siemens/Picker/GE/DICOM/VoxBo
ImageJ w. Analyze plugin Unix/Windows/Macintosh Analyze/DICOM
Space Windows Analyze/VOL [beta release]

comsol matlab

http://www.stanford.edu/services/softwarelic/comsol/

un blog mort: http://comsol-users.blogspot.com/

MATLAB

External links

Wikibooks
Wikibooks’ Programming has more about this subject:

Tutorials

FEM et éléments finis-english and « Francais »

Some examples of FEM software available on the market

Some examples of explicit software:

See also

References

  1. ^ Clough, Ray W.; Edward L. Wilson. Early Finite Element Research at Berkeley (PDF). 2007

External links

———

Quelques exemples de logiciels d’éléments finis appliqués à la mécanique des structures

Quelques exemples de logiciels généralistes utilisant la méthode des éléments finis en mécanique des structures

  • ABAQUS: logiciel américain
  • CosmosWorks : Logiciel Franco-Américain appartenant à SolidWorks qui lui même appartient à Dassault CosmosWorks
  • ANSYS: logiciel américain
  • CAST3M: logiciel français mis à disposition gratuitement pour l’enseignement et la recherche CASTEM
  • SYSTUS: logiciel français, traite des calculs mécaniques, thermiques et thermo-mécaniques linéaires et non-linéaires
  • SYSWELD: logiciel français, basé sur SYSTUS et permettant le calcul de traitement thermique, thermo-chimique, soudage, avec couplage mécanique/thermique/métallurgique voir éléctromagnétisme (trempe par induction)
  • Code Aster: logiciel libre français Aster
  • Nastran: logiciel américain
  • PERMAS: logiciel allemand PERMAS
  • SAMCEF: logiciel belge SAMCEF
  • Morfeo: logiciel belge Morfeo
  • JMAG: logiciel Japonais (distribué en Europe par Powersys Powersys) permet un couplage entre les analyses électromagnétiques et structurelles.

Quelques exemples de logiciels de dynamique non linéaire (explicite) des structures utilisant la méthode des éléments finis en mécanique des structures

Sitographie

SOLSI, http://www.solsi.fr

aide en génie mécanique

http://www.cnr-cmao.ens-cachan.fr/

un ensemble de données issus des dossiers techniques:

http://www.cnr-cmao.ens-cachan.fr/index/?Ind=tout&ssi=ChronoInv&t=13

Solidedge V19

Solid Edge is a 3D CAD parametric feature solid modeling software. It runs on Microsoft Windows and provides solid modeling, assembly modelling and drafting functionality for engineers.

Through third party applications it has links to many other Product Lifecycle Management (PLM) technologies.

Originally developed and release by Intergraph in 1996 using the ACIS geometric modeling kernel it later changed to using the Parasolid kernel. In 1998 it was purchased and further developed by UGS Corp (the purchase date correspond to the kernel swap).

In 2007, UGS was acquired by the Automation & Drives Division of Siemens AG. UGS company was renamed Siemens PLM Software on oct 2007.

Since Sep 2006 Siemens also offers a free 2D version called Solid Edge 2D Drafting.

  • Solid Edge V1 (1995)
  • Solid Edge V2 (1996)
  • Solid Edge V3 (Spring 1997)
  • Solid Edge V3.5 (October 1997 – introduced the sheet metal environment)
  • Solid Edge V4 (1998)
  • Solid Edge V5 (1998 – UGS + switched from ACIS modeling kernel to Parasolid )
  • Solid Edge V6 (1999)
  • Solid Edge V7 (1999)
  • Solid Edge V8 (2000)
  • Solid Edge V9 (2001)
  • Solid Edge V10 (2001)
  • Solid Edge V11 (2002)
  • Solid Edge V12 (2002)
  • Solid Edge V14 (2003 – « Rapid Blue »)
  • Solid Edge V15 (2003)
  • Solid Edge V16 (2004)
  • Solid Edge V17 (March 2005)
  • Solid Edge V18 (September 2005)
  • Solid Edge V19 (June 2006)
  • Solid Edge V20 (August 2007)
  • Solid Egde with Synchronous Technology (2008)

For some time now Solid Edge has been in a curious place within the mainstream modelling market.

The organisational changes within UGS had seen a much greater concentration on the NX and Teamcenter product – but this changed with the release of the Velocity Series offering last year and a renewed commitment to Solid Edge from UGS (V19). This saw Solid Edge combined with industrial strength, production proven, management tools from Teamcenter and Nastran-based analysis from Femap to create a compelling offering that raised its profile massively.

Reviewing the sales figures with UGS, it’s clear that this has done wonders for Solid Edge sales in the last twelve months and while in terms of total numbers of seats, Solid Edge is still behind its competition (SolidWorks and Inventor), it is gaining ground – which is as things should be. It’s always been a capable tool whose development has been based on depth of functionality.

As with all software releases, the vendor has chosen to break down new functionality into specific workflows or areas of benefit, while we prefer to present things in terms of workflow and how each update applies to each area of a system’s functionality. The first area we’re going to look at are the updates made to the core part and assembly modelling tools within the system.

The focus for the core modelling tools of this release seems to be aimed at the handling of assemblies. While it might not sound much considering Solid Edge already has existing tools to do this, the workflow means that, as ever, the introduction of new functionality in one area to solve a specific task has downstream effects, particularly when you look at how it’s been implemented and integrated with other tools to create a raft of new functionality.

So, let’s start with the basics – motion simulation.

While Solid Edge has always been able to create intelligent assembly models and allow the user to inspect how mechanisms work, as with many mainstream modelling tools this type of tool has been limited in its usefulness. The last few releases, in part due to some acquisitions from the major vendors, has seen this change. Autodesk has acquired dynamic simulation tools and started their integration into Inventor and SolidWorks has taken over the reins of the Adams-based CosmosMotion product to bump it forward. As a response, Solid Edge V19 has taken on similar tools that allow users to take things a little further in terms of mechanism simulation, with two key new features – gears and motor assembly relationships.

Gear relationships, although quite specific in their name, are a new class of ‘super-relationships’ within Solid Edge and allow you to define interaction between rotary components and linear components. This single relationship type can create rotary to rotary, rotary to linear and linear to linear conditions. Components don’t need to be in contact, so you can define everything from gears, belts and chains, right through to rack and pinion set-ups and hydraulics/pneumatics – all using the same feature. Motor relationships, on the other hand, are used to put gears into motion. This allows users to define a rotary or linear input (direction, speed and travel where appropriate) to drive a mechanism or system and use that to drive the motion simulation.

While at present you can’t use these tools to conduct kinematic or load transfer analysis, they do allow you to achieve a much closer approximation of how your mechanisms are going to perform. Following on from this, and to extend this functionality further, there’s been a complete rework of the tools available to create exploded views, then subsequent renderings and animations of products – all wrapped up under the banner of Explode, Render and Animate (ERA).

Right Hemisphere

Right Hemisphere

Tomorrow is the day Right Hemisphere releases version 5 of (most of) its software suite, and today was the day Rix Kramlich, the company’s new vp of worldwide marketing, described it for me.

What sets Right Hemisphere apart from other technical documentation providers is that they encourage you to stay with the CAD and graphics software you already use. Some 130 file formats are translated into and out of their own .rh format. What this means is that CATIA users continue using CATIA, and that Illustrator users continue using Illustrator. Right Hemisphere does the grunt work in the background, translating between CATIA to Illustrator, and also modifying the images from solid CAD models to isometric 2D line drawings. As required, PMI and ERP data is automatically added to diagrams.

The name, by the way, comes from its origins in the creative industry, and the Right Hemisphere is supposed to be the creative side. [I am not sure what that means for people who claim to not have a creative BONE in their body.] The company became better-known last year as the one who provided Adobe with the U3D technology used in Acrobat 3D.

The other items being announced tomorrow are:

o Deep Publisher and Deep View will be free. (I hope I got the names right; I’m working to deadline here). o Deep Server and Enterprise ship in early summer. o New API and SDK allows customers to make their own applications using any programming language, but Flex has been found to work well. o Workflow Designer allows you to interactively define the workflow of technical documents.

I asked Mr Kramlich who his competitors were. People like Seemage and Bunkspeed do some things but none do it all as does Right Hemisphere. I mentioned PTC, but then the CAD end of their tech doc system is Pro/E.

I had to chuckle at Mr Kramlich defining PLM as « Pain, Labor, Misery. » You’ll get to chuckle too, when Right Hemisphere launches its new ads using that slogan.

http://www.righthemisphere.com

u3D acrobat PRo extended

http://www.adobe.com/products/acrobat/matrix.html

for full 3D objects or contents in a pdf:  Acrobat 9 Pro Extended.

The new format u3d that can be used in pdf files for interactive explanations.

For example, anyone know how to output a file in Adobe 3D format from Matlab?
That would be a REALLY powerful way to demonstrate Matlab results
in the pdf of your papers – it could even include animations.

Now one way to do something nice is to save your graphs in .wrml and then transform them into .u3d
with Acrobat 3D or Right Hemisphere (on which Acrobat 3D is based but which has much more capabilities).

——

I found a very interesting solution for exporting 3D-Plots.
Look at this webpage and download « Saveobjmesh.m »
http://www.nada.kth.se/~asa/Ray/matlabobj.html

Try to build a 3D plot and save this plot to ‘parab.obj’.
[u,v]=meshgrid(-6:0.5:6,-6:0.5:6);
x=u; y=v; z=u.^2+v.^2;
mesh(x,y,z)
saveobjmesh(‘parab.obj’,x,y,z)

Now you are able to import this obj file to Adobe Acrobat 3D
Toolkit (30 days demo available). You can save this file as
an U3D file, name it « matlabplot.u3d ».

Go to your favourite latex editor.
Create a file named « views.vws » containing only one line:

[frontview]{-0.000000193670558701 -0.000000028775016148
36}{0.7103724479675293 0.7032560706138611
-0.0283149853348732}{140.5486495578774}{42.73490890549407}{}

Now create a new latex file and copy and paste these lines:

\documentclass[a4paper]{article}
\usepackage[3D]{movie15}
\begin{document}
\section*{my first 3d plot from matlab in \LaTeX}
\includemovie[autoplay, toolbar,
label=3dplot,3Dviews=views.vws]{.5\linewidth}{.5\linewidth}{matlabplot.u3d}

\\
\movieref[3Dgetview]{3dplot}{Get View!}
\end{document}

If you want to add another view of your plot, zoom and
rotate to the view and click on the « Get view! » text. Copy
this line into the « views.vws » files. The first line ist the
starting view.

Only works with new versions of Adobe Acrobat Reader.


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