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  • Re: MRI/CT SCAN to 3D IGES Image Converter?

    Dear People,
    Thank you verymuch for your flooded response. I have attached some of the
    replies I got for this query. Hope this may be useful for some of the other
    researchers who are working in this field.
    Thank you once again,
    With regards,
    Dr.Siva

    ------------------------------------------------------------------
    Try using 3D doctor or Mimics.

    Nilesh Billade

    -------------------------------
    From: nithyasatish@hotmail.com
    To: sivasankar@iitg.ernet.in
    Subject: RE: [BIOMCH-L] MRI/CT SCAN to 3D IGES Image Converter?
    Date: Wed, 3 Jun 2009 15:36:33 +0000


    Dear Dr Siva

    If you are using the Spiral Ct Scan machine they themself have converters.

    If you need any further help can feel free to contact
    ------------------------------------------------------------------------

    Dear Dr Sivasankar

    You should use mimics software for creating the model. Then I think you need
    not convert
    ---------------------------------------------------------------------------------

    Hello Dr. Sivasankar,
    I believe the task you are trying to do is a little more involved than a
    simple file conversion. To create a computer model of the anatomy from
    image data, you will first need to segment the bone from the image
    (label what part of the image is femur, and what is not). You will then
    need to run an algorithm (like marching cubes) on the labeled image that
    can convert the image into a surface model. Then you can save the
    surface model into a format suitable for FEA. There are a few software
    packages that are available depending on whether you want to use ready
    made software or if you will need to build your own. I would recommend
    that you first take a look at the excellent open-source itk-snap
    (http://www.itksnap.org/pmwiki/pmwiki.php) as I think it will do what
    you need. If you need to build your own software, you will probably be
    very interested in ITK (http://www.itk.org/) and VTK
    (http://www.vtk.org/) as they have all the necessary algorithms to this
    type of task.

    -bryan
    ---------------------------------------------------------
    Dear Dr. Diva,
    Yes you sure can do that . There are a couple of softwares available
    such as amira , simpleware, mimics etc . They can convert image data
    into dr models

    Cheers
    Srinivas
    --------------------------------------------------------------
    Dear Dr.M.Sivasankar,

    I read your post at the BIOMCH-L about 3D reconstruction of bone tissue from
    medical images. Me and some colleagues have gathered experience over the
    past couple of years regarding this issue. I can recommend the reading of
    the following papers:

    http://www.iacm-eccomascongress2008.org/cd/offline/pdfs/a2566.pdf

    http://www.informaworld.com/smpp/content~content=a910351161~db=all~jumptype=rss
    (this one I attached to the e-mail)

    If any further questions arise, do not hesitate on asking.


    Best regards,
    ________________________________________________
    Daniel Simões Lopes, PhD Student

    Instituto Superior Técnico - Technical University of Lisbon

    IDMEC/IST
    Av. Rovisco Pais
    1049-001 Lisboa
    Portugal
    --------------------------------------------------------------------
    Dear Prof. Sivasankar,

    There are software programs like Mimics, 3D Doctor, Amira, etc. do
    convert CT/MRI scan images into 3D models. The segmentation of these
    images to reconstruct a perfect 3D bone model is a time consuming job.
    Also, the generated IGES file would huge in size due to islands and
    errors in segmentation. Also, getting a solid IGES model out of CT
    slices is a difficult task. If you have medical modelling software at
    your lab, please ask your student to segment the CT scan images
    manually drawing boundaries of the bone and reconstruct it. Also,
    Mimics has a module to export directly into FE mesh for some FEA
    systems (Nastran, Ansys,.....). Instead of exporting it into IGES and
    import, i would prefer to use the mesh generated by these softwares.

    All the best for your bioengineering research.

    with warm regards,

    K. Subburaj
    Research Scholar
    Biomanufacturing Lab
    Dept. of Mechanical Engg.
    Indian Institute of Technology Bombay
    Powai, Mumbai - 400 076, MH, India
    +91.98.6915.2700 (Cell) +91.22.2576.7510 (Lab)
    www.me.iitb.ac.in/~subbu
    http://orthocad.iitb.ac.in (Lab)
    ----------------------------------------------------------------------------
    Dear Dr. Sivasankar

    You can use Materialize Mimics software to do this, some other software
    like ScanFE can also.


    Zq.Lian,lianzq75@gmail.com
    2009-06-03
    -------------------------------------------------------------------------------

    Mr. SivaSankar. In order to convert DICOM images to Iges file, you need to
    use either Mimics software or softwares similar to that. Even these
    softwares do not convert Dicom images directly to Iges file . They only
    convert imgaes to STL file, then you might need to use software like 3Matic
    to convert STL file to Iges file. Hope this helps.

    Best Regards,
    Satya Nambu
    ----------------------------------------------------------------
    Dear Dr Sivasankar
    Following is my reply to Sarah's post yesterday. Hopefully you find it
    helpfiul.

    There is a little extra to say on this though if you want to get the scan
    data into IGES or a CAD readable format.

    Forgive me if I am making assumptions about what your student wants to do.
    If the principle purpose is to get geometry into your FEA package simply so
    that it can prepare a mesh for your analysis this may not be necessary, as a
    number of the following packages will generate an FE mesh directly that can
    be imported into your analysis software.

    3D Scan data is often developed as a faceted triangulated surface, and often
    output in STL format. This contains no information about surface curvature
    etc which are used in NURBS surfaces. Therefore the generation of an IGES
    file or other NURBS surfaces from either point cloud or faceted data are not
    trivial tasks.

    Having said that there are options. Reverse engineering tools do this. I am
    sure that there are more out there than I am aware of. Following are
    packages that I am aware of that might be able to help you do this.
    1. Geomagic is one that I have used that can do this. Seems to work well
    2. A number of CAD packages probably have modules for reverse engineering
    that do this
    3. Simpleware mentioned below has an IGES export option
    4. MIMICS I believe has an IGES export option
    5. ANALYZE from the Mayo clinic has an IGES export option
    6. ICEM Surf (automotive package)

    Hope this is helpful. Following is my reply to Sarah's post yesterday.

    Good luck.

    Andrew Sims

    ----------------------------------------
    I do quite a bit of this. There are a number of options that I am familiar
    with in no particular order of preference (I will give some of my thoughts
    at the end) Hope you don't mind the length. Good luck with your work! There
    are a number of packages that could do the job.
    1. Simpleware:
    Simpleware is a suite of programs ScanIP, ScanFE and ScanCAD. I have used
    ScanIP and ScanFE. As the names suggest ScanIP is the image processing part
    of the suite. ScanIP can import DICOM, raster images and raw files, and
    export some of these also. It allows multiple "masks" for different
    materials/volumes etc. There are both manual and automatic segmentation
    tools, and boolean operations to allow union, subtraction, intersection and
    inversion of masks. A number of operations are valid over the entire volume,
    a region or a local slice.
    There are a number of background filters, ranging from gaussian to nonlinear
    edge preserving filters. Other filters and operations include morphological
    mask operations, and a number of different level set segmentation
    implementations. The surfaces/volumes that you define in ScanIP can be then
    exported to ScanFE. ScanFE exists to convert the surfaces defined in ScanIP
    to FE/CFD meshes using solid elements. The features that I find nice in this
    are 1.) material allocation based on underlying greyscale value and 2)
    native export of mesh to various solvers (eg I use ANSYS and this is the
    only tool that I use that exports a file in ANSYS' text format directly,
    otherwise I need to add another step).
    2. AMIRA/AVIZO
    AMIRA and AVIZO are similar products, they used to simply be AMIRA, but a
    year or so ago the program was rebundled and split into AMIRA for life
    sciences and AVIZO for simulation, materials science and several other
    things. This probably means that there is more flexibility in what you
    licence but if you need breadth of product there are more modules to buy. I
    am not sure of how AMIRA has changed since the split as the installation
    that I use is now on AVIZO. These are general purpose high end
    visualisation, reconstruction and analysis packages. There are all the usual
    segmentation procedures. There is a neat level set contour tool for active
    highlighting. One of the features that I find very helpful in AVIZO is the
    registration module to align different scan volumes. There is also a link
    between the packages and MATLAB so that you can pass information back and
    forth for example to incorporate a custom filter. You can import just about
    anything. There is tcl scripting to automate repetitive tasks. There are
    good tools to downsample and clean up triangulated surfaces, this can be a
    little time consuming if you have intersections. Tet meshes can be generated
    from triangulated surfaces. In the version I use I needed to do an extra
    conversion step to import it into ANSYS, but this is not a real problem.
    These programs can also be used for presentation of data and postprocessing
    and diffusion tensor imaging (maybe only AMIRA for DTI).
    3. 3D Slicer
    3D slicer is a free open source program used for research. I have used it
    but not extensively. I believe that it incorporates the VTK as its basis. I
    may be wrong here, so others may fill you in on this better. There is a
    broad scope of modules incorporated to generate surfaces, volumes, it looks
    like there is a new meshing module, registration and alignment, DTI etc.
    4. MIMICS
    I have not had much experience with MIMICS but it is a commercial product by
    MATERIALISE. It is used for 3D reconstruction, rapid prototyping and FE mesh
    generation, and possibly other things as well. Worth checking out. I think
    it includes marterial allocation based on greyscale value
    My thoughts.
    All of these packages are powerful. I personally like AMIRA/AVIZO and
    Simpleware. Amira for the manual segmentation tools and general flexibility
    of the product, and Simpleware for some meshing features.
    The general purpose nature of AMIRA and AVIZO are very powerful, it is a
    fully featured visualisation package. I have benefited from being able to
    script a number of repetitive tasks across a number of models. I find the
    user interface clean, although I feel that the help leaves a little to be
    desired. I have found that I can do pretty much what ever I want in it, but
    it might take me a while to work it out. Calculations etc can be performed
    on your data to give all manner of things. You are probably limited by your
    imagination.
    Simpleware makes good meshes and some of the tools are nice such as contact
    region definition on volume boundaries which can save time downstream, and
    material property allocation. Some of the other people at our school like
    the direct link to COMSOL also.
    3D Slicer appears to be powerful, but there will be others more experienced
    in it than me. I did have problems with it crashing heaps several releases
    ago on a particular operation I needed to do but I understand that bug is
    fixed now.
    MIMICS also seems powerful, but I cannot say much more about it.

    Andrew Sims
    PhD Student
    University of New South Wales
    Sydney, Australia
    a.sims@student.unsw.edu.au
    +61 2 9385 3916
    ------------------------------------------------------------------------
    Have you tried MIMICS or one of their other products? I think 3-Matic is
    another one of their conversion products.

    Lieselle

    Lieselle Trinidad
    Doctoral Candidate
    Mechanical Engineering Deptartment
    E-Lab Building, Complex 207e
    160 Governors Drive
    Amherst, MA 01003
    ---------------------------------------------------------------------------
    Good afternoon,

    MIMICS from Materialise does a fantastic job of this task - it can export to
    IGES as well as a number of other engineering formats. We use it in our lab
    to deal with CT imaging and finite element analysis.

    Have a good one,

    Dan
    -----------------------------------------------------------------------------
    Hello Dr. Siva

    There are many software packages that convert image data (dicom) to models
    (.iges, .vtk, .stl). Some of the well-known ones are ScanIP, Slicer, and
    Mimic. Slicer is open source, so it is free. It is fairly intuitive. You
    can download Slicer from www.slicer.org. Depending on your application, the
    output models from Slicer may need to be smoothed in order to run FE
    analyses.

    Good luck!

    Saikat Pal
    Post doc
    Department of Bioengineering
    Stanford University
    --------------------------------------------------

    Dr. Siva,

    I use SliceoMatic (Tomovision, Montreal, Canada) to segment my MR images and
    turn them into 3-D polygon surfaces for FEA analysis. This program allows
    you to use several different semi-automated techniques to segment your
    images (region growing, snakes, thresholding, etc.). It also allows you to
    save your solid model in a variety of formats (i.e. stl,mov,dxf,VRML) for
    processing. I'm not sure if it is the best software out there but it is user
    friendly and fairly easy to use. I hope this helps. Thanks.

    Shawn Farrokhi, DPT
    PhD Candidate
    Musculoskeletal Biomechanics Research Laboratory
    Division of Biokinesiology and Physical Therapy
    School of Dentistry
    University of Southern California
    1540 East Alcazar St. CHP-155
    Los Angeles, CA 90089
    -------------------------------------------------------------------------
    Hello Dr. Sivasankar,

    We use a version of the Mimics software from Materialise (
    http://www.materialise.com/materialise/view/en/92462-Why+choose+Mimics.html)
    to help us convert our CT data to iges/ and stp files. I am in the dental
    implant industry with a focus on guided surgery. This software/ company, I
    believe will do what you need it to.

    Thanks,
    Alexis Goolik
    Project Manager
    Biomet 3i
    Palm Beach Gardens, FL USA
    ----------------------------------------------------------------
    Dear Dr. Sivasankar,

    You may try

    http://www.ablesw.com/

    and there are two more software's like SurfDriver and
    http://www.visageimaging.com/pdf/amira_web.pdf.

    I guess there is a demo for these software's that you can try. Hope this
    helps.

    Srianjana.
    ----------------------------------------------


    On Tue, Jun 2, 2009 at 4:07 PM, Dr.M.Sivasankar wrote:

    > Hi,
    > Greetings , I am Dr.Sivasankar from India. One of my research
    > students has come across a problem while scanning the femoral bone for the
    > finite element analysis, he got the scanned image from the Orthopaedic
    > hospital and wants to bring that image into the FEA software as IGES file
    > for the analysis. But we could not able to find a suitable software to
    > convert that scanned image (DICOM) to IGES, could you please help him in
    > converting this scanned image to IGES file. Results will be collected and
    > published in this same thread. Good day to you all.
    > Best regards,
    > Dr.Siva.
    >
    >
    > --
    > -------------------------------------------------
    > "To
    > win...you must stay in the game"
    >
    > Prof.Dr.M.Sivasankar
    > Ph.D
    > Professor,
    > Dept of Mechanical Engg,
    > Arunai Engg
    > College,
    > Tiruvannamalai
    > Tamilnadu, India, Asia.
    > PIN:606603
    >
    > please send a cc to sivasankar.iitg@gmail.com
    >
    >
    > ---------------------------------------------------------------
    > Information about BIOMCH-L: http://www.Biomch-L.org
    > Archives: http://listserv.surfnet.nl/archives/Biomch-L.html
    > ---------------------------------------------------------------
    >



    --
    Prof.Dr.M.Sivasankar.Ph.D
    Professor,
    Department of Mechanical Engineering,
    Director (Centre for Biomedical Engineering),
    Arunai Engineering College,
    Tiruvannamalai,
    Tamilnadu,
    South India.
    ASIA.PIN:606603
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