FEWarp on 3D Imagestack Setup Troubleshooting

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  • shochmut
    Junior Member
    • Aug 2019
    • 3

    FEWarp on 3D Imagestack Setup Troubleshooting

    Hello,

    I am currently trying to run the FEWarp plugin on a .raw file that contains an image stack. The 3d image is 50x50x20 with 20 being the slices in the z direction.
    I am able to run the FEWarp on each slice separately but I am having trouble figuring out how to setup the mesh/geometry for the analysis on the whole 3d imagestack. How do I go about setting up the geometry/FE model for the 3d analysis? Should I be setting up a regular mesh of 20 slices stacked on top of each other and then run FEWarp with the range, template z slices, and target z slices modified to 20?

    Any help would be greatly appreciated.
    Thank you very much,

    Skyler Hochmuth
  • maas
    Lead Code Developer
    • Nov 2007
    • 3400

    #2
    Hi Skyler,

    You should be able to apply the warping to the entire image stack. Just make sure you specify the three dimension of the image stack in the size parameter. E.g.

    Code:
    <template file="temp.raw">
      <size>50,50,20</size>
    </template>
    And similarly for the target. If that does not work please send us the model file and we'd be happy to take a closer look.

    Cheers,

    Steve
    Department of Bioengineering, University of Utah
    Scientific Computing and Imaging institute, University of Utah

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