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Re: [shapeworks-users] Rescaling NRRDs for Shapeworks Studio or full install


Chronological Thread 
  • From: Shireen Elhabian <shireen@sci.utah.edu>
  • To: shapeworks-users@sci.utah.edu, Bob Cieri <bob.cieri@utah.edu>
  • Cc: Shireen Elhabian <shireen@sci.utah.edu>
  • Subject: Re: [shapeworks-users] Rescaling NRRDs for Shapeworks Studio or full install
  • Date: Mon, 2 Dec 2019 16:38:58 -0700
Hi Bob,

We have been working on a similar use case where the input is surface meshes (vtk or ply) rather than binary segmentations (volumes). The grooming pipeline starts with converting meshes to binary segmentations (and distance transforms) which have common voxel spacing, origin and image size. To convert stl to vtk or ply, please use the stl2vtk or stl2ply tools in ShapeWorks command line tools.

As of now, this pipeline is not yet merged to master. Please build from the “FemurUseCase” branch which has all of the added functionality necessary for starting from .vtk in the Python scripts.  The output of this pipeline could then. be loaded into Studio (from the release or master build) for shape model optimization. 

Hope this helps ...

thanks and best regards
Shireen


------------------------------------------
Shireen Elhabian, M.Sc., Ph.D.
Research Assistant Professor
School of Computing
Scientific Computing and Imaging Institute
University of Utah
WEB 2815
72 Central Campus Drive, Salt Lake City, UT, 84112
Phone (801) 587-3206
Fax (801) 585-6513
Home Page: http://www.sci.utah.edu/~shireen

On Dec 2, 2019, at 4:13 PM, Bob Cieri <bob.cieri@utah.edu> wrote:

Hi,

We are interested in using Shapeworks for comparative shape analysis research of long bones. It looks very promising. I've got the GUI version of the Shapeworks Studio up and running on Mac but I am having some issues getting data into the software. Most of the data I have already is in STL format. I can get it into NRRD by converting things in 3DSlicer, but I can't get the NRRDs to be the same size - I consistently get the same error when importing the NRRDS (file.nrrd does not match spacing with otherfile.nrrd).

Is there an easy way to go from STL to NRRD and use the studio build, or is better to use the FullPipelinePrepRunMeshtoDT.sh script in the full build. If so, I'm having difficulty getting the build to run on Mac but I might give it another shot. Is it typical to use cMake to compile?

Thanks,

Bob Cieri


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