hi, ShapeWorkers,

Thank you for developing this great tool!

I am trying to use ShapeWorks to model the shape of hippocampus.

I try to use the binary release on all three platforms but encounter similar problems. I have attached an example file in a link. The file is converted to nrrd from nifti using Convert3D.

FYI, I can successfully run the example you provide. So I think the problem may be at parameter selection for this particular shape. However, I did try a range of parameters but had similar problem.

The first problem is at Groom: if I select center or autocrop, it will generate an empty image. This is ok, since I can use other methods to align and crop them. But it would be great if I can do it in this pipeline.

The second and third problem are at Optimization and seem related to the Groom settings. The problem should be replicated using default parameter settings.

If I use fastmarching in Groom, I will get following error. I didn't provide any initial points.

itk::ExceptionObject (0x7fa989f89448)

Location: "typename PointListType::iterator itk::PowerOfTwoPointTree<3>::AddPoint(const PointType &, unsigned int, NodePointerType &) [VDimension = 3]" 

File: /shapeworks-1.4/src/ITKParticleSystem/itkPowerOfTwoPointTree.txx

Line: 125

Description: itk::ERROR: PowerOfTwoPointTree(0x7fa98a8013e0): Point [13.8866, 10.9929, 22.8239] is not contained within tree domain [-129.496, 115.37, 163.315] - [126.504, -140.63, -92.6846]

If I don't use fastmarching in Groom, the program will stuck. In Linux, it kept generating empty output.

Thank you very much!

Michael X. Feng

Columbia University

File: https://www.dropbox.com/s/kiovmmh0ek29ow8/HippoMask1_bin.nrrd?dl=0

HippoMask1_bin.nrrd www.dropbox.com Shared with Dropbox