Running GeodesicDepthMain

[iamjoostjanssen]

Hi,

Our goal: to run the geodesic depth binary (GeodesicDepthMain).

Within our docker container we can run the mindboggle command (from command line) and use it to generate e.g. traveldepth AND geodesic depth. we can also run the TravelDepthMain binary: TravelDepthMain:

/root/mindboggle/vtk_cpp_tools/bin/travel_depth/TravelDepthMain Usage: TravelDepthMain [Options] InputVTKMesh MeanCurvatureOutput Options: -n: Normalize the output values beteween 0 and 1 -w outputWrapperMesh: export the wrapper mesh Example: TravelDepthMain -n -w wrapper.vtk lh.pial.vtk lh.travel_depth.vtk

but when we run the GeodesicDepthMain binary we get: ERROR: In /home/maxcg/miniconda3/conda-bld/work/VTK-7.0.0/IO/Legacy/vtkDataReader.cxx, line 392 vtkPolyDataReader (0x22ed230): No file specified!

ERROR: In /home/maxcg/miniconda3/conda-bld/work/VTK-7.0.0/Filters/Core/vtkHull.cxx, line 495 vtkHull (0x22fb0f0): There must be >= 3 points in the input data!!!

ERROR: In /home/maxcg/miniconda3/conda-bld/work/VTK-7.0.0/Filters/Core/vtkSmoothPolyDataFilter.cxx, line 331 vtkSmoothPolyDataFilter (0x2309300): No data to smooth!

ERROR: In /home/maxcg/miniconda3/conda-bld/work/VTK-7.0.0/Common/DataModel/vtkCellLocator.cxx, line 1213 vtkCellLocator (0x230e210): No cells to subdivide

Euclidean depth allocated for very close points Geodesic depth computed ERROR: In /home/maxcg/miniconda3/conda-bld/work/VTK-7.0.0/IO/Legacy/vtkDataWriter.cxx, line 163 vtkPolyDataWriter (0x230e210): Unable to open file: VTK_DIR=/usr/local/miniconda//lib/cmake/vtk-7.0

vtk file written Elapsed time (geodesic depth): 0 s

Any pointers?

[iamjoostjanssen]

Solved.

[binarybottle]

@iamjoostjanssen -- How did you resolve this issue?

[iamjoostjanssen]

If you provide GeodesicDepthMain with the required inputs it runs. It thus appears that in our docker mindboggle distribution when running TravelDepthMain as a standalone without any input will give the Usage options whereas GeodesicDepthMain does not.

[binarybottle]

Thank you!