[vmtk-users] using vmtksurfacetransformtoras

[Hoppe, A. L <ann...@ui...>]

Hi Luca,

I'm trying to use vmtksurfacetransformtoras to convert a surface generated via vmtk in xyz image space to RAS space. The script I'm using is this:

vmtkimagereader -ifile /path/image_volume.dcm --pipe vmtksurfacetransformtoras -ifile /path/surface.vtp -ofile /path/transformedtoras_surface.vtp

from the vmtk terminal output I see (among other things):
Output vmtkimagereader members:
    Id = 0
    Image = vtkImageData
    RasToIjkMatrixCoefficients = [-3.8400001464843805, 7.875971109312715e-10, 0.0, 348.0000131671146, -7.875971109312715e-10, -3.8400001464843805, -0.0, 526.7215631329591, 0.0, -0.0, 2.0, 111.08353424072266, -0.0, 0.0, -0.0, 1.0]
    XyzToRasMatrixCoefficients = [-1.0, -2.0510340648094427e-10, 0.0, 181.25000002813343, 2.0510340648094427e-10, -1.0, 0.0, 274.33413694430317, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0]
.
.
.
Input vmtksurfacetransformtoras members:
    Id = 0
    Disabled = 0
    Surface = None
    SurfaceInputFileName = /var/tmp/alhoppe/BIOMOST/Fe_MRI_Study/CFD/2319/RAS_coord_model/2319_MCA_Clipped_triangle_ex.vtp
    XyzToRasMatrixCoefficients = [-1.0, -2.0510340648094427e-10, 0.0, 181.25000002813343, 2.0510340648094427e-10, -1.0, 0.0, 274.33413694430317, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 1.0]
    SurfaceOutputFileName = /var/tmp/alhoppe/BIOMOST/Fe_MRI_Study/CFD/2319/RAS_coord_model/2319_MCA_Clipped_triangle_ex_transformedtoras.vtp

>From this output I see that the proper xyztoras matrix coefficients (identical to the xyztoras matrix coeficients from vmtkimagereader) are being read in by vmtksurfacetransformtoras. However, when I load the transformedtoras_surface.vtp into 3DSlicer, which I know uses the RAS coordinate system, the transformedtoras_surface.vtp is misaligned from the image_volume.dcm. What am I missing in my script?

Thanks for everything!
Anna Hoppe