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RE: [shapeworks-users] NRRD Files Not Loading Properly


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  • From: Murat Maga <maga@uw.edu>
  • To: "shapeworks-users@sci.utah.edu" <shapeworks-users@sci.utah.edu>, "salewis@buffalo.edu" <salewis@buffalo.edu>
  • Subject: RE: [shapeworks-users] NRRD Files Not Loading Properly
  • Date: Fri, 6 Sep 2019 04:06:20 +0000
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I assume what it means that the XYZ dimensions of the individual datasets are
not the same.

Assuming you used 'segment editor' to create your mandible meshes (and
Segmentations module to convert them to labelmaps). If so, install the
'segment registeration' extension of Slicer, and choose one of your samples
as reference, and rigidly register each against them. That will preserve the
geometry of the segment, while making sure that they all have the same grid
structure. You can then export to labelmap and try again.

By the way setting the voxel spacing to 1,1,1mm arbitrarily is a bad idea if
your original volumes have not this resolution. Basically you are messing
with the spatial scale of your data. If your input volumes are higher spatial
resolution, consider using ResampleScalarVolume to bring them to 1x1x1mm.



-----Original Message-----
From: shapeworks-users-request@sci.utah.edu
<shapeworks-users-request@sci.utah.edu> On Behalf Of salewis@buffalo.edu
Sent: Thursday, September 5, 2019 8:01 PM
To: shapeworks-users@sci.utah.edu
Subject: [shapeworks-users] NRRD Files Not Loading Properly

Hi, I am new to ShapeWorks and am having a problem loading in my NRRD files.
I have created several mandible meshes that I converted to binary labelmaps
using 3D Slicer and when I go to import them it loads the first, but says the
subsequent ones do not have the same spacing. However, when creating the
binary meshes I made sure that the voxel spacing was set to 1mmX1mmX1mm and
that the image origin was set to 0,0,0. Finally, all of the image directions
are set to [[-1,0,0], [0,-1,0], [0,0,1]]. What else can I do to get the files
to work?

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