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[SCIRUN-USERS] Shifting of the files

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  • From: Andjela Davidovic <>
  • To:,
  • Cc: Jess Tate <>, ayla <>
  • Subject: [SCIRUN-USERS] Shifting of the files
  • Date: Tue, 4 Aug 2015 06:18:13 +0200 (CEST)


It seems there is some problem with file import/export in Seg3D and SCIRun, with spacings and origins. 

So, my original files are of the following formats in .vtk:
MRI data: 256x256x512, spacing  0.05, 0.05, 0.05,  origin 0, 0, 0
Fibers files: 64x64x128, spacing 0.2, 0.2, 0.2, origin 0, 0, 0

Then I use Seg3d to segment my MRI data, and for some reason the output of the segmentation in .nrrd format becomes:
256x256x512, spacing  0.05, 0.05, 0.05,  origin  -0.025, -0.025, -0.025

I also use Seg3d to convert Fiber files in .nrrd format, and for some reason th output becomes
64x64x128, spacing 0.2, 0.2, 0.2, origin -0.1, -0.1, -0.1

This messes finally also with the size of the domain, and then SCIRun thinks that the data are not of the same size, and does not want to ComputeFieldData - in order to project fibers onto segmentation.

I tried to use Transform in Seg3d, to force origin to 0, 0, 0, and it appears to work at first. When I open the file in vi it shows origin at 0, 0, 0, but when I import file in SCIRun it seems to be shifted again and of the wrong size.

Any advice?


Andjela Davidovic
PhD Student, CARMEN team

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