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Re: [Seg3D] [SCIRUN-USERS] Shifting of the files


Chronological Thread 
  • From: Brett Burton <bburton@sci.utah.edu>
  • To: Andjela Davidovic <andjela.davidovic@inria.fr>
  • Cc: Brett Burton <bburton@sci.utah.edu>, scirun-users@sci.utah.edu, seg3d@sci.utah.edu, Jess Tate <jess@sci.utah.edu>, ayla <ayla@sci.utah.edu>
  • Subject: Re: [Seg3D] [SCIRUN-USERS] Shifting of the files
  • Date: Tue, 4 Aug 2015 15:32:32 -0600
Hopefully there is an actual fix for getting the origins to remain unshifted, but in the meantime, I have a hack you can use.

Use AlignMeshBoundingBoxes in SCIRun to get the regions to occupy the same bounded area.  Then you should be able to map the fibers.  I have a SCIRun 4 network (not compatible with SCIRun 5) that deals with this exact issue.  I can attempt to recreate it in SCIRun 5, but some of the features will not be available.  Let us know if that works.

Brett Burton

PhD Candidate in Bioengineering | University of Utah





On Aug 3, 2015, at 10:18 PM, Andjela Davidovic <andjela.davidovic@inria.fr> wrote:

Hi,

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


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Andjela Davidovic
PhD Student, CARMEN team
INRIA
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  • Re: [Seg3D] [SCIRUN-USERS] Shifting of the files, Brett Burton, 08/04/2015

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