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Re: [SCIRUN-USERS] Importing .nrrd failed


Chronological Thread 
  • From: Jess Tate <jess@sci.utah.edu>
  • To: Andjela Davidovic <andjela.davidovic@inria.fr>
  • Cc: scirun-users@sci.utah.edu
  • Subject: Re: [SCIRUN-USERS] Importing .nrrd failed
  • Date: Wed, 29 Jul 2015 13:28:32 -0600
Hi Andjela,

I think that SCIRun4 does not like the commas in the spacing and axis fields.  Try changing them to periods:
spacings: 0.20000000000000001 0.20000000000000001 0.20000000000000001
axis mins: -0.10000000000000001 -0.10000000000000001 -0.10000000000000001

it is possible that SCIRun5 is reading them incorrectly, but it is hard to say without see what you did.  To combine the three fields into one vector (this will work in SCIRun4 too), use CalulateFieldData, put the three field as inputs, then use parser code like this:
RESULTS=vector(DATA1,DATA2,DATA3);
Assuming that the order of inputs was the X,Y,Z components of the vectors.  

Does that help?

cheers,
Jess




On Jul 29, 2015, at 1:14 PM, Andjela Davidovic <andjela.davidovic@inria.fr> wrote:

Hi,

I have some files in .vtk format. These are MRI images of the heart and DT vector files for fiber orientations. I want to read them with SCIRun. I did the following:
- take one vector .vtk file and convert it into 3 scalar .vtk files.
- import these files ,vtk files into Seg3D and export them, unchanged as .nrrd files. - this worked, as I was able to import them back into seg3d.
Now I want to use SCIRun4, in order to create and visualise fibers (and later on to map them to the segmentation - since I am not going to use the whole heart data).
The problem is that SCIRun4 does not want to import them - it says there is a spacing error.

The header of one of these files looks like this:

NRRD0001
# Complete NRRD file format specification at:
# http://teem.sourceforge.net/nrrd/format.html
type: float
dimension: 3
sizes: 64 64 128
spacings: 0,20000000000000001 0,20000000000000001 0,20000000000000001
axis mins: -0,10000000000000001 -0,10000000000000001 -0,10000000000000001
centerings: cell cell cell
endian: little


SCIRun5 imports them, but it does not plot what I would like to see, although maybe I am plotting it wrong.
And anyway, in SCIRun5 I did not find the module to crate a vector field out of 3 scalar fields.

Any advice?

Andjela


--
Andjela Davidovic
PhD Student, CARMEN team
INRIA
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