[Elastix] Syntax for reading raw data..?

S. Klein s.klein at erasmusmc.nl
Fri May 9 16:05:07 CEST 2014


Hi David,
It would be possible with a bit of hacking. You could extend the 2D transform parameter file to 3D transformation, by changing the transform parameters (depending on which transform you use, you need to add a number of "dummy parameters", such that the transformation remains the same for all frames/bands, and you need to modify the definitions of the resample domain (Size, Spacing, Origin, Index).
Best,
Stefan

On 09/05/2014 14:42, McInnis, David wrote:

Is there a way to have transformix  apply the transform to just a certain range of bands?  This is where to IO hit would be the worst if I had to split the cubes, apply, then reassemble.

BTW, I learned that the 'raw' output is actually ENVI's format (raw plus a header file meant for envi).  Quite nice.

On May 9, 2014 6:41 AM, "S. Klein" <s.klein at erasmusmc.nl<mailto:s.klein at erasmusmc.nl>> wrote:
Hi David,
No, it's better to split as separate 2D files. As they are just 2D files, the amount of IO time should not be too much, relative to other tasks such as the registration itself.
Kind regards,
Stefan

On 08/05/2014 18:32, McInnis, David wrote:
Sounds like a good idea, thanks Stefan.

Is there a way to use a specific band in a cube as the fixed image and another as the moving?
Or would I need to pull the bands out as separate 2D image files?

I'm assuming this is not possible, but thought I'd ask.
It's trivial to pull the slices but I'd like to take the resulting transform and apply it to a certain range of bands within the cube.  Not to the whole cube.
I could split the cube, apply the transform to one piece, and reassemble..  but the IO time would double.

 ( These are spectral cubes: spatial, spatial, spectral. )








On Thu, May 8, 2014 at 11:12 AM, S. Klein <s.klein at erasmusmc.nl<mailto:s.klein at erasmusmc.nl>> wrote:
Hi David,
It is not directly possible like this.
The most easy solution would be to write a little .mhd header file next to your .raw file.
In the elastix example, there is an example .mhd/.raw file. Just open it with a text editor, and you will probably figure out how it works.
Cheers,
Stefan


On 08/05/2014 17:07, McInnis, David wrote:
Hi,

I'm just learning about Elastix and am trying to figure out how to read in raw data cubes.
I got as far as finding the module:  ITKIORAW   at    http://www.itk.org/Doxygen45/html/group__ITKIORAW.html
but I'm not a great coder and cannot find where the syntax structure is.   And how would it translate to Elastix's syntax?

In ITK's own software guide they simply say you can read raw files..  but should avoid doing so with medical data.   :-/

Anyway I tried guessing, without luck:
>   elastix -f myfile.dat 800 600 712 2<tel:800%20600%20712%202>   ...
meaning a 712 band cube of 800x600 as 2B ints

Anyone have a clue?

Thanks,
David


btw..  I may not be much of a coder but I do appreciate how well Elastix is written and commented and documented (ummm..  excepting my question :-)   ).    This is just beautiful work.





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Stefan Klein
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David McInnis  -  MTEQ Inc
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--
Stefan Klein
+31 10 7043442<tel:%2B31%2010%207043442>
http://www.bigr.nl/people/StefanKlein


--
Stefan Klein
+31 10 7043442
http://www.bigr.nl/people/StefanKlein
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