[Elastix] Syntax for reading raw data..?

McInnis, David dmcinnis at mteq.com
Fri May 9 14:42:37 CEST 2014


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> 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> 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   ...
>>  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.
>>
>>
>>
>>
>>  _______________________________________________
>> Elastix mailing listElastix at bigr.nlhttp://lists.bigr.nl/cgi-bin/mailman/listinfo/elastix
>>
>>
>> --
>> Stefan Klein+31 10 7043442http://www.bigr.nl/people/StefanKlein
>>
>>
>
>
> --
> David McInnis  -  MTEQ Inc
> 505-510-1818     dmcinnis at mteq.com
> NVESD bldg 357, rm 225
> Ft Belvoir, VA
>
>
> --
> Stefan Klein+31 10 7043442http://www.bigr.nl/people/StefanKlein
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.bigr.nl/pipermail/elastix/attachments/20140509/3020ccbc/attachment.html>


More information about the Elastix mailing list