[Insight-users] 3D Resampling

[Luis Ibanez]

Hi Kevin,


If you don't know what the spacing in your image is, you should go
back to whoever provided this image to you and obtain that information.



                      What is certain,
                is that a Z spacing of 0.0
                      is *not* real.


There is no point in having a 3D dataset with a null Z spacing...



Maybe you should go back to the tool that you used for converting
your "Bruker" file.

Maybe you should use another tool...


If your dataset has a collection of slices that are not at equal
spacing, you *will not* be able to process it with ITK anyways,
because ITK only supports datasets with uniform spacing.


You probably don't need to be concerned about brightness or
contrast until you solve the spacing issues...


What is the original source of this dataset ?



    Please let us know,


      Thanks


         Luis



=================
Kevin Ming wrote:
> Hi Luis,
> 
> I'm actually not too sure what the Z spacing should be, but when I tried 
> it with different values (e.g. 0.001, 0.01, 0.1) it gave me black images 
> for all but the 1st slice.
> 
> But in the ANALYZE format it gives me Size z (mm) = 0.00, so I assume 
> it's meant to be 0.  Actually, though, I had to convert the Bruker file 
> format into ANALYZE before using it, and during the conversion it gives 
> me something along the lines of "your slices don't appear to be 
> equi-distance, ANALYZE assuming equal spacing between slices."  Do you 
> think that may be the problem, or is it something else?
> 
> What about the brightness and contrast issues?
> 
> Thank You,
> Kevin
> 
> On 5/1/06, *Luis Ibanez* <luis.ibanez at kitware.com 
> <mailto:luis.ibanez at kitware.com>> wrote:
> 
> 
> 
>     Hi Kevin,
> 
>     Is this a typo in your email ?
> 
> 
>      >> Spacing (or in ANALYZE, Size) (mm):  x = 0.01, y = 0.01, z = 0.00
> 
> 
>     or
>     do you *really* expect the Z spacing of your 3D dataset to be NULL ?!!
> 
> 
>     If that's the actual spacing in your dataset, that can easily be
>     the source of the problems that you are experiencing.
> 
> 
>       Please let us know,
> 
> 
>         Thanks
> 
> 
>            Luis
> 
> 
>     =======================
>     Karthik Krishnan wrote:
>      > Hi Kevin
>      >
>      > I would first check if you can read your Analyze file. (There
>     have been
>      > reports in the past of certain Analyze files not being read in
>     correctly).
>      > Use InsightApplications/ImageViewer to open your Analyze file and
>     check
>      > if you see what you expect to see.
>      >
>      > bye
>      > -karthik
>      >
>      > Kevin Ming wrote:
>      >
>      >> Hi,
>      >>
>      >> I'm trying to rigidly transform some 3D image data for test in
>      >> registration, but can't seem to figure out what kind problems I'm
>      >> running into:
>      >>
>      >> 1)  The program only seems to resample the 1st out of a total of 12
>      >> slices from my 3D image, all other slices are just a repeat of the
>      >> first slice.  I tried playing around with spacing[2] = x for
>     Dimension
>      >> = 3 where x is any value greater than 0, but instead the program
>     would
>      >> give me every slice other than the 1st one black.
>      >>
>      >> 2)  Also, all the output images seem to give me really high
>     brightness
>      >> and contrast values.  For example my original images have
>     brightness =
>      >> 2204933.4355 and contrast = 4277002.0027, and the output would be
>      >> brightness = 44324303030.1732 and contrast = 9999999.0000
>     .  Does this
>      >> have to do with the fact that I changeed the InputPixelType and
>      >> OutputPixelType to float?
>      >>
>      >> In generally I think it's my spacing and maybe origin values
>     that are
>      >> creating these problems, so here are what I think they should be:
>      >>
>      >> Spacing (or in ANALYZE, Size) (mm):  x = 0.01, y = 0.01, z = 0.00
>      >> Origin (same name in ANALYZE) (vxl):  x = 0.00 , y = 0.00, z = 0.00
>      >>
>      >>
>      >> Thank You,
>      >> Kevin
>      >>
>      >>
>     ------------------------------------------------------------------------
>      >>
>      >> _______________________________________________
>      >> Insight-users mailing list
>      >> Insight-users at itk.org <mailto:Insight-users at itk.org>
>      >> http://www.itk.org/mailman/listinfo/insight-users
>     <http://www.itk.org/mailman/listinfo/insight-users>
>      >>
>      >>
>      > _______________________________________________
>      > Insight-users mailing list
>      > Insight-users at itk.org <mailto:Insight-users at itk.org>
>      > http://www.itk.org/mailman/listinfo/insight-users
>      >
>      >
> 
> 
>