[Insight-users] 3D Resampling
Luis Ibanez
luis.ibanez at kitware.com
Thu May 4 09:21:00 EDT 2006
Hi Kevin,
Thanks for letting us know that you found the solution
to the problem.
Regards,
Luis
=================
Kevin Ming wrote:
> Hi Luis,
>
> Just wanted to let you know that we were able to figure out the
> resampling problem: The z = 0 spacing for the image was incorrect, and
> the resampling worked fine once the appropriate changes have been made
> to header file and the algorithm. Also, for the brightness and contrast
> issue, it's due to the fact that the ANALYZE format we work with are
> 32-bit images, so once we convert it to 8-bit ones the algorithm no
> longer gives us any problems.
>
>
> Thank you for all your help,
> Kevin
>
> On 5/2/06, *Kevin Ming* <ming.kevin at gmail.com
> <mailto:ming.kevin at gmail.com>> wrote:
>
> Hi Luis,
>
> Let me know if you need further information.
>
>
> Thank You,
> Kevin
>
>
> On 5/2/06, * Luis Ibanez* < luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>> wrote:
>
>
> Hi Kevin,
>
>
> You can upload the image at the following web link:
>
> http://www.kitware.com/KitwareScripts/uploadfile.cgi
>
>
> Please include all the information you have about the
> Bruker file format.
>
>
> Thanks
>
>
> Luis
>
>
>
> =====================
> Kevin Ming wrote:
>> Hi Luis,
>>
>> I've confirmed the following spacing specs for my image:
>>
>> x = 0.1 mm
>> y = 0.1 mm
>> z = 1 mm
>>
>> *But* the resampling only seems to kind of work for x = 0.01
> mm and y =
>> 0.01 mm, "kind of" meaning only the 1st slice shows up
> correctly, all
>> other slice our black. For the z spacing, I've tried quite a few
>> different kinds of values between 0.001 mm and 2 mm (inclusive),
>> including 1 mm of course, and the same problem persists.
>>
>> All the MRI images that I have come directly from the MR
> imaging centre,
>> where I participate in the imaging process as well, so the images
>> themselves should be of no problem. But agian, the raw data I
> get are
>> in the Bruker format (the company that made the MRI machine),
> so I have
>> to convert them into ANALYZE format and go from there. Would
> it help if
>> I sent you the images?
>>
>> Thank You,
>> Kevin
>>
>> On 5/2/06, *Luis Ibanez* < luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>
>> <mailto:luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>>> wrote:
>>
>>
>>
>> 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>
>> <mailto: luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>>
>> > <mailto: luis.ibanez at kitware.com
> <mailto:luis.ibanez at kitware.com>
>> <mailto: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
>> > >>
>> > >>
>> >
>>
> ------------------------------------------------------------------------
>> > >>
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