[Insight-users] MetaIO, large volume (>2GB) and HeaderSize

[Bill Lorensen]

Looks like a bug to me.


On Thu, Apr 18, 2013 at 12:03 PM, Simon Rit
<simon.rit at creatis.insa-lyon.fr>wrote:

> Sorry if I did not make myself clear: I have solutions for this (here
> I used HeaderSize = -1), I'm actually reporting what I consider being
> a bug! By the way, your solution will result in reading the whole
> image, I would rather use Matt's solution which might read only what's
> required.
> Thank you for your help and sorry for not being clearer. If you
> consider this a minor issue, I'll just keep in mind the limitation of
> HeaderSize to 2GB. But my advice would be to consider replacing int by
> something more robust, e.g., size_type...
> Simon
>
> On Thu, Apr 18, 2013 at 5:57 PM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
> > Hello Simon,
> >
> > If you need a quick way to mung an image file SimpleITK is very good for
> this purpose. In Python it'd just be:
> >
> > import SimpleITK as sitk
> > img = sitk.ReadImage("myfile.mhd")
> > sitk.WriteImage(img[:,:,-1], "outfile.mhd")
> >
> > Brad
> >
> > On Apr 18, 2013, at 11:16 AM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
> wrote:
> >
> >> It is a lot handier to directly modify the header file rather than
> >> adding an optional extract filter in my software with the gui (here,
> >> http://vv.creatis.insa-lyon.fr/). And it does not change the fact that
> >> this is a bug or a limitation of MetaIO...
> >>
> >> On Thu, Apr 18, 2013 at 5:07 PM, Matt McCormick
> >> <matt.mccormick at kitware.com> wrote:
> >>> Hi Simon,
> >>>
> >>> Hacking the .mhd file may not be a good way to select a slice.
> >>> Instead, try something like
> >>> http://www.itk.org/Doxygen/html/classitk_1_1ExtractImageFilter.html.
> >>>
> >>> MetaIO is maintained alongside ITK/VTK.
> >>>
> >>> HTH,
> >>> Matt
> >>>
> >>> On Thu, Apr 18, 2013 at 2:55 PM, Simon Rit
> >>> <simon.rit at creatis.insa-lyon.fr> wrote:
> >>>> Hi,
> >>>> I'm using the mhd format to read one slice of a 4GB raw volume. At
> >>>> some point, I wanted to display the last slice of my volume so I put
> >>>> "HeaderSize = -1" at the beginning of my mhd file which was pointing
> >>>> to the raw data. Doing the same with the exact position, i.e.,
> >>>> "HeaderSize = 4278190080" failed... I found out that m_HeaderSize is
> >>>> an int in metaImage.cxx so the value is read as negative.
> >>>> Is this a bug or a known limitation? In the second case, any
> >>>> alternative suggestion? In the first case, where should I report this
> >>>> since it's a third party library?
> >>>> Thanks,
> >>>> Simon
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