[ITK-users] [ITK-dev] Problem reading a big nifti volume.

Tue Dec 2 10:27:28 EST 2014

Hello,

What software did you use to create and validate that this image is correct?

Thanks,
Brad

On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:

> Hi all,
> 
> I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. The image cannot loaded correctly when I use the itk::ImageFileReader.
> The test image contains non-zero values only at indexes (350,350,i)  where i=0 to 8300.
> The pixelType is short.
>  
> Thanks
> Fotis  
> 
> On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <matt.mccormick at kitware.com> wrote:
> Thanks! Added.
> 
> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at gmail.com> wrote:
> > Hi,
> > I signed up for the ITK community on midas.
> >
> > Thanks,
> > Fotis Drakopoulos
> >
> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick
> > <matt.mccormick at kitware.com> wrote:
> >>
> >> Hi Fotis,
> >>
> >> Thanks for helping to improve large nifti file support.
> >>
> >> The file can be uploaded on midas3.kitware.com.  Sign up for the ITK
> >> community [1], let the list know the name of your account, and myself
> >> or one of the other administrators will add upload priviledges to the
> >> account.
> >>
> >> The file could then be added to
> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.
> >>
> >> Thanks,
> >> Matt
> >>
> >> [1] http://midas3.kitware.com/midas/community/12
> >>
> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrakopo at gmail.com>
> >> wrote:
> >> > Hi all,
> >> >
> >> > I created a test nifti image that reproduces the problem I mentioned
> >> > before.
> >> > How can I share this image with the ITK community?
> >> >
> >> > Best,
> >> > Fotis Drakopoulos
> >> >
> >> >
> >> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
> >> > <blowekamp at mail.nih.gov>
> >> > wrote:
> >> >>
> >> >> Shareable test data greatly helps determine the cause and fix these
> >> >> types
> >> >> of issues.
> >> >>
> >> >> Got data?
> >> >>
> >> >> Brad
> >> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> >> >>
> >> >> This is reminiscent of the previous problem with big TIFF images, now
> >> >> fixed.
> >> >>
> >> >> Gib
> >> >> ________________________________
> >> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
> >> >> Drakopoulos [fdrakopo at gmail.com]
> >> >> Sent: Monday, 24 November 2014 10:51 a.m.
> >> >> To: insight-users at itk.org; insight-developers at itk.org
> >> >> Subject: [ITK-users] Problem reading a big nifti volume.
> >> >>
> >> >> Hi all,
> >> >>
> >> >> For the last couple of days I have been trying reading (unsuccessfully)
> >> >> a
> >> >> big nifti volume labeled image from my disk.
> >> >>
> >> >> The pixel type is unsigned char and the rest specs of the image are:
> >> >> Size : [1001, 1001, 8345]  (in voxels)
> >> >> Spacing : [0.012, 0.012, 0.012]  (in mm)
> >> >> Origin : [0, 0, 0]
> >> >> Direction :
> >> >> 1 0 0
> >> >> 0 1 0
> >> >> 0 0 1
> >> >>
> >> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea
> >> >> how it looks like. Indeed the object in the volume looks as it was
> >> >> expected.
> >> >> So far no problems. The specs of the image on Slicer are the same as
> >> >> above
> >> >> (except the direction which has flipped signs for the first two
> >> >> diagonal
> >> >> entries, as we know ).
> >> >>
> >> >> Then I tried to load the image in the memory using the
> >> >> itk::ImageFileReader  from ITK4.6.0 (64 bit-linux) version. After
> >> >> loading
> >> >> the image I noticed that there are pixels with zero values instead of
> >> >> non-zero by comparing the same indexes with the loaded image on Slicer.
> >> >>
> >> >> Then I decided to write the loaded image on the disk using the
> >> >> itk::ImageFileWriter.
> >> >>
> >> >> After opening the (written from ITK) image on Slicer I checked the
> >> >> specks
> >> >> and were the same with the original image as above. However I noticed
> >> >> that a
> >> >> big portion of the image is completely empty (black)!
> >> >>
> >> >> My workstation has enough memory to load the image (768 GB 1600MHz
> >> >> DDR3L)
> >> >> and is using Red Hat Enterprise Linux Server 6.5.
> >> >> The size of the original nifti volume is :
> >> >>
> >> >> 25.7 MB (.nii.gz)
> >> >> 8.36 GB (.nii)
> >> >>
> >> >> Has anybody experienced similar difficulties trying to load so big
> >> >> volume
> >> >> data?
> >> >>
> >> >> Best,
> >> >> Fotis Drakopoulos
> >> >> CRTC
> >> >>
> >> >> _____________________________________
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> >> >>
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> >> >>
> >> >> ________________________________
> >> >>
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> >> >
> >> >
> >> >
> >> > _______________________________________________
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