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

[Fotis Drakopoulos]

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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