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

[Fotis Drakopoulos]

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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