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

[Jerome Plumat]

Hi,
Have you correctly specified the pixel type? I had similar problem and 
mine was due to pixels specifications.
Hope it helps.

Jerome Plumat
-------
School of Medical Sciences
University of Auckland

If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? – Hillel HaZaken

On 24/11/14 10:51, Fotis Drakopoulos wrote:
> 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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