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

[Fotis Drakopoulos]

Hi  Jerome,

Yes, I correctly specified the pixel type to unsigned char.

On Sun, Nov 23, 2014 at 5:15 PM, Jerome Plumat <j.plumat at auckland.ac.nz>
wrote:

>  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
>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects athttp://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:http://public.kitware.com/mailman/listinfo/insight-users
>
>
>  ------------------------------
>
> Spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=01Njag6QE&m=e24f9d3be5a0&t=20141123&c=s>
> Not spam
> <https://www.spamtrap.odu.edu/canit/b.php?i=01Njag6QE&m=e24f9d3be5a0&t=20141123&c=n>
> Forget previous vote
> <https://www.spamtrap.odu.edu/canit/b.php?i=01Njag6QE&m=e24f9d3be5a0&t=20141123&c=f>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/insight-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-developers/attachments/20141123/3fcee160/attachment-0001.html>