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

[Gib Bogle]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20141123/dd4d47ee/attachment.html>