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.bo...@auckland.ac.nz> wrote: > This is reminiscent of the previous problem with big TIFF images, now fixed. > > Gib > From: Insight-users [insight-users-boun...@itk.org] on behalf of Fotis > Drakopoulos [fdrak...@gmail.com] > Sent: Monday, 24 November 2014 10:51 a.m. > To: insight-us...@itk.org; insight-developers@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 > > _____________________________________ > 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
_______________________________________________ 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://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-developers
