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 <[email protected]> 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 <[email protected]> wrote: > > This is reminiscent of the previous problem with big TIFF images, now > fixed. > > Gib > ------------------------------ > *From:* Insight-users [[email protected]] on behalf of Fotis > Drakopoulos [[email protected]] > *Sent:* Monday, 24 November 2014 10:51 a.m. > *To:* [email protected]; [email protected] > *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 > > > ------------------------------ > > Spam > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s> > Not spam > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n> > Forget previous vote > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f> >
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