Hi, I created and wrote the image on the disk using ITK 4.6.0. I visualized the image using Slicer 4.4.0.
The properties are: Size : [1001, 1001, 8345] Spacing : [1,1,1] Origin : [0, 0, 0] Direction : 1 0 0 0 1 0 0 0 1 Fotis On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <blowek...@mail.nih.gov> wrote: > Hello, > > What software did you use to create and validate that this image is > correct? > > Thanks, > Brad > > On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <fdrak...@gmail.com> wrote: > > Hi all, > > I added a big test image to ITK/Public/ITK/Modules/IO/NIFTI/test/Input. > The image cannot loaded correctly when I use the itk::ImageFileReader. > The test image contains non-zero values only at indexes (350,350,i) where > i=0 to 8300. > The pixelType is short. > > Thanks > Fotis > > On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick < > matt.mccorm...@kitware.com> wrote: > >> Thanks! Added. >> >> On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrak...@gmail.com> >> wrote: >> > Hi, >> > I signed up for the ITK community on midas. >> > >> > Thanks, >> > Fotis Drakopoulos >> > >> > On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick >> > <matt.mccorm...@kitware.com> wrote: >> >> >> >> Hi Fotis, >> >> >> >> Thanks for helping to improve large nifti file support. >> >> >> >> The file can be uploaded on midas3.kitware.com. Sign up for the ITK >> >> community [1], let the list know the name of your account, and myself >> >> or one of the other administrators will add upload priviledges to the >> >> account. >> >> >> >> The file could then be added to >> >> ITK/Public/ITK/Modules/IO/NIFTI/test/Input. >> >> >> >> Thanks, >> >> Matt >> >> >> >> [1] http://midas3.kitware.com/midas/community/12 >> >> >> >> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <fdrak...@gmail.com >> > >> >> wrote: >> >> > 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 >> >> > <blowek...@mail.nih.gov> >> >> > 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 <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 >> >> >> >> >> >> >> >> >> ________________________________ >> >> >> >> >> >> Spam >> >> >> Not spam >> >> >> Forget previous vote >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > 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 >> >> > >> >> >> >> >> >> -- >> >> >> > >> >> >> -- >> BEGIN-ANTISPAM-VOTING-LINKS >> ------------------------------------------------------ >> >> Teach CanIt if this mail (ID 03NkpHcqT) is spam: >> Spam: about:blank >> Not spam: about:blank >> Forget vote: about:blank >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> >> > > ------------------------------ > > Spam > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=s> > Not spam > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=n> > Forget previous vote > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmDyijL&m=0a26c0248a9e&t=20141202&c=f> >
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