The image contains a single non-zero voxel on each axial slice. When I load the image on Slicer the non-zero voxels are preserved as you traverse the image using the window slider. When I read the image using a simple main program a big portion of the the non-zero voxels do not exist.
I had the same issue when the file was .nii (not compressed). Fotis On Tue, Dec 2, 2014 at 10:58 AM, Bradley Lowekamp <blowek...@mail.nih.gov> wrote: > So if you wrote and read with ITK ( via Slicer ), how do you know that the > file is correct as you expect? > > I see the file has a ".nii.gz" extension, meaning that it's compressed. > Does the same issue occur when it's not compressed? > > Brad > > > > On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <fdrak...@gmail.com> wrote: > > 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 >> Not spam >> Forget previous vote >> > > > ------------------------------ > > Spam > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=s> > Not spam > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=n> > Forget previous vote > <https://www.spamtrap.odu.edu/canit/b.php?i=03NmE09Ru&m=eb19ac9fd119&t=20141202&c=f> >
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