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 03Nk3J6v4) is spam: >> Spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Nk3J6v4&m=9e79d1b816aa&t=20141125&c=s >> Not spam: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Nk3J6v4&m=9e79d1b816aa&t=20141125&c=n >> Forget vote: >> https://www.spamtrap.odu.edu/canit/b.php?i=03Nk3J6v4&m=9e79d1b816aa&t=20141125&c=f >> ------------------------------------------------------ >> END-ANTISPAM-VOTING-LINKS >> > _______________________________________________ Powered by www.kitware.com
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