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: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=s > Not spam: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=n > Forget vote: > https://www.spamtrap.odu.edu/canit/b.php?i=03NkpHcqT&m=cd686a1f4aec&t=20141126&c=f > ------------------------------------------------------ > END-ANTISPAM-VOTING-LINKS > >
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