[ITK] [ITK-dev] [ITK-users] Problem reading a big nifti volume.

[Matt McCormick]

Thanks! Added.

On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <fdrakopo at 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.mccormick at 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 <fdrakopo at 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
>> > <blowekamp at 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.bogle at auckland.ac.nz> wrote:
>> >>
>> >> This is reminiscent of the previous problem with big TIFF images, now
>> >> fixed.
>> >>
>> >> Gib
>> >> ________________________________
>> >> From: Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
>> >> Drakopoulos [fdrakopo at gmail.com]
>> >> Sent: Monday, 24 November 2014 10:51 a.m.
>> >> To: insight-users at itk.org; insight-developers at 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
>> >>
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