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

Bradley Lowekamp blowekamp at mail.nih.gov
Tue Dec 2 10:58:40 EST 2014 

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 <fdrakopo at 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 <blowekamp at 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 <fdrakopo at 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.mccormick at kitware.com> wrote:
>> 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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>> >> >>
>> >> >> ________________________________
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>> >> >
>> >> >
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