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

Tue Dec 2 11:14:46 EST 2014

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 <blowekamp at 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 <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
>>> >> >>
>>> >> >> _____________________________________
>>> >> >> Powered by www.kitware.com
>>> >> >>
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>>> >> >>
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>>> >> >>
>>> >> >> Please keep messages on-topic and check the ITK FAQ at:
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>>> >> >>
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>>> >> >>
>>> >> >>
>>> >> >> ________________________________
>>> >> >>
>>> >> >> Spam
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>>> >> >
>>> >> >
>>> >> >
>>> >> > _______________________________________________
>>> >> > 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:
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>>> >>
>>> >>
>>> >> --
>>> >>
>>> >
>>>
>>>
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