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

[Matt McCormick]

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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>> ________________________________
>>
>> Spam
>> Not spam
>> Forget previous vote
>
>
>
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