[ITK-users] Reading nifti files

[Cyril Mory]

Thanks for this answer.
By manipulation, I essentially mean reading a 6D .nii file, extracting 
sub images, and writing them to .mhd format, hopefully keeping the 
correct image information throughout the process.
I'll see if my colleague can write to a more recent format, and 
otherwise follow your advice about ReadUnknownImageType.

Best,
Cyril

On 17/03/2017 16:34, Sarthak P wrote:
> For NIfTI I/O, I'd suggest you stick to the latest tags as they up to 
> date regarding the latest standards.
>
> What exactly do you mean my manipulation? There is an ITK filter to 
> change image information 
> (https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html) 
> but that only happens AFTER itk::ImageFileReader has done its work.
>
> Could you possibly try to get your collaborator to write a few images 
> using a latest variant of ITK (preferably version matched with yours 
> for consistency)? If not, then perhaps try to read the information in 
> the header using the example in 
> https://itk.org/Wiki/ITK/Examples/IO/ReadUnknownImageType and then do 
> comparisons between what you expect.
>
> All the best,
> S
>
> On Fri, Mar 17, 2017 at 11:21 AM, Cyril Mory 
> <cyril.mory at creatis.insa-lyon.fr 
> <mailto:cyril.mory at creatis.insa-lyon.fr>> wrote:
>
>     Hi ITK users,
>
>     I have recently started working with nifti files, to collaborate
>     with a colleague that uses this format. But the
>     itk::ImageFileReader does not correctly open the nifti files I
>     have (image size, offset and direction matrix are wrong). I use a
>     recent version of ITK (commit from Feb 6 18:02:49 2017), but my
>     colleague has his own fork from nifti_reg, which is several years old.
>
>     Two questions:
>     - Does someone have experience in manipulating nifti files from
>     ITK, and if so, is it supposed to work fine ?
>     - Have there been important modifications in the nifti format in
>     the last years, which the ITK reader would have followed, and
>     which could cause the issues I'm seeing when opening old ones ?
>
>     Best regards,
>     Cyril
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