[ITK-users] Reading nifti files
Cyril Mory
cyril.mory at creatis.insa-lyon.fr
Fri Mar 17 11:46:56 EDT 2017
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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