Visualization of 5d Nifti RGB images in Anatomist

[ylep]

Hi fellow BrainVISA users,

It seems that Nifti has two ways of encoding RGB images:

• the NIFTI_TYPE_RGB24 data type,
• or images encoded as a 5-dimensional array of size (x, y, z, 1, 3), possibly having nifti_intent = NIFTI_INTENT_RGB_VECTOR = 2003.

The former type is handled very well by Anatomist. I was wondering if there was a way to visualize the latter type (5d) in Anatomist? I can get such an image to load as a multi-channel greyscale visualization, but could not find a way to display it as RGB.

[denisri]

In Aims/Anatomist we don't really use the intent code, which is rather a hint on how to interpret the data. We could of course build a RGB/RGBA volume from such a file but there is currently no automatic conversion tool.
We could add support for it and read it as a RGB volume, but is it always what the user will expect ?
Should the two shapes you mention be equivalent ? (and if so, why having those 2 shapes ?)
However the fact is that we cannot currently reinterpret the 5D volume as a RGB volume (using strides), because the Aims RGB volumes assume the voxels are a tight structure {R, G, B} (AimsRGB class in C++), channels cannot be split or bound without duplicating the data, and we don't have a notion of RGB defined via separate channels.

[denisri]

I have a proposal in a feature branch of anatomist: a new fusion type in Anatomist taking a 5D volume and building a RGB or RGBA volume. But it needs a user action (or a line of code in a program) to be done. Would that suit your needs ?
feature branch: vol5d
brainvisa/anatomist-free@bf9a4ed

[ylep]

Thanks a lot @denisri, the new Fusion works great for visualizing my 5D RGB data! I have created a pull request, feel free to merge it if you think it is ready for release!