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miykael / gif_your_nifti

How to create fancy GIFs from an MRI brain image
BSD 3-Clause "New" or "Revised" License
113 stars 31 forks source link

Add overlay? #8

Open EmilyLars opened 3 years ago

EmilyLars commented 3 years ago

Might it be possible to visualize two images, anatomical base with an overlay with a different color scheme?

ofgulban commented 3 years ago

Hi @EmilyLars , thanks for opening this issue. Do you mean an overlay to show activation maps etc. ? This is possible but needs to be implemented. I might have a look into it.

EmilyLars commented 3 years ago

Yes - I do structural imaging but same idea - I'm imagining a figure where I've color coded certain brain structures or cluster to display my results. Could be really useful to use your tool to scan through instead of having to show all the different slices. Thank you!

miykael commented 3 years ago

Yes, that might be useful. However, the problem with these gifs are that you cannot really stop them. So for some results the loop might be too fast or not focused enough.

Perhaps something like nilearn's plotting rountines might be better for this? For example the glass_brain plot could be used for a quick overview of your results. Nilearn also has an interactive visualization plot feature which allows you to scroll through the images. And if you want to have everything automaed, what about atlasreader to quickly create a multitude of figures and output tables?

ofgulban commented 3 years ago

@miykael I think @EmilyLars means the gif as a complementary figure (to other interactive visualizers) to give a quick impression of the activation blobs. I can imagine that e.g. in a blog post such animation would convey the 3D extend of the more easily.

EmilyLars commented 3 years ago

Yes I agree - alone it would be hard to appreciate the results but could be a useful complement for talks for example

araikes commented 5 months ago

@miykael,

I'll just give this a small bump. I working on mask generation for rodent brains and the GIFs work with my brains. Being able to overlay the mask or an atlas would be helpful as a QC step. If there's a way to that, I'd be very interested.