Combine orthogonal stacks

Dear Experts,

I don’t know if this is even possible, but I’m hoping you can help. I have 3 clinical T1 scans in NIFTI format:

one has good resolution in the axial plane

one has good resolution in the coronal plane

one has good resolution in the sagittal plane

My dream is to combine the 3 orthogonal planes into a single high-resolution 3d image.

Is such a thing possible? Does anyone have suggestions?

Thanks so much,


Hi Dianne (@dkp),

Welcome to the forum!

It certainly is possible, but I’m afraid there is no single “standard” way to accomplish it. And because of that, there are not plugins / algorithms available in standard software for it (afaik).

Okay, correction: this is kind-of like “image fusion” that happens after “stitching.”
It may be worth trying to “stitch” then “fuse” your datasets. BigStitcher is a nice tool for this.

The first step that would need to happen is that all the volumes would need to be registered / aligned. When I tried this (long ago), small errors in the alignment ended up having the effect of “blurring” the result, and so it wasn’t really worth it.

Is there a particular task that you’d like to use the higher resolution 3d volume to do?


Edit: pointed to bigstitcher

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We have stroke data and we need to map the lesion.

On research scans, we do this mapping in 3D. It is more cumbersome to load the 3 separate clinical images and draw.

Thanks for the insight. I’ll have a look at BigStitcher.


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