How to extract brain to STL when I have 3 different files with one HD resolution in one direction each?


I am trying to do it for such a long time and find no answer anywhere.

I have few files from my brain MRI and I am trying to extract it to STL file so I can 3D print it.
I have been trying to do it with FreeSurfer (I successfully have done it with other, good volume) an Slicer, and even combinign the images with NiftyMIC but results are bad.

The problem is that scan was taken multiple times in one direction only (in T1 and T2 variants, and one with flare (but only one direction).

So I have multiple overlapping imagings and I would like to have stl model.

I can add nii.gz files if you are interested, but just give me some anonymization metod.

What I have (form my scan, best result):

What I want (done using great MRI scan and freesurfer):

Unfortunately, you cannot combine 3 anisotropic images into one high-resolution image because lots of information is missing between the slices. See this topic for more details: Combining volumes - what am I missing?

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