Hi there,

I have an animal brain's MRI with 3 volumes, each with a good resolution in one of the planes.

(i. 768x768x88, ii. 768x768x150,  iii. 768x768x140)

As far as I  understand freeSurfere doesn't have a 3D ihgh-res reconstruction tool, right?

So I tried to reconstruct a high-resolution 3D volume with NiftyMIC (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/gift-surg/NiftyMIC), but unfortunately it didn't work for me.

My final goal is to get good tissue segmentation (pial-, grey-, and white-matter labels).

So now I am considering rescaling one of the scans in a high-dim. space (768x768x768) using imresize3 (or something similar for interpolation) with MATLAB.

The rescaling works, but the non-high-resolution planes turn out to be elongated. I am not sure how to get past this issue, and register the new rescale volume with one of the old ones (trying some params with mri_vol2vol might work?)

At the end I want to visualize rescaled 3D volume on top of the original scans, so I can at least (semi-automatically and then) manually segment it.

thanks in advance :)

- malav