Do you just need to change the voxel size for that dimension? If so, you can use mri_convert, something like
mri_convert -iis newvoxsize input.mgz output.mgz
where -iis means the change the voxel size of the first dimension. Use -ijs or -iks for the 2nd and 3rd. You may have to play with it to get the right dimension

On 10/6/2023 12:00 PM, Malav Shah wrote:

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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

Malav Shah
PhD candidate, Michael Brecht Lab,
Humboldt University zu Berlin.
(+49) 163-216-9391
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