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:
External Email - Use Caution
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
<https://secure-web.cisco.com/1pycZ_2SF5XqnaigDfeUBVSUx6el0NqrRFY73S86xcHKBmENAMDW0UImRthmw5ABzQXy4HbR5YvrmPrKqVtps7XvPuj-FM18syDXhXobeyvrjYZXzCWNWL5XrFc_x6F6sXZmNJiaiqVbTgleW5W_JFX66v_8fxOYC_3g0Abw3qcNVhxtjB-lKCNvkgLJTBNfRoIcFNdptMbIJnJJLw4ctFkad0nyy3QrWENp1yPh_-VKqjYY9w45GedHmEn_vICXVD7bRQL8wfM64bNFfHnw7J19BvbmjjLeCH7Qd0TqPUlRbcIblAFj6bGvn1TJXdj1sHiz8ZcMieEXj42iBoIrFCg/https%3A%2F%2Fgithub.com%2Fgift-surg%2FNiftyMIC>),
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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