Have you looked at this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat ?

On 7/29/2025 2:37 AM, Razieh Salesi wrote:

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Dear FreeSurfer team,

I have a workflow question and would appreciate your guidance:

I ran `recon-all` on the original `T1.nii.gz` image (208×240×256), which produced the standard FreeSurfer outputs, including `mri/aseg.mgz`, conformed to 256×256×256.
Separately, I performed N4 bias correction using ANTs and denoising (non-local means) on the original `T1.nii.gz`, resulting in a denoised volume (`T1_N4_naonlm3d.nii.gz`) with the original dimensions (208×240×256).

My goal is to:
1. Create an accurate white matter (WM) mask aligned with this denoised native-space T1,
2. Use it with an EPC image (T1/T2 ratio) for perivascular space (PVS) mapping using Frangi filtering.

My main question is: What is the best approach to transform `aseg.mgz` (in conformed space) to this denoised T1 native space, preserving anatomical accuracy?

Should I:
- Use `mri_label2vol` with `--regheader` and `--temp T1_N4_naonlm3d.nii.gz`?
- Register `T1_N4_naonlm3d` back to `orig.mgz` and invert the matrix?
- Or is there a more accurate method (e.g., using `tkregister2`, `bbregister`, or resampling via FreeSurfer)?

Any recommendations or practices would be very helpful.

Best regards,  
Razieh Salesi

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