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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
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:
External Email - Use Caution
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:
- 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
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
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I truly appreciate your help. It worked.
On Thu, Jul 31, 2025 at 5:04 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Have you looked at this page https://secure-web.cisco.com/14frzEOOKtYjpn80fU1gCUnGB_Lmrxc3Nj1KxJ38sgMi_Ky... ?
On 7/29/2025 2:37 AM, Razieh Salesi wrote:
External Email - Use CautionDear 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:
- 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
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...
Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
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Douglas N. Greve -
Razieh Salesi