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Perhaps it smooths the data some and that would impair the gradient placement of the final white and pial surfaces?

Matt.

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Alexopoulos, Dimitrios" dimitriosalexopoulos@wustl.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, August 25, 2020 at 3:56 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] use of ANTs Denoising in FS 7.1

External Email - Use Caution Hi all,

In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline.

“ANTS denoise is used when creating the orig surface (but not thefinal surfaces)”

Does this mean the denoised image is only used in the segmentation part of the pipeline (to generated the aseg.mgz) and does not propagate through to final surfaces? Why not use denoised T1 through the surface-generation phase of the pipeline.

Can you provide some further clarification.

Thx. Jim

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