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I'm looking through the pipeline table , looking to see where the orig surfaces
are created, which appear to be in autorecon2 /tessellation step . What
advantage is gained by denoising the image (which image is actually denosed?)
at this stage if id does not contribute the final surfaces?
Sorry for asking for more detail, just want to make sure I understand the
application of the utility. Many groups are now denoising their input images
into many pipelines.
Jim
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Tuesday, August 25, 2020 4:05 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
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It is only used to create the orig surface. It is not used in the volume
segmentation or the final placement of the surfaces. Volume smoothing of any
kind has the potential to bias the surface placement so we recommend against
denoising the input.
On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote:
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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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