brain.mgz is denoised to create antsdn.brain.mgz. This volume is then
used to create the initial surface. The final surfaces are created from
the unfiltered brain.mgz but using the orig surface created with the
denoised brain.mgz. So the denoising helps to create the orig surface
which is then used to initialize the final surfaces.
On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote:
External Email - Use Caution
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
** External Email - Caution **
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:
* 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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