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Thanks for clarifying.
Some initial results on a cohort of 1-2 yo subjects we have run through both the infant FS and 7.1.1 pipelines, seem to benefit from using a denoised T1 image as input. Specifically, denoising in images with motion generates better WM segmentations in complexly folded regions (i.e. occipital/calcarine). We are still evaluating.
Jim
Get Outlook for Androidhttps://aka.ms/ghei36 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, August 25, 2020 10:17:43 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
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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:
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, August 25, 2020 4:05 PM To: freesurfer@nmr.mgh.harvard.edumailto: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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