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Dear Jim,
I had been looking at the effect of denoising the data to improve processing
speed in case of noisy data in an ISMRM abstract couple of years ago. However,
I haven't had the time to follow up on this. Glad to see something similar now
being implemented in recon-all.
As Doug and Matt pointed out, denoising the input data will bias your results
potentially which is why it is not recommend to do at all. However, denoising
the data just for the initialization will reduce defects and errors of the
initial white matter surface, reducing processing time from many to a few hours
in case of noisy data. As the actual surface is fitted using the unfiltered
data this should not impair surface placement.
Best,
Falk
Von: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Alexopoulos, Dimitrios
Gesendet: Mittwoch, 26. August 2020 06:04
An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Betreff: Re: [Freesurfer] use of ANTs Denoising in FS 7.1
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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
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________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>>
Sent: Tuesday, August 25, 2020 10:17:43 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto: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<mailto: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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