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I found in the source code about the use of fwhm. It decides the number of
iterations to achieve a gaussian filter with the specified fwhm in mm
Best,
Jiaen
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From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jiaen Liu
<jiaen....@utsouthwestern.edu>
Sent: Thursday, April 11, 2024 3:58:18 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface-based filtering
External Email - Use Caution
I thought N controls the number of smoothing iterations and the smoothing in
each iteration is defined by fwhm which is some measurement of the smoothing
kernel width.
Can I ask how to achieve smoothing effect similar to gaussian smoothing with
certain sigma, where sigma is defined by voxel unit?
Thanks!
Best
Jiaen
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surface-based filtering
Hi Jiaen
I’m not sure what you mean by “stacked smoothing”. I think the N in nsmooth is
the number of iterations of nearest neighbor smoothing to apply, which
converges to Gaussian as N gets bigger. Not sure about the units for fwhm – I
defer to Doug on that
Bruce
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 Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering
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Hi Bruce
Thanks for your response. In the help, I found the following options. Is the
fwhm based on voxel unit? Does nsmooth-in or-out control the number of stacked
smoothing?
--fwhm-src fwhmsrc: smooth the source to fwhmsrc
--fwhm-trg fwhmtrg: smooth the target to fwhmtrg
--nsmooth-in N : smooth the input
--nsmooth-out N : smooth the output
Best
Jiaen
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 Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering
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Yes, we support surface-based smoothing. Check out the help for mri_surf2surf
Cheers
Bruce
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 Jiaen Liu
Sent: Thursday, April 11, 2024 2:14 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] surface-based filtering
External Email - Use Caution
I’m wondering if freesurfer provides functions to filter the surface data
within certain neighborhood exclusively on the surface. It’s essentially
similar to regular smoothing in 3D space. But the filtering kernel only runs on
the surface.
I can think of a solution to filter adjacent vertex in the surface file. But
I’m not sure if the adjacent vertex is also close in space.
Thanks!
Best regards,
Jiaen Liu Ph.D.
Assistant Professor
Advanced Imaging Research Center & Radiology
UT Southwestern Medical Center
2201 Inwood Ln
Dallas, TX, USA, 75390
Office: 214.645.2750
Website: Liu (Jiaen) Lab | UT Southwestern, Dallas,
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