Hi,
I would like to know the relationship between number of iteration in surface smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr/ http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
Hi Hae-Jeong,
it is:
fwhm = (2.3*sqrt(niter*2/pi));
cheers, Bruce
On Mon, 27 Jun 2005, Hae-Jeong Park, PhD wrote:
Hi,
I would like to know the relationship between number of iteration in surface smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr/ http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
Is this FWHM in centimeter unit or in millimeter unit? Thanks a lot.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 27, 2005 8:51 PM To: Hae-Jeong Park, PhD Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on FWHM in surface smoothing
Hi Hae-Jeong,
it is:
fwhm = (2.3*sqrt(niter*2/pi));
cheers, Bruce
On Mon, 27 Jun 2005, Hae-Jeong Park, PhD wrote:
Hi,
I would like to know the relationship between number of iteration in
surface
smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr/ http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
I am sorry. I made a mistake. It cannot be the centimeter unit. Thanks.
Hae-Jeong -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, June 27, 2005 8:51 PM To: Hae-Jeong Park, PhD Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question on FWHM in surface smoothing
Hi Hae-Jeong,
it is:
fwhm = (2.3*sqrt(niter*2/pi));
cheers, Bruce
On Mon, 27 Jun 2005, Hae-Jeong Park, PhD wrote:
Hi,
I would like to know the relationship between number of iteration in
surface
smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr/ http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
Dear Dr. Park,
I guess you are asking about freesurfer related surface smoothing. Although I am not exactly sure how FreeSurfer is implmenting surface smoothing, the general theory of suface-based smoothing and FWHM can be found in two of my previous publications:
Chung, M.K., Worsley, K.J. , Paus, T., Cherif, C., Giedd, J.N., Rapoport, J.L, Evans, A.C. 2001. A Unified Statistical Approach to Deformation-Based Morphometry, NeuroImage 14:595-606. http://www.math.mcgill.ca/chung/deformation/ni_deformation.pdf
Chung, M.K., Robbins,S., Dalton, K.M., Davidson, Alexander, A.L., R.J., Evans, A.C. 2005. Cortical thickness analysis in autism via heat kernel smoothing. NeuroImage 25:1256-1265. http://www.stat.wisc.edu/~mchung/papers/ni_heatkernel.pdf
These softwares implemented in MATLAB can be found in my webpage http://www.stat.wisc.edu/~mchung/softwares/sotfwares.html for other type of triangular meshes.
Moo.
On 6/27/05, Hae-Jeong Park, PhD parkhj@yumc.yonsei.ac.kr wrote:
Hi,
I would like to know the relationship between number of iteration in surface smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Moo,
I actually implemented your diffusion smoother but could not quite get it to work. It might have been related to the delta t parameter. Can you give some guidance as to how to set it? What's the difference between heat kernel smoothing and diffusion smoothing? btw, the link to the "Diffusion smoothing on cortex" software on your web page is broken.
thanks
doug
Moo K. Chung wrote:
Dear Dr. Park,
I guess you are asking about freesurfer related surface smoothing. Although I am not exactly sure how FreeSurfer is implmenting surface smoothing, the general theory of suface-based smoothing and FWHM can be found in two of my previous publications:
Chung, M.K., Worsley, K.J. , Paus, T., Cherif, C., Giedd, J.N., Rapoport, J.L, Evans, A.C. 2001. A Unified Statistical Approach to Deformation-Based Morphometry, NeuroImage 14:595-606. http://www.math.mcgill.ca/chung/deformation/ni_deformation.pdf
Chung, M.K., Robbins,S., Dalton, K.M., Davidson, Alexander, A.L., R.J., Evans, A.C. 2005. Cortical thickness analysis in autism via heat kernel smoothing. NeuroImage 25:1256-1265. http://www.stat.wisc.edu/~mchung/papers/ni_heatkernel.pdf
These softwares implemented in MATLAB can be found in my webpage http://www.stat.wisc.edu/~mchung/softwares/sotfwares.html for other type of triangular meshes.
Moo.
On 6/27/05, Hae-Jeong Park, PhD parkhj@yumc.yonsei.ac.kr wrote:
Hi,
I would like to know the relationship between number of iteration in surface smoothing and Gaussian kernel size in FWHM.
Would you give me some information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park, PhD Assistant Professor, Department of Diagnostic Radiology, Yonsei University, College of Medicine and Division of Nuclear Medicine, Severance Hospital Director, Laboratory of Molecular Neuroimging Technology http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax) 82-2-393-3035 Cellur) 82-10-4220-1003
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi all,
heat kernel smoothing and diffusion smoothing are supposed to give the same solution to an isotropic heat equation on the cortex. the difference is that heat kernel smoothing is simpler and there is no need to worry about the convergence. in diffusion smoothing, there might be a ringing effect (divergence) on smoothed data if "delta t" is not small enough. to avoid this problem, you may want to implement backward Euler scheme in solving the diffusion equation, which i haven't done. to avoid this instability problem, i developed the heat kernel smoothing. i feel heat kernel smoothing is far simpler and better approach than diffusion smoothing.
SUMA pacakage (AFNI add on) uses diffusion smoothing ported from my original MATLAB code but they are trying to replace with heat kernel smoothing soon. :)
i am sorry i will fix the link on diffusion smoothing soon.
moo.
On 6/29/05, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Moo,
I actually implemented your diffusion smoother but could not quite get it to work. It might have been related to the delta t parameter. Can you give some guidance as to how to set it? What's the difference between heat kernel smoothing and diffusion smoothing? btw, the link to the "Diffusion smoothing on cortex" software on your web page is broken.
thanks
doug
Moo K. Chung wrote: Dear Dr. Park,
I guess you are asking about freesurfer related surface
smoothing.
Although I am not exactly sure how FreeSurfer is implmenting
surface
smoothing, the general theory of suface-based smoothing and FWHM
can
be found in two of my previous publications:
Chung, M.K., Worsley, K.J.
, Paus, T., Cherif, C., Giedd, J.N.,
Rapoport, J.L, Evans, A.C. 2001. A
Unified Statistical Approach to
Deformation-Based Morphometry, NeuroImage
14:595-606.
http://www.math.mcgill.ca/chung/deformation/ni_deformation.pdf
Chung,
M.K., Robbins,S., Dalton, K.M., Davidson, Alexander, A.L.,
R.J., Evans, A.C.
- Cortical thickness analysis in autism via heat
kernel smoothing.
NeuroImage 25:1256-1265.
http://www.stat.wisc.edu/~mchung/papers/ni_heatkernel.pdf
These
softwares implemented in MATLAB can be found in my webpage
http://www.stat.wisc.edu/~mchung/softwares/sotfwares.html for
other type of triangular meshes.
Moo.
On 6/27/05, Hae-Jeong Park, PhD
parkhj@yumc.yonsei.ac.kr wrote:
Hi,
I would like to know the relationship between number of iteration in
surface
smoothing and Gaussian kernel size in FWHM.
Would you give me some
information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park,
PhD
Assistant Professor, Department of Diagnostic Radiology, Yonsei
University, College of Medicine
and Division of Nuclear Medicine, Severance
Hospital Director,
Laboratory of Molecular Neuroimging
Technology
http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax)
82-2-393-3035
Cellur) 82-10-4220-1003
_______________________________________________ Freesurfer
mailing list
Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone
Number: 617-724-2358
Fax: 617-726-7422
The heat kernel sounds cool :). I'll check it out.
doug
Moo K. Chung wrote:
Hi all,
heat kernel smoothing and diffusion smoothing are supposed to give the same solution to an isotropic heat equation on the cortex. the difference is that heat kernel smoothing is simpler and there is no need to worry about the convergence. in diffusion smoothing, there might be a ringing effect (divergence) on smoothed data if "delta t" is not small enough. to avoid this problem, you may want to implement backward Euler scheme in solving the diffusion equation, which i haven't done. to avoid this instability problem, i developed the heat kernel smoothing. i feel heat kernel smoothing is far simpler and better approach than diffusion smoothing.
SUMA pacakage (AFNI add on) uses diffusion smoothing ported from my original MATLAB code but they are trying to replace with heat kernel smoothing soon. :)
i am sorry i will fix the link on diffusion smoothing soon.
moo.
On 6/29/05, Doug Greve greve@nmr.mgh.harvard.edu wrote:
Hi Moo,
I actually implemented your diffusion smoother but could not quite get it to work. It might have been related to the delta t parameter. Can you give some guidance as to how to set it? What's the difference between heat kernel smoothing and diffusion smoothing? btw, the link to the "Diffusion smoothing on cortex" software on your web page is broken.
thanks
doug
Moo K. Chung wrote: Dear Dr. Park,
I guess you are asking about freesurfer related surface
smoothing.
Although I am not exactly sure how FreeSurfer is implmenting
surface
smoothing, the general theory of suface-based smoothing and FWHM
can
be found in two of my previous publications:
Chung, M.K., Worsley, K.J.
, Paus, T., Cherif, C., Giedd, J.N.,
Rapoport, J.L, Evans, A.C. 2001. A
Unified Statistical Approach to
Deformation-Based Morphometry, NeuroImage
14:595-606.
http://www.math.mcgill.ca/chung/deformation/ni_deformation.pdf
Chung,
M.K., Robbins,S., Dalton, K.M., Davidson, Alexander, A.L.,
R.J., Evans, A.C.
- Cortical thickness analysis in autism via heat
kernel smoothing.
NeuroImage 25:1256-1265.
http://www.stat.wisc.edu/~mchung/papers/ni_heatkernel.pdf
These
softwares implemented in MATLAB can be found in my webpage
http://www.stat.wisc.edu/~mchung/softwares/sotfwares.html for
other type of triangular meshes.
Moo.
On 6/27/05, Hae-Jeong Park, PhD
parkhj@yumc.yonsei.ac.kr wrote:
Hi,
I would like to know the relationship between number of iteration in
surface
smoothing and Gaussian kernel size in FWHM.
Would you give me some
information on this? Thank you in advance.
Hae-Jeong
-- Hae-Jeong Park,
PhD
Assistant Professor, Department of Diagnostic Radiology, Yonsei
University, College of Medicine
and Division of Nuclear Medicine, Severance
Hospital Director,
Laboratory of Molecular Neuroimging
Technology
http://neuroimage.yonsei.ac.kr Tel) 82-2-2228-2363, Fax)
82-2-393-3035
Cellur) 82-10-4220-1003
Freesurfer
mailing list
Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone
Number: 617-724-2358
Fax: 617-726-7422
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Hae-Jeong Park, PhD -
Moo K. Chung