subject:"\[Freesurfer\] surface\-based filtering"

Re: [Freesurfer] surface-based filtering

2024-04-18 Thread Douglas N. Greve


Yes, you can also run
mris_fwhm --smooth-only --i input.surf-values.mgz --fwhm FWHM --s 
subject --hemi hemi --o output.surf-values-smoothed.mgz --cortex

This will give the same result as mri_surf2surf

On 4/12/2024 10:07 PM, Jiaen Liu wrote:


External Email - Use Caution

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
Sent with my mobile device

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 


*Sent:* Thursday, April 11, 2024 3:58:18 PM
*To:* Freesurfer support list 
*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 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 15:50
*To:* Freesurfer support list 
*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 
 *On Behalf Of *Jiaen Liu

*Sent:* Thursday, April 11, 2024 4:41 PM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*External Email - Use Caution *

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 
 *On Behalf Of *Fischl, Bruce 
R.,PHD

*Sent:* Thursday, April 11, 2024 14:24
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] surface-based filtering

*EXTERNAL MAIL*

Yes, we support surface-based smoothing. Check out the help for 
mri_surf2surf


Cheers

Bruce

*From:*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
*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, Texas 
<https://secure-web.cisco.com/1LRODsNbioejkgSU5esL6oghgOFFyz4pTQi641G4D5xNfMfbb_ofdI5eybtyfWaW7xPb4NqQdgcaRwfi1LSDsTRIVHxeOQpjqT8bE0Hnp_jBK0zjSzuUEljjFUH_UlE0N1h88bm8SWVtCKGoag3Z486QQdGpBkNLHPhs2oWluOVVqfzgpey18qwTWJrT5GZM6uVHV5NKb6AfBfbrzNLOepRTGs_i3HWr8ONQEyXtHd-ILU0jxAl5xPMqTTOMdeS9prrqIn4NOjsHSL8CAh52eUw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1yHhAPHTBcTc91EqCySD8GmE6Xsvmij6jPIUMgKqvaf7ygg_jKCOH3HhvGl3bLmLQTcZzc4nsXdJ2NrOgn5qkU554SYwjLxVVX_rpnEaCBNLECHAaFAnNQNjKvI9WzY3FQeYV0bejhraZaayMd8vgc8Y3-xz4SVY36D2tzk3wW_dMCUzxHi-6NNHZvXOBDXRZ_Ic5i5vA6bHUjvOBd68L13We7dE-7iclSA0faig-ekvMnVnXAgbi0ykIwLebJ4IMI-jzXcFSYUGc9gJeN6ieDb0sOh3vOq93ip494F45T6kiHBL9vwKQtkGRiTDuMn0ynnVgTmC6lX28T51pTExngw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1Lg6Gap_08UIPjUEXgULmXlS4zrJtCKXh_D8gzP6AUrh_9A2Eof9YqougNuu8ga8NqJkulQMSh5GHo6mQn4Cg1wxXLbmxy2WAT_vg7Kb_xmdIDAm8SN_bkyuaF0dQ-vSB7rKuko4Mv4AIUz-UwQ95m-C3uRwhDMvNBGv2Kul_OhZjHyQMGcdWpD5edirXbbnoeC_aee3IczFARImkHq57PA8q6L7AHzQhiga3vvW3T3LY_YNLu2vGObI2xxpY18T7MJ8YWEcIyFsKRfgPvPzje3TlOtUARIj5BiuLiUhZ3ZI64GD8qF7DWkkq_bCBTI3QEbedt-HO3tZ4cJIS3yqL_g%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo7GEHEbOnDKFEjLXVg2eEwVhiG9uT2Hc7asFEYCYcbSB7QpBiE-gWNQtxXdY21-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2

Re: [Freesurfer] surface-based filtering

2024-04-12 Thread Fischl, Bruce R.,PHD

Makes sense
Bruce

On Apr 12, 2024, at 10:08 PM, Jiaen Liu  wrote:



External Email - Use Caution

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
Sent with my mobile device

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 

Sent: Thursday, April 11, 2024 3:58:18 PM
To: Freesurfer support list 
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 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering



External Email - Use Caution

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>
 
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 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering



EXTERNAL MAIL

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>
 
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, 
Texas<https://secure-web.cisco.com/1LRODsNbioejkgSU5esL6oghgOFFyz4pTQi641G4D5xNfMfbb_ofdI5eybtyfWaW7xPb4NqQdgcaRwfi1LSDsTRIVHxeOQpjqT8bE0Hnp_jBK0zjSzuUEljjFUH_UlE0N1h88bm8SWVtCKGoag3Z486QQdGpBkNLHPhs2oWluOVVqfzgpey18qwTWJrT5GZM6uVHV5NKb6AfBfbrzNLOepRTGs_i3HWr8ONQEyXtHd-ILU0jxAl5xPMqTTOMdeS9prrqIn4NOjsHSL8CAh52eUw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1yHhAPHTBcTc91EqCySD8GmE6Xsvmij6jPIUMgKqvaf7ygg_jKCOH3HhvGl3bLmLQTcZzc4nsXdJ2NrOgn5qkU554SYwjLxVVX_rpnEaCBNLECHAaFAnNQNjKvI9WzY3FQeYV0bejhraZaayMd8vgc8Y3-xz4SVY36D2tzk3wW_dMCUzxHi-6NNHZvXOBDXRZ_Ic5i5vA6bHUjvOBd68L13We7dE-7iclSA0faig-ekvMnVnXAgbi0ykIwLebJ4IMI-jzXcFSYUGc9gJeN6ieDb0sOh3vOq93ip494F45T6kiHBL9vwKQtkGRiTDuMn0ynnVgTmC6lX28T51pTExngw%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1Lg6Gap_08UIPjUEXgULmXlS4zrJtCKXh_D8gzP6AUrh_9A2Eof9YqougNuu8ga8NqJkulQMSh5GHo6mQn4Cg1wxXLbmxy2WAT_vg7Kb_xmdIDAm8SN_bkyuaF0dQ-vSB7rKuko4Mv4AIUz-UwQ95m-C3uRwhDMvNBGv2Kul_OhZjHyQMGcdWpD5edirXbbnoeC_aee3IczFARImkHq57PA8q6L7AHzQhiga3vvW3T3LY_YNLu2vGObI2xxpY18T7MJ8YWEcIyFsKRfgPvPzje3TlOtUARIj5BiuLiUhZ3ZI64GD8qF7DWkkq_bCBTI3QEbedt-HO3tZ4cJIS3yqL_g%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fsecure-web.cisco.com%2A2A2F1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6

Re: [Freesurfer] surface-based filtering

2024-04-12 Thread Jiaen Liu

External Email - Use Caution

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
Sent with my mobile device

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Jiaen Liu 

Sent: Thursday, April 11, 2024 3:58:18 PM
To: Freesurfer support list 
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 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering



External Email - Use Caution

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>
 
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 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering



EXTERNAL MAIL

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>
 
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, 
Texas<https://secure-web.cisco.com/1yuL9in4QQVLDnBFljaD949DgCPH6sG-Bg_nLKIIMto8RJkPUnxGE9Db3HNWq6RB6768IWGdupuUyEgzIyMfp6ufkQWhhfRRomkzKTOGxSzPvik0C-CoW1uITNBMbrz-4UvZMGj7b7OBwCKyf0aKxECGXaYXJtpgPvxh_rONGgWqGqRZtD_91eCOZAyrmxCvd87fN3Som-B5iOdRemaP4tUceddYjKqupf7dwivJ5CJxzIoMRA2V3J0Ap09p8dhr068b7GLFl2EY8SzH_0Y5ipbDbXMRyylt0MRzoV0A4KQwVcItqOmbjgu4g4Hgkf1sIwte1ze6Ktxy6qVeC1ibajA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsecure-web.cisco.com%2F1yHhAPHTBcTc91EqCySD8GmE6Xsvmij6jPIUMgKqvaf7ygg_jKCOH3HhvGl3bLmLQTcZzc4nsXdJ2NrOgn5qkU554SYwjLxVVX_rpnEaCBNLECHAaFAnNQNjKvI9WzY3FQeYV0bejhraZaayMd8vgc8Y3-xz4SVY36D2tzk3wW_dMCUzxHi-6NNHZvXOBDXRZ_Ic5i5vA6bHUjvOBd68L13We7dE-7iclSA0faig-ekvMnVnXAgbi0ykIwLebJ4IMI-jzXcFSYUGc9gJeN6ieDb0sOh3vOq93ip494F45T6kiHBL9vwKQtkGRiTDuMn0ynnVgTmC6lX28T51pTExngw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1Lg6Gap_08UIPjUEXgULmXlS4zrJtCKXh_D8gzP6AUrh_9A2Eof9YqougNuu8ga8NqJkulQMSh5GHo6mQn4Cg1wxXLbmxy2WAT_vg7Kb_xmdIDAm8SN_bkyuaF0dQ-vSB7rKuko4Mv4AIUz-UwQ95m-C3uRwhDMvNBGv2Kul_OhZjHyQMGcdWpD5edirXbbnoeC_aee3IczFARImkHq57PA8q6L7AHzQhiga3vvW3T3LY_YNLu2vGObI2xxpY18T7MJ8YWEcIyFsKRfgPvPzje3TlOtUARIj5BiuLiUhZ3ZI64GD8qF7DWkkq_bCBTI3QEbedt-HO3tZ4cJIS3yqL_g*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsecure-web.cisco.com*2A2F1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo

Re: [Freesurfer] surface-based filtering

2024-04-11 Thread Jiaen Liu

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 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 15:50
To: Freesurfer support list 
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>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering


External Email - Use Caution
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>
 
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 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
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>
 
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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Re: [Freesurfer] surface-based filtering

2024-04-11 Thread Fischl, Bruce R.,PHD

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 
 On Behalf Of Jiaen Liu
Sent: Thursday, April 11, 2024 4:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface-based filtering


External Email - Use Caution
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>
 
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 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
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>
 
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, 
Texas<https://secure-web.cisco.com/1Lg6Gap_08UIPjUEXgULmXlS4zrJtCKXh_D8gzP6AUrh_9A2Eof9YqougNuu8ga8NqJkulQMSh5GHo6mQn4Cg1wxXLbmxy2WAT_vg7Kb_xmdIDAm8SN_bkyuaF0dQ-vSB7rKuko4Mv4AIUz-UwQ95m-C3uRwhDMvNBGv2Kul_OhZjHyQMGcdWpD5edirXbbnoeC_aee3IczFARImkHq57PA8q6L7AHzQhiga3vvW3T3LY_YNLu2vGObI2xxpY18T7MJ8YWEcIyFsKRfgPvPzje3TlOtUARIj5BiuLiUhZ3ZI64GD8qF7DWkkq_bCBTI3QEbedt-HO3tZ4cJIS3yqL_g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo7GEHEbOnDKFEjLXVg2eEwVhiG9uT2Hc7asFEYCYcbSB7QpBiE-gWNQtxXdY21-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2rC5UlPB-7QMlqM4JpE_pt1pg6NAQPr9R4knE_k_am2zSouWWDFcLBzyqyeq66PzCx2mc7p%2Fhttps%2A3A%2A2F%2A2Flabs.utsouthwestern.edu%2A2Fliu-jiaen-lab__%3BJSUlJQ%21%21MznTZTSvDXGV0Co%21GYydHkcWwUUxabPeUXMIfHXTRAhASBjUkmJqIr4DPmWnqI0toQo_t8rspwASUsJdE6zgrg9VtJr56Vi486yNvBqyq5czr0ey%24>




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Medical Center

The future of medicine, today.

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Re: [Freesurfer] surface-based filtering

2024-04-11 Thread Jiaen Liu

External Email - Use Caution

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 
 On Behalf Of Fischl, Bruce R.,PHD
Sent: Thursday, April 11, 2024 14:24
To: Freesurfer support list 
Subject: Re: [Freesurfer] surface-based filtering

EXTERNAL MAIL
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>
 
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, 
Texas<https://secure-web.cisco.com/1AofbNbSj-GEQlw3J-B-1P0p5HCFqRSfw2t5l2kVpOTayqkHgE6Mupf6pIwXP62LhQrsVbH-xtVJ-GU01COmhHlJALv_Ct4gDt9fwUeEQQuBHQxJ-oo3cs3D87_i-MCk8r7Z_vAgMNvW8rzTQEXErcxXBTNaK0guWGaJI7UIASvstJWCZQnkb2OXXIOvsTPXDqCbxjLSPhLskImcnQMA-k0I754rzbf_A6uMgZvyq5ZoD_y3vPxd-bBJFymhj0ow4-teRRLxsrfU17L96nGZ7ZBLrOLqr3xZDc4tHbYIwmhn1Y6UlYzxKCuRrsYimrw5S4qKUJOnPpkgOyYFDOrkjZQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo7GEHEbOnDKFEjLXVg2eEwVhiG9uT2Hc7asFEYCYcbSB7QpBiE-gWNQtxXdY21-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2rC5UlPB-7QMlqM4JpE_pt1pg6NAQPr9R4knE_k_am2zSouWWDFcLBzyqyeq66PzCx2mc7p%2Fhttps*3A*2F*2Flabs.utsouthwestern.edu*2Fliu-jiaen-lab__;JSUlJQ!!MznTZTSvDXGV0Co!GYydHkcWwUUxabPeUXMIfHXTRAhASBjUkmJqIr4DPmWnqI0toQo_t8rspwASUsJdE6zgrg9VtJr56Vi486yNvBqyq5czr0ey$>




UT Southwestern

Medical Center

The future of medicine, today.

CAUTION: This email originated from outside UTSW. Please be cautious of links 
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] surface-based filtering

2024-04-11 Thread Fischl, Bruce R.,PHD

Yes, we support surface-based smoothing. Check out the help for mri_surf2surf

Cheers
Bruce

From: 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
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, 
Texas<https://secure-web.cisco.com/1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo7GEHEbOnDKFEjLXVg2eEwVhiG9uT2Hc7asFEYCYcbSB7QpBiE-gWNQtxXdY21-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2rC5UlPB-7QMlqM4JpE_pt1pg6NAQPr9R4knE_k_am2zSouWWDFcLBzyqyeq66PzCx2mc7p/https%3A%2F%2Flabs.utsouthwestern.edu%2Fliu-jiaen-lab>

UT Southwestern

Medical Center

The future of medicine, today.

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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail.

[Freesurfer] surface-based filtering

2024-04-11 Thread Jiaen Liu

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, 
Texas




UT Southwestern

Medical Center

The future of medicine, today.
___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

Re: [Freesurfer] surface-based filtering

[Freesurfer] surface-based filtering

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