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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 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-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 Fischl, Bruce R.,PHD Sent: Thursday, April 11, 2024 14:24 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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 Jiaen Liu Sent: Thursday, April 11, 2024 2:14 PM To: freesurfer@nmr.mgh.harvard.edumailto: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, Texashttps://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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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jiaen Liu Jiaen.Liu@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-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 Jiaen Liu Sent: Thursday, April 11, 2024 4:41 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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 Fischl, Bruce R.,PHD Sent: Thursday, April 11, 2024 14:24 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-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 Jiaen Liu Sent: Thursday, April 11, 2024 2:14 PM To: freesurfer@nmr.mgh.harvard.edumailto: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, Texashttps://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_obcKaq5oL2yqeKgViqZIVcrcWMEYsMRClqQNWgXfENeuG6GalScCAKIRCo7GEHEbOnDKFEjLXVg2eEwVhiG9uT2Hc7asFEYCYcbSB7QpBiE-gWNQtxXdY21-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2rC5UlPB-7QMlqM4JpE_pt1pg6NAQPr9R4knE_k_am2zSouWWDFcLBzyqyeq66PzCx2mc7p*2A2Fhttps*2A2A3A*2A2A2F*2A2A2Flabs.utsouthwestern.edu*2A2A2Fliu-jiaen-lab__*2A3BJSUlJQ*2A21*2A21MznTZTSvDXGV0Co*2A21GYydHkcWwUUxabPeUXMIfHXTRAhASBjUkmJqIr4DPmWnqI0toQo_t8rspwASUsJdE6zgrg9VtJr56Vi486yNvBqyq5czr0ey*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUl*21*21MznTZTSvDXGV0Co*21BjvDUA9rj9bjxQZSdIFXWGVuPvNDPLT2Mv3QQ9roMPSfXmOb3keJe00XMG6RpWmdJs-amHvEpQSZj0H9ZjFNqrpamXdhojPO*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!MznTZTSvDXGV0Co!GpoccVRyDMP_g2wC9xgWtAr8H-AcLxB3Clq8Qty32ed9HEtsD51KQz4ksL496hSWerrLd9lhpT_33zoW8ykb6SycExRNhPJjCEO1$

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Medical Center

The future of medicine, today.

CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Jiaen Liu Jiaen.Liu@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 *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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 *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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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-NvJL9ayiMgvf0vjPZ58ihtEDDpktkt3FKuEygFF36UU3ITL19Rh5Ry95xi3ybBhPid2IvMWLczOnfoVUCoAq6XIptCy4h2rC5UlPB-7QMlqM4JpE_pt1pg6NAQPr9R4knE_k_am2zSouWWDFcLBzyqyeq66PzCx2mc7p%2A2A2Fhttps%2A2A2A3A%2A2A2A2F%2A2A2A2Flabs.utsouthwestern.edu%2A2A2A2Fliu-jiaen-lab__%2A2A3BJSUlJQ%2A2A21%2A2A21MznTZTSvDXGV0Co%2A2A21GYydHkcWwUUxabPeUXMIfHXTRAhASBjUkmJqIr4DPmWnqI0toQo_t8rspwASUsJdE6zgrg9VtJr56Vi486yNvBqyq5czr0ey%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSUlJSUl%2A21%2A21MznTZTSvDXGV0Co%2A21BjvDUA9rj9bjxQZSdIFXWGVuPvNDPLT2Mv3QQ9roMPSfXmOb3keJe00XMG6RpWmdJs-amHvEpQSZj0H9ZjFNqrpamXdhojPO%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU%21%21MznTZTSvDXGV0Co%21GpoccVRyDMP_g2wC9xgWtAr8H-AcLxB3Clq8Qty32ed9HEtsD51KQz4ksL496hSWerrLd9lhpT_33zoW8ykb6SycExRNhPJjCEO1%24

---

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The future of medicine, today.

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