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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/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.
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, Texashttps://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.
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.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/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 or attachments, and validate the sender's email address before replying.
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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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.
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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/1N6eTMZttMhK9NfGA4NvBve3j31ow_cnxb1OMdgoW-5AAUjP1znXD5cS6iQrWtzxlAsjJAgK6qhcpZw8FCWB8Vpq5Utrcc0_HJ4GMTqRM-q425Z9zXhYT9B8DJgVVFp19EPF4Lri0D0x7etYM_bboKh9LwBYLdj5MYDzczUgXuUHyTtunEF6-O42ERfT1-8BsZb9OMJJVtheEY_PTqPEnjnjcBACOgWHmvoLNvA_p5UfqsK5AbzmCAuq9nhTF0zGvnJFuAN0ZwxhOS4fXbO2wJkJjI3pOoR1kSQ_4YkA5DyVb0UI0gt3CW4MPWCQ9Ht3b60w59bvBEBJkXw0xj87JXQ/https%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*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__;JSUlJSUlJSUlJSUlJSUlJSUl!!MznTZTSvDXGV0Co!BjvDUA9rj9bjxQZSdIFXWGVuPvNDPLT2Mv3QQ9roMPSfXmOb3keJe00XMG6RpWmdJs-amHvEpQSZj0H9ZjFNqrpamXdhojPO$
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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.
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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
________________________________
UT Southwestern
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.
Makes sense Bruce
On Apr 12, 2024, at 10:08 PM, Jiaen Liu Jiaen.Liu@utsouthwestern.edu 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.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
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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
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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
________________________________
UT Southwestern
Medical Center
The future of medicine, today.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
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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
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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
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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-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
*UT**Southwestern*
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu