Hi there, Hope all is well
Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration.

Nárlon Cássio
Nárlon C Boa Sorte Silva, PhD (He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia
+15196944893 https://secure-web.cisco.com/1WOyPTiy1S37KSd-TKeW2x9b9p4Iz3oChJj2C73O4_E4RmA... https://secure-web.cisco.com/11fPHF_NbaiAS9OznZllbCbArfM8-LaAlHeQDjv3l-NN6eD...
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Can you send your recon-all.log file?
On 11/14/2024 6:17 PM, Boa Sorte Silva, Narlon wrote:
Hi there, Hope all is well
Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration.
Sample 1.pngSample 2.png
Nárlon Cássio
Nárlon C Boa Sorte Silva, PhD(He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia
+15196944893 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://twitter.com/boanarlon https://secure-web.cisco.com/1WOyPTiy1S37KSd-TKeW2x9b9p4Iz3oChJj2C73O4_E4RmATlXuqi-zepGC9ToMMke_9EMkGtUFxFokWVfD6C_FOLv8-fTgq2TmpCRxGeO6omM39qMwGcX_GwqWA__4duu_igxgMehhM86VQ5a08fTlWYJtt5UpxvqvS9LNcLsSPZqhmvhUTtoaq9vHjIQqMYqJiTBYD1Y1MXi_BUxH4vporVp0MMXtkHowOMAYUXtLvwzecjcxB9bgz4-P9FnlcxrEDkJArnJ_jk7sg7KoSg08lg8b2UvEtvr55CtOWnPQITQKIQ-4Y9_5HnpjaKGEE7_9ERlwPoL1OGQ9t6kP8Gmw/https%3A%2F%2Ftwitter.com%2Fboanarlon
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oh yes, see it attached

Thanks
Nárlon Cássio
Nárlon C Boa Sorte Silva, PhD (He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia
+15196944893 https://secure-web.cisco.com/1ehNfqK8oWU6VuDbwVQsO40xzylb_zhp0sxtyWZjnQLL8nO... https://secure-web.cisco.com/1pR5p4Q2ukzbc04LYcafHV-1fdv40EjijwNlZZkmD1KFM80...
On Nov 20, 2024, at 10:14 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
[CAUTION: Non-UBC Email] Can you send your recon-all.log file?
On 11/14/2024 6:17 PM, Boa Sorte Silva, Narlon wrote:
Hi there, Hope all is well
Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration.
<Sample 1.png><Sample 2.png>
Nárlon Cássio
Nárlon C Boa Sorte Silva, PhD (He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia
+15196944893 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ehNfqK8oWU6VuDbwVQsO40xzylb_zhp0sxtyWZjnQLL8nO... https://secure-web.cisco.com/1WOyPTiy1S37KSd-TKeW2x9b9p4Iz3oChJj2C73O4_E4RmATlXuqi-zepGC9ToMMke_9EMkGtUFxFokWVfD6C_FOLv8-fTgq2TmpCRxGeO6omM39qMwGcX_GwqWA__4duu_igxgMehhM86VQ5a08fTlWYJtt5UpxvqvS9LNcLsSPZqhmvhUTtoaq9vHjIQqMYqJiTBYD1Y1MXi_BUxH4vporVp0MMXtkHowOMAYUXtLvwzecjcxB9bgz4-P9FnlcxrEDkJArnJ_jk7sg7KoSg08lg8b2UvEtvr55CtOWnPQITQKIQ-4Y9_5HnpjaKGEE7_9ERlwPoL1OGQ9t6kP8Gmw/https%3A%2F%2Ftwitter.com%2Fboanarlon MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1pR5p4Q2ukzbc04LYcafHV-1fdv40EjijwNlZZkmD1KFM80... https://secure-web.cisco.com/11fPHF_NbaiAS9OznZllbCbArfM8-LaAlHeQDjv3l-NN6eDQhM5AVSoySW8azDVEqa0N_Kv-2FMU8cGsnTFVpPS8wTWtBElIRIhcBBJehu3a9QQZmLMH4oqUjo_zwyGiCDFVvnG8iiFyHXQEfCwBAUfpLBXGALbf1Kv5rnymYHPQQL7AtEIkiBFZoAGuL4OYVwNOT2tIZdhQYTqsAzjAEzJZuEh-IK58qS-ZxfrwgNoXrafMDAqaDXGf14pe4eE5XkRj1bhBp-K4ioysKTvx4r_uTWY4glYIj75qKVHy-iAs-IZ2pNzDjrmgMd8_89c4NaJ6AtaIScqCFt-vPpKA0lA/https%3A%2F%2Fwww.linkedin.com%2Fin%2Fnarlonsilva
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1YpEPYl8vE0ayKqQ0DfZu2M1PSeKGSj3edINL2zsPXJJc13... 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://secure-web.cisco.com/1Fp8lg65-fvcL1Q5SVaYdT2EW50QFA0MCYNemI_CBG29LvO... https://secure-web.cisco.com/1Fp8lg65-fvcL1Q5SVaYdT2EW50QFA0MCYNemI_CBG29LvOH8dYQ6o3sQqwr8pkbXnvk7QJljWNtzJ_uK46UoTWdg0T-BrQyxe0v0Fovby3u7twRy5AqhNLCNBijL9ruQO71fJlQOdWVGty8vyzOip9NKso54BYo-0RIx_tno64EVzYjzbO5xgpheTYReoiLFbqg3hQXlUe0K8p6ps8Wh0jT1jlXD2nQQfKGKaiz8S65DsM71YA_raSBEDyKf9t5RjkXermhniTR-aRuzuq2hLd17JumgGdAKdBNkdreubhZR3wp8B0zyPV7s--dRmpbX8JpkkaUB42uFkoBVtQe9jA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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My guess is that this is a problem with the bias field correction. You can try putting in control points in to the WM around those areas (make sure they are fully in WM). From an automatic perspective, you could try running your own bias field correction and then pass that to recon-all. Eg, you could run something like samseg --i inputvol.mgz --o samseg This will create a samseg folder with a bias field corrected volume. Visualize that to make sure nothing bad happened, then pass that to recon-all
On 11/14/2024 6:17 PM, Boa Sorte Silva, Narlon wrote:
Hi there, Hope all is well
Is there any preprocessing or additional steps within FreeSurfer that could help with issues like the ones in the images attached (aside from manual edits)? Granted this is an example of a sample of older individuals with marked neurodegeneration.
Sample 1.pngSample 2.png
Nárlon Cássio
Nárlon C Boa Sorte Silva, PhD(He, Him, His) Postdoctoral Fellow Centre for Aging SMART, Vancouver Coastal Health Research Institute Djavad Mowafaghian Centre for Brain Health, Vancouver Coastal Health Research Institute Department of Physical Therapy, University of British Columbia
+15196944893 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://twitter.com/boanarlon https://secure-web.cisco.com/1WOyPTiy1S37KSd-TKeW2x9b9p4Iz3oChJj2C73O4_E4RmATlXuqi-zepGC9ToMMke_9EMkGtUFxFokWVfD6C_FOLv8-fTgq2TmpCRxGeO6omM39qMwGcX_GwqWA__4duu_igxgMehhM86VQ5a08fTlWYJtt5UpxvqvS9LNcLsSPZqhmvhUTtoaq9vHjIQqMYqJiTBYD1Y1MXi_BUxH4vporVp0MMXtkHowOMAYUXtLvwzecjcxB9bgz4-P9FnlcxrEDkJArnJ_jk7sg7KoSg08lg8b2UvEtvr55CtOWnPQITQKIQ-4Y9_5HnpjaKGEE7_9ERlwPoL1OGQ9t6kP8Gmw/https%3A%2F%2Ftwitter.com%2Fboanarlon
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Boa Sorte Silva, Narlon -
Douglas N. Greve