External Email - Use Caution
Hi Arianna,
1) Yes. Please note that the method was tuned and mostly tested on MS patients.
2) These two versions of SAMSEG model WMH/ WM lesions differently and cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563).
3) Yes. Note that SWI data might not add valuable information to the lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data.
Stefano
Sent on behalf of Arianna Menardi:
----
Dear Experts,
I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions.
I am new to the approach so I have 3 main questions: 1. Can I use Samseg for MS lesions even if my patients present WM lesions but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images?
Thank you for your help, Arianna
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/1Kb8pmdPdKdYdZdQofh1Zs9Y9vJBM9d8tTBbuN-azPwq2Up... https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELlJj_fUE5E2mrg9cDatPEQ-geElCrjJuTaB-qazWOXa5iGBZGLOgpj8pOQP2xaeiKGMTBx0gJLJ7v0j63ezQaAKtr1se2Q3DMPeaMz4eb-wWvG8dFTZuW5tVyAjfVcNFQ--_l8RLrQU0ggiPnC_v6suCGnlD6zxvQ0OURakuse4JLh8gb6PMUJubZMmp2jUneM7KDdD26KmfMDAJzwHmJK0cF0jGYRkc-eaOiWNxVi_rlvwTx1v4BnOH0X2DDI0vtRbTxaUbBooGZawK9XZUCCy5Yyb6piU6khHHqMAPrAg/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C02%257Cstce%2540di.ku.dk%257Ca91a682c46ca40db5bef08dd929178e4%257Ca3927f91cda14696af898c9f1ceffa91%257C0%257C0%257C638827875690801147%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DZ85vGQiqeULorQXYJrw9WfWWKxixOUCDLs98nEZLA28%253D%26reserved%3D0 .
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.
External Email - Use Caution
Thank you Stefano!
Just an additional curiosity, is there any function within Freesurfer that you think could be used to map and quantify microbleeds in SWI data?
Thanks for the help, Arianna
Il giorno mer 14 mag 2025 alle ore 17:26 Stefano Cerri ste.45.ste@gmail.com ha scritto:
External Email - Use CautionHi Arianna,
- Yes. Please note that the method was tuned and mostly tested on MS
patients.
- These two versions of SAMSEG model WMH/ WM lesions differently and
cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563 ).
- Yes. Note that SWI data might not add valuable information to the
lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data.
Stefano
Sent on behalf of Arianna Menardi:
Dear Experts,
I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions.
I am new to the approach so I have 3 main questions:
- Can I use Samseg for MS lesions even if my patients present WM lesions
but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images?
Thank you for your help, Arianna
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/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoG... https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELlJj_fUE5E2mrg9cDatPEQ-geElCrjJuTaB-qazWOXa5iGBZGLOgpj8pOQP2xaeiKGMTBx0gJLJ7v0j63ezQaAKtr1se2Q3DMPeaMz4eb-wWvG8dFTZuW5tVyAjfVcNFQ--_l8RLrQU0ggiPnC_v6suCGnlD6zxvQ0OURakuse4JLh8gb6PMUJubZMmp2jUneM7KDdD26KmfMDAJzwHmJK0cF0jGYRkc-eaOiWNxVi_rlvwTx1v4BnOH0X2DDI0vtRbTxaUbBooGZawK9XZUCCy5Yyb6piU6khHHqMAPrAg/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C02%257Cstce%2540di.ku.dk%257Ca91a682c46ca40db5bef08dd929178e4%257Ca3927f91cda14696af898c9f1ceffa91%257C0%257C0%257C638827875690801147%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DZ85vGQiqeULorQXYJrw9WfWWKxixOUCDLs98nEZLA28%253D%26reserved%3D0 .
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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1PfT23qIe_lDJXa9HtHHeTFPTahJpTNiK_CMSmDfOXqJ7CI... 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/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoG... < https://secure-web.cisco.com/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoG... .
No, I don't think so.
On 5/14/2025 11:51 AM, Arianna Menardi wrote:
External Email - Use Caution
Thank you Stefano!
Just an additional curiosity, is there any function within Freesurfer that you think could be used to map and quantify microbleeds in SWI data?
Thanks for the help, Arianna
Il giorno mer 14 mag 2025 alle ore 17:26 Stefano Cerri ste.45.ste@gmail.com ha scritto:
External Email - Use Caution Hi Arianna, 1) Yes. Please note that the method was tuned and mostly tested on MS patients. 2) These two versions of SAMSEG model WMH/ WM lesions differently and cannot be directly compared. The basic SAMSEG is not designed for accurate WMH or WM lesion estimation. Note that you can use the lesion version of SAMSEG on scans without lesions (see Fig. 6 here <https://secure-web.cisco.com/1KM7GJ1i4uKDVvBOOHjfxLxbNpEbDV37ju32_ri0-iGtre9ZQKasYmqnwK6bi5vzt5-BaRS02ywgcOcI--IezHyHTAKt807vpLrXUZvO33iKmYOL0EeUkqkVhKXj38poEFY9bY4Djm69SgNrHqC2TpJRpU5OQUybXs5s7nPnXPv0ArkvG_YpXaiip_cs58dLk8TygUTgVuRtW8x9gYHo_BSTpTQs6pwsWwQ2nel-ejGeDe1nkcKTJcqBaT8vZrbLqyVpzVwZRXQDIXUhOjCyNPkbtTJdnT8BSGUjOyXcMp0Etejbfjh9bThJhaEK0tzEhXSLDLIgxCcSmrxk53keXlg/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS1053811920309563>). 3) Yes. Note that SWI data might not add valuable information to the lesion and whole-brain segmentation task. My suggestion is to visually inspect a couple of subjects with and without SWI data. Stefano Sent on behalf of Arianna Menardi: ---- Dear Experts, I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions. I am new to the approach so I have 3 main questions: 1. Can I use Samseg for MS lesions even if my patients present WM lesions but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images? Thank you for your help, Arianna 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 <https://secure-web.cisco.com/1tDmFFExvcidAJHTtPomz2TcTR-cmBcLvo3q_epfYYnELlJj_fUE5E2mrg9cDatPEQ-geElCrjJuTaB-qazWOXa5iGBZGLOgpj8pOQP2xaeiKGMTBx0gJLJ7v0j63ezQaAKtr1se2Q3DMPeaMz4eb-wWvG8dFTZuW5tVyAjfVcNFQ--_l8RLrQU0ggiPnC_v6suCGnlD6zxvQ0OURakuse4JLh8gb6PMUJubZMmp2jUneM7KDdD26KmfMDAJzwHmJK0cF0jGYRkc-eaOiWNxVi_rlvwTx1v4BnOH0X2DDI0vtRbTxaUbBooGZawK9XZUCCy5Yyb6piU6khHHqMAPrAg/https%3A%2F%2Feur02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fwww.massgeneralbrigham.org%252Fcomplianceline%26data%3D05%257C02%257Cstce%2540di.ku.dk%257Ca91a682c46ca40db5bef08dd929178e4%257Ca3927f91cda14696af898c9f1ceffa91%257C0%257C0%257C638827875690801147%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DZ85vGQiqeULorQXYJrw9WfWWKxixOUCDLs98nEZLA28%253D%26reserved%3D0> . 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1PfT23qIe_lDJXa9HtHHeTFPTahJpTNiK_CMSmDfOXqJ7CIuWnNbs-eqVAyeyK1QV015Ze-lCocqmRIaremDavd2FiyOegA7IFrVJ8qngx4E-qZdnAIQr2v-HQmKCI8ibFznM6Rlzt4K-2-x676Ftj3NBMjLnj9aRAakpdyEY_hjrKXRSNsltYRe66aYxE_YBVYe0Fc-JJQLggUJhq1ZFQbuSDcpMNyEy4Io2-IbaLjIzMKIzwfarF6uxKM11MU-orJ4Ttv14aCAQoeGQl5YwBp-gs4R7-euXCSG7Iv5NNjsneeNZkx2aOND0uAhP-PfPNPPcQHnY0GP8DxMparxYEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> 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 <https://secure-web.cisco.com/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoGUYISc1eGF7rB4Vuq0hhEG28UJtwbUf_YgI0KVpppHZB1LWnNQxVqixBOZWnbUx6lvko0EcawkeqdxKA6GbMfwMfu4M2nIgrJdkSEaj_0oQA8ZOk7_ZtNg-AvWI1hzsM0ex5prLqGd8eZPlPXiNr444pJK7y8ktVBm1s-sz2R3FVRICOZqk10BhBs0ZfhUjo8lsCllb8doj6DxRUEAIAs9F52FaObTrvh7U1rkNaTRM9G_q7kjdez9f8XFrccxhPqY1yZuOkgi3O3u97__aiOTPXkzS-QDOFZXapyoBMQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1XXzeUVIlswRYB32b4Im8HqpGqypNx3qr57S_8rr-pZADoGUYISc1eGF7rB4Vuq0hhEG28UJtwbUf_YgI0KVpppHZB1LWnNQxVqixBOZWnbUx6lvko0EcawkeqdxKA6GbMfwMfu4M2nIgrJdkSEaj_0oQA8ZOk7_ZtNg-AvWI1hzsM0ex5prLqGd8eZPlPXiNr444pJK7y8ktVBm1s-sz2R3FVRICOZqk10BhBs0ZfhUjo8lsCllb8doj6DxRUEAIAs9F52FaObTrvh7U1rkNaTRM9G_q7kjdez9f8XFrccxhPqY1yZuOkgi3O3u97__aiOTPXkzS-QDOFZXapyoBMQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Arianna Menardi -
Douglas N. Greve -
Stefano Cerri