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Dr Sunniva Fenn-Moltu (she/her) Postdoctoral Research Associate Department of Forensic and Neurodevelopmental Science Institute of Psychiatry, Psychology & Neuroscience King’s College London 16 De Crespigny Park, Denmark Hill, London, SE5 8AF ________________________________ From: [email protected] <[email protected]> Sent: 02 July 2025 15:23 To: [email protected] <[email protected]> Subject: Freesurfer Digest, Vol 257, Issue 14 Send Freesurfer mailing list submissions to [email protected] To subscribe or unsubscribe via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Recon-all clinical vs. FS version 8.0.0 (Iglesias Gonzalez, Juan E.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 2 Jul 2025 14:23:09 +0000 From: "Iglesias Gonzalez, Juan E." <[email protected]> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 To: Freesurfer support list <[email protected]> Message-ID: <[email protected] prd04.prod.outlook.com> Content-Type: multipart/alternative; boundary="_000_PH0PR04MB83888D 5F6E0D1EB14A99250EFD40APH0PR04MB8388namp_" Oh, I see. They are fairly different in the way that they try to place cortical surfaces. Recon-all uses T1 intensities directly, and only works with high-resolution near-isotropic T1w scans. Recon-all-clinical uses machine learning and is compatible with scans of any contrast and resolution, BUT is less accurate than recon-all if you actually do have 1mm T1 data. So, I would try recon-all first. Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1K25c8GgtPaI1iQbFYGnNILxny8Ubj0djw1dmJIKkZgr4Fvj4ofJhgaNLMoKv2bwFWe7oUB2M7bBuuTjakAaEaIMDHxnMexY3mLLRzVExDrMQ8D4-GXrUXw8_MexKKbnnCn4TAShV1jEThCPBwUI-OGMbUmr8Pm8vAl-l6kanInEWs15WvNRqPeg4hA5o5XSHApo89vGYki88d7xPDKlUrXTLqvvLRJgLKl5XjesNWctfrukaSXaPnOAft8RBetsXDvXrK1AGn34FuygkADOzscSBuCQtEVAiA2-YVoQy7N-wusQIrv_NpJG5dscOXuzS/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.jeiglesias.com%252F%26data%3D05%257C02%257Csunniva.fenn-moltu%2540kcl.ac.uk%257C31c3752bbb93455eeefb08ddb97409a1%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C638870630244364781%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DCQAbsRQi3TBKEZ8CXxyn9%252FU1AlqVxfv25KlLMT0gL%252BU%253D%26reserved%3D0<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO64zkOLOidmfkT4pdSz9W6I8YhOnb73_J1MT4-j4JkHYOVMfErS70AcRZDllPVmbQ-PxdWl6eKgplk-aRRZvrHlhgnVaq0f48Fme1fg0ztfA7gRtxHc7sph49dJHUclJjhl1NvKFOyjkZcQN6kay3TfoYjrF3J1owSX71w8O1jdVufNXhc0pe3INuUahPEKx44mUbs9nxh41hfakKKMTrIcWwjCmCJvluN9mCPyRY7rrx0DZFlsHWrXIQ1MJ4I56vAuq5OPtszS2Dmohnt0N/http%3A%2F%2Fwww.jeiglesias.com%2F> From: Stefanie Bradley <[email protected]> Date: Wednesday, July 2, 2025 at 09:24 To: Freesurfer support list <[email protected]> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 External Email - Use Caution Hi Eugenio, Thanks for your response. I was more wondering if the standard recon-all pipelines (v8.0) are the same for recon-all clinical, since it seems like recon-all in version 8 uses Synthseg by default. My population is children aged 4-6 years old with cerebral palsy. The T1-weighted scans are MPRAGE, 0.8mm isotropic. Thanks, Stefanie ________________________________ From: Iglesias Gonzalez, Juan E. <[email protected]> Sent: Tuesday, July 1, 2025 8:35 PM To: Freesurfer support list <[email protected]> Subject: [Freesurfer] Re: Recon-all clinical vs. FS version 8.0.0 Dear Stefanie, What type of pathology are we discussing? What ages? What MRI sequence and resolution? Cheers, /Eugenio -- Juan Eugenio Iglesias https://secure-web.cisco.com/1HDqa2YX4Xwt8w_hiXJZ0lyV8Spi72Rzf-J41A6uWqy-QZnntaWXIetzO_aAiL73bgRnjJfKIBYKvxy0PsaG59UBQTOmKKeRwHeWrdGtdQaS8oYpYzUBce5IXPYfE702CM_Ms9a0hnlan2wV8-b6u9YNvNI9Wo3qWbk54CUSkQiAFGxgCzBdNnBEuIA_7uULHH8lf964UU32K0RmgwmLalvOY1MYyBQvvb77U3TxgNXBmDRfkrmzybUkqFKtc8w-r074uKyftR4iPn1DIfTTmZYyvLVw6DRiAes30zBfQIrRmHX9PLZDMvdZPAp_jhsnx/https%3A%2F%2Feur03.safelinks.protection.outlook.com%2F%3Furl%3Dhttp%253A%252F%252Fwww.jeiglesias.com%252F%26data%3D05%257C02%257Csunniva.fenn-moltu%2540kcl.ac.uk%257C31c3752bbb93455eeefb08ddb97409a1%257C8370cf1416f34c16b83c724071654356%257C0%257C0%257C638870630244384054%257CUnknown%257CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%253D%253D%257C0%257C%257C%257C%26sdata%3DsUAYvPOGHhin%252FMUV9g6gMTGgIh99M3YZsnYM1ZWExjg%253D%26reserved%3D0<http://secure-web.cisco.com/19dk633J8cDfEYmJaTrtHSBYKUttUKjsNwNDCuKAZXv-UO64zkOLOidmfkT4pdSz9W6I8YhOnb73_J1MT4-j4JkHYOVMfErS70AcRZDllPVmbQ-PxdWl6eKgplk-aRRZvrHlhgnVaq0f48Fme1fg0ztfA7gRtxHc7sph49dJHUclJjhl1NvKFOyjkZcQN6kay3TfoYjrF3J1owSX71w8O1jdVufNXhc0pe3INuUahPEKx44mUbs9nxh41hfakKKMTrIcWwjCmCJvluN9mCPyRY7rrx0DZFlsHWrXIQ1MJ4I56vAuq5OPtszS2Dmohnt0N/http%3A%2F%2Fwww.jeiglesias.com%2F> From: Stefanie Bradley <[email protected]> Date: Tuesday, July 1, 2025 at 5:49 PM To: Freesurfer support list <[email protected]> Subject: [Freesurfer] Recon-all clinical vs. FS version 8.0.0 External Email - Use Caution Hi there, I am analyzing some pediatric brains with clinical pathology, and I was wondering if I would expect a difference in the reconstructions from regular recon-all (Freesurfer version 8.0.0) vs. recon-all clinical, since they both use SynthSeg from what I understand? 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