External Email - Use Caution Hi Simone,
Based on your other recent question, I would recommend running samseg the way it is documented here: https://secure-web.cisco.com/1J42u65oQ1VRxZxUyRLQ0WfsPO92xbqHhvftl-50s4v7BtSkaxkqj9Uth8zkhUbE5ltPY6CmgzIx_1mP4ycP1j7W8fDqhKLTDHkGmI-DqSRGDbBcbVvD2ZYxadS3PEMABQR530EszSNiOS7P3awiDYnrJ_BT9Z_jWWQtA-6UpIv8bH-27XY-kylkZaYZaNmM5KNxFT1_dPoOAldmsiYqbaTq2yWdSVfWoQyFrZxT22GVZoY1AjZzvu7jb8GLFMbglRnbd6UX6s79VCV2KVDA74NAOpWXROIDzdFspEjG6ujb53KX6PCtoVLpnG4JSoYd944qWtAIRjCbarYFsvueWDQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSamseg In general, you will need the lesion pattern mask as otherwise you'll get a ton of false positive lesion detections. Koen On Mon, Mar 31, 2025 at 8:07 AM Simone Cauzzo <cauzzo.sim...@gmail.com> wrote: > External Email - Use Caution > > Dear support > I'm running samseg using Freesurfer 7.4.0. I'm using t1, t2 and flair as > input. I'm not sure if it's necessary to specify --lesion-mask-pattern but > if I try, I get an unrecognized flag error as it reads the second input to > --lesion-mask-pattern as a new flag. > > Log: > > ERROR: Flag 1 unrecognized. > --t1w [...]/001.mgz --flair [...]/oFL.mgz --t2w [...]/oT2.mgz --s [...]01 > --recon --use-flair --refmode t1w --pallidum-separate --lesion --fill > --threads 16 --lesion-mask-pattern 0 1 1 > > if I remove the "--lesion-mask-pattern 0 1 1" I don't get any error. > Any suggestion? > Thanks > > Simone > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ovE-Lo9_DCOscpXV6QW9kC4X7QcTHKapTjW07w2PrcGlGmH1HI5FND6e7GRuBe-q-46HkFnhG7zHD6ezKa_ZD8aJ8sU2jnir_2clAXBYUMqew-Vdybl0vqSHIugBtvM0GNLj6ED5ACmnD68EWCTKmY4CDAl3RC-opjIFG1_KvrpPjsi9x7XOv3E_HQwEowNdzAphHs-2Sj8QMLIY9J4fz8h4G1QpUsid6VBMkDCekIBFVYhG1hjBgjx4Uib5hftVpC-atKMVxOMuDBp-lqabxFfBLy73MzD_8eo28o2LUzzBLM8asXTaNpb_bgR_TzPtFLkWXJZlQMK4LBhlbKSs0Q/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://secure-web.cisco.com/1CZK5PL0tU561Hr8UbH4_GIBgBJBdrQ2WCxkPmb57Z0g3sqyFSsn-b2CoByVIK5mVYUw879-2a4pKaC5mfBzX-dm7uzn1Udh5rdJGHbVbOyqO0h61dOXc11ME_tFZ6XjWczWdw9lZuw26_AabcmIYclkJgwsxX70bwxcVMJNuoLepRw3WDdEWWRshDSOnQxyOtZjsDvrsmEw9xrf5qZg8dLJ-3h_a_DGKsjtN-wmh46K0DGMPjCzWIwW41lg_1hkl-7j2KWKX2Ne97qV7dw_DJdeqb-LN6gmHYnHs2n8jSko-kb6MZj7iHb2r7C6dPy98cJM6O_-2nWRxD3LhTWR9LA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1CZK5PL0tU561Hr8UbH4_GIBgBJBdrQ2WCxkPmb57Z0g3sqyFSsn-b2CoByVIK5mVYUw879-2a4pKaC5mfBzX-dm7uzn1Udh5rdJGHbVbOyqO0h61dOXc11ME_tFZ6XjWczWdw9lZuw26_AabcmIYclkJgwsxX70bwxcVMJNuoLepRw3WDdEWWRshDSOnQxyOtZjsDvrsmEw9xrf5qZg8dLJ-3h_a_DGKsjtN-wmh46K0DGMPjCzWIwW41lg_1hkl-7j2KWKX2Ne97qV7dw_DJdeqb-LN6gmHYnHs2n8jSko-kb6MZj7iHb2r7C6dPy98cJM6O_-2nWRxD3LhTWR9LA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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