External Email - Use Caution Hi,
For SAMSEG: Are you using the --lesion-mask-pattern flag with the value "1" on the FLAIR scan? You can try to relax the masking by excluding darker than WM mean intensities voxels rather than darker than GM ones, i.e., by adding to your command: --lesion-mask-structure "White" For WMH-SynthSeg: It looks like a memory error (the process was killed). On the Wiki: https://secure-web.cisco.com/1HuCfTaru0pjBRImg5FBdnCDAClGBp2QhQDG_ONxySiD4aBpb8dX_9OWokS_PrsTYfMYUj6Dub6piUJi2g2Zpl7rhqLNDkcwSORd5hQ3SUk7_fYeGPCEOrfp3QjhjjHebnuj-k3zV_yc_wRKAI-jbX5BHqaNgPByMMc7-bhmMcBGophr1_lP4tmBxmq-SvMcZ0iWerp81-cOXMxo4NtbhS5gIUIhprFiFtLhcXjlwCtPcMIaIHbmTzL5XjtfzOLAg-22R7Awi6o7400qTCzIKXxyS473rB0txewIziNjlNmHT6MgPBPh5iwHokUj3naGQ_jEESDEujufpSbUwtVxLbA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FWMH-SynthSeg they recommend 32GB of RAM. Do you have access to a machine with more RAM? Stefano [Freesurfer] WMH-SynthSeg vs. SAMSEG for WM lesions <https://secure-web.cisco.com/10UF5Sfsck6gBiuQyh4tRFtvmnzLpFEUi-WgbbCbj9UG2boB9N5XjVjTMWP2Y5j0lQtS3keltoGD7fPWDgtVe4_5zwOh3es5NY-BMN0A-JNk3wH3si-segJF_xIACeMG_YaMeVT-mTgyjusr2X32cUZsjuXj60HXiGVdQp0SfFDc9lQHUzFNKP3zkFwCj3pM52K3KI10F1CmH4AxI-FtLil2AAV-fRw1C8_HdbId3ZjXeXMyJ7gC8DUXEWapUSmiRGZACymUMayzcIvfmH1L1S2za6QCGAGCsPoM8UG7wXCdJkTPJuWZKCpJPNYKouK85kbjGj8LeyF54sUq5M5VR-A/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dsubject%3A%2522%255C%255BFreesurfer%255C%255D%2BWMH%255C-SynthSeg%2Bvs.%2BSAMSEG%2Bfor%2BWM%2Blesions%2522%26o%3Dnewest> SudEEpti <https://secure-web.cisco.com/1oJN1ySIU6hTF6KozyWDOxPUxnfQT6NbHWVuqvL4RV_PNw-mjuH5HUIQ_4CrcrA2nB92UzWiqt0sldQoX7neyVBIx5YQ_ClIloJhwjfN3Wr-65IptS-tt7ZRgYRK4ptYQGQfsFX5B8cKOsc0-XY7SOZxDPnLT5_SQDK_zbCwXForrAFt6h-C4TbVXo15OSdI9A8_Wa4dkPrebnymfACMnEVmCmQyBjnkS71J2FBFdGJ1m8j_Gmkg7V-5nKiYy-Loc0f8uI6uvcCDH2wkofUf0wC8tT9K0feA_coqMJR_k3brvE_FKWAKCcp4TEUfmxhx39s2jcXEa0Kk6Ko5v93TwIA/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Dfrom%3A%2522SudEEpti%2522> Thu, 04 Jan 2024 23:54:04 -0800 <https://secure-web.cisco.com/1JsH5pJG8BzMI3v8LKsEGcmt1J0aRmNdo-KqIrQw8arF8BP4GEGTyt7o7BBWBpoBhFnf7H2f8hDDHgVlApzrrpJd2B6CFkE6_1l2GHF-la-9yG9VlF8r8WARQiwmJu8zcMm1Lo6NFMGySBH954XRq9sg_4lBw_KdBCO3c04OTsh4eiUGXUNVO4_ev_uGvK9CaGTT5qsKtJouRpJarF-2rJi15G4_C7HH3EQu1fTC-ZfCnZR_Iu-HmfT3RIgmWaGcMQ39UdoH5yjZTKXI60uUiVnYj8_pwvoQ1Je2JsEFnyBS_EBQIAzYniwh1Cqk6q8EevaCdjfZi-bisWeUEnjws8g/https%3A%2F%2Fwww.mail-archive.com%2Fsearch%3Fl%3Dfreesurfer%40nmr.mgh.harvard.edu%26q%3Ddate%3A20240104> External Email - Use Caution Hello Freesurfer I am reaching out for some advice on unsupervised WM lesion detection using SAMSEG and WMH-SynthSeg. *SAMSEG: * Our use case prioritizes maximizing true positives over minimizing false positives. However, even with a low threshold of 0.1, SAMSEG misses some areas (on FLAIR). Are there any strategies or parameters to force SAMSEG to be more "aggressive"? *WMH-SynthSeg:* Unfortunately, I have not been able to get WMH-SynthSeg to work. The error message is pasted below. Does this point to a memory issue (I have 24GB RAM)? *Arguments seem correct; loading Python packages...Using cpuUsing 1 thread(s)Preparing model and loading weightsWorking on image 1 of 1: /home/localuser01/southekal/TEMP/101-001_3scans_FLAIR/101-001-1_reg.mgz Loading input volume and normalizing to [0,1] Upscaling to target resolution Pushing data through the CNNKilledreal 3m33.897suser 2m48.028ssys 0m32.337s* Any insights or suggestions would be greatly appreciated! Thank you in advance. _______________________________________________ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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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