External Email - Use Caution Hi Stefano,
For samseg isn't there also an option to disable the VAE shape model? I forgot the details, but if false positives are not an issue maybe that could also help? Koen On Friday, January 5, 2024, Stefano Cerri <ste.45....@gmail.com> wrote: > 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: > *MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" claiming > to be* > https://secure-web.cisco.com/1AbDUq0LXLC_wuj398BG4fYmP5OWi3BKCYXWtf4bYDiSc_gRavwq4Lsf_kjrX7zOkfYzH1a8Hz778SM3PXH9arnJnR9tpssWl7WlcQ47q_cjiXicNwkAEpJ8EvEmUvRb8cXd3gqbGgsV_q_a-H8vZUfK7WNGttlzZ8gYQ8obvUuGHuez0dYnwLU9ToLIX_VXTPJUkaThticFDR6m44AWbHMgzuMUUoOkjOEVptePMlj95qHTOrEzIyufEe_5LQfRr0iJ58zaDBm5ldwkPNgijWEqqUW8Wa5wirouJ0fCmEHyMNZgQGlgV6CHeqlJV-sqvI9RrOEwNEQP6dMYyIB0HOw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FWMH-SynthSeg > <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.edu*MailScanner has > detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1awKJbDMWjF_mXt9-XwZ6DAb4vg28mBXVqAu4ULpFDT9Cd1NgHZMuNhrCVUAMSkI4DycYP75NAFsF97ZPT7S70UNpGY66FF1GQzH_MgZNzxNj_YZLJbVLkvwFFuEaue0bTrAL1AQRo2-ORSPGexnTWcBTwJoGktLCZGc7rdIYNGHWB6HSvGLhzFXiQoRemjkU7lB54NVb2voz1o3_c9QhR0sCrk7WvLduVHnLORM8kxgMM_yohlENm7xzgi1UYV3YQpK-_Mi9AzgO5xeLUNRgBXA4G9pGZIzCDTmBe6uqy7hVwPNUNWGx9sL9u3S0w0Y3A8Bqxw6dujA_dhLhiruZ4A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > <https://secure-web.cisco.com/1L5bfw4JEkXOrhY8TbJ8DAIk6FHVJxNUWzVkU8Ueq6fQY5XqhPfvgjXxlg3X2muiBxW5BsnLz05HdvKtXjfwp2IXX4Hqn0PCfa7VynsizJ5YgIYDSZ1dc8AvYd7R3IA-NqcNwrwwTM0S3CFe1vKNaJbITTsCLRnLtzlyD8iXAZrCAG3nVCO8QZTi-RC1lQ9kx9ekO0eorj8dpx6oMQ62MMUtq-6-JKSkvH41LdhhA6JmH5BJpGemqfMjLr4wB8SUAKUINRO4TmZ7X18mVBtib09PBik62Pe9rvjtFS6J7Fi_R52V_O2hbGA0OLu5eZgVO-T698cN-xoglHC_x1hwB6g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > Please note that this e-mail is not secure (encrypted). 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