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I've just exposed the option to the user. It might take some days before it will be available in the development version.
@sudeepti: In the new development version, if you add to your samseg command the following flag "--do-not-use-shape-model", the lesion shape model (VAE) will not be used. This will most probably produce a lesion segmentation with more true positives *and* more false positives. Please double-check the results if you're using this option.
Stefano
On Fri, Jan 5, 2024 at 11:20 AM Koen Van Leemput leempko@gmail.com wrote:
External Email - Use CautionHi 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.ste@gmail.com wrote:
External Email - Use CautionHi,
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/1n6HHxGODqkOuO4bNnigMhWKnI-nKae-t26hw5s_Sdz9GzW... 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
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 CautionHello 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.
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