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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-50s4v7BtS...

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.simone@gmail.com wrote:

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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

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