External Email - Use Caution Hi Alberto, Koen and Stefano,
You can get the behavior you want/expect by counting the number of voxels > assigned to lesions in the seg.mgz file - there is a ready tool for that in > FreeSurfer but I don't remember off the top of my head what the correct > command is (a search on the mailing list should be able to reveal it) > You should be able to do this with mri_segstats, e.g. ``` mri_segstats --seg /path/to/seg.mgz --o test.txt ``` You'll also need to know the label number in the FreeSurfer lookup table > for lesions - perhaps Stefano can tell you what it is (?) The label for lesions should be specified in `$FREESURFER_HOME/FreeSurferColorLUT.txt`, right now there seems to be 2 entries: ``` # wm lesions 498 wmsa 143 188 143 0 499 other_wmsa 255 248 220 0 ``` A few months ago Stefano Cerri wrote some code to correct this behavior > (and apply different thresholds without having to re-run everything from > scratch), but it never made it into the repository (my fault). Koen/Stefano, just to double-check my understanding, and you referring to this script that Stefano wrote? - https://secure-web.cisco.com/12C09A1Pra-JQ3_eWwPneWHlTs8QZ2h-wDRi-AlByffQ_QIWIu17tflIF58pjQ9HLOtYBcmztu3euel_eLN7G38YXnAiDKnrzjd9K1QkAIh__uGT3yzeUplTZQgapM7wy_YWlhiWM1RXYX2WaRXDo1zP1ebLFpkCRmHKg11fXHSnWHutLwcl_ZnMKb4uZdQOe860OOFv_t1YAMwYZHLoHErw4f8FUZ0JvyxrNHd5msiz_sja5bAEgN7-3ZqR957S1Ad-OOZunTyOSFWOzdwljxQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Fsamseg%2Fgems_compute_binary_atlas_probs My understanding is that this could be used to update the priors of the model without having to re-run everthing. Not sure if what is being discussed here is related or something completely different. I've been working on generalizing that script to n-classes here: - https://secure-web.cisco.com/1VNfWVD_6T2AndQf1rq6BsPpYglmbJ3GzN01rptI6VZge7qfAmTxcMGIRwfyS5UFa94DGFk9puvQZ-aB22F7cAqEIaEAViRRfPmOh7v6j4oW0TT6wL4ZK9XyceRl2GA6yAbXcimGQj4dNZDAz6ACpxkTlMDbPOH3hmKvLE09mHQVuXanZu-iYF5s3VdKf8padIKNW2YCaC3Nmslowctma-X6lcGzwXCR4L3TiG_jou_E-tE_DVRuWrqWCtp7Z7aLTIxpQ-9P2iEKFt9C3XQsoAw/https%3A%2F%2Fgithub.com%2Fpwighton%2Ffreesurfer%2Fblob%2F20210513-fs-infant-dev-merge%2Fsamseg%2Frecompute_atlas_probs -Paul
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