Hi all,

Just few clarifications:

1) Lesions are segmented in SAMSEG with the label 99.

2) @Paul: The script Koen was talking about is not yet in the repo (hopefully we will commit it soon)

@Alberto: if you are just interested in *only* the volume of vascular lesions for different thresholds you can also run SAMSEG with the --save-posteriors flag to obtain lesion probabilities (in yourSeg/posteriors/Lesions.mgz). Then you can play with mri_binarize and mri_segstats to obtain lesion volumes for different thresholds without re-running anything.

Hope it helps.

Best,

Stefano

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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