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?
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:
-Paul