External Email - Use Caution Hi Alberto,
In the current implementation the volume reported in the table is simply the sum of the lesion posterior probabilities, i.e., it is not affected by the threshold used to create the crisp segmentation result for the lesions. 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). 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'll also need to know the label number in the FreeSurfer lookup table for lesions - perhaps Stefano can tell you what it is (?) Koen On Thursday, July 1, 2021, Alberto Del Cerro Leon <[email protected]> wrote: > External Email - Use Caution > > Hello FreeSurfer team, I have a question about SAMSEG thresholds. I am > analyzing the vascular lessions aplying several thresholds. I would expect > that lower thresholds results in lower volumes but dont seems like that. > What is the reason? >
_______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
