Hi Mehul,

I think -write-probs still works, although it's been a long time since I used it. You would then find the voxels in the aseg that are the class you want (e.g. wm) and their probabilities would be given in the volume you write with -write-probs (or maybe something monotonically related to the probability)

Bruce

On Wed, 7 Jul 2010, Mehul Sampat wrote:

Hi Folks,

I believe that I can create a binary white matter mask using "mri_wmfilter".

I was wondering if there is a way to create a probabilistic white matter mask ? (for each voxel, I would like to obtain the probability of it being white matter)

I did a search on the mailing list and found the following related message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11786.html

The message suggests to use "-write_probs" flag with the mri_ca_label command but I dont see this flag as on option in the usage instructions for mri_ca_label. If this is the right way, should i just add "-write_probs wm.mgz" to mri_ca_label to get a probablistic white matter mask ?

Thanks Mehul