I found a couple older threads about creating a probabilistic mask in Freesurfer: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11790.html https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-July/014953. html
I have modified mri_ca_label with the flag -write-probs and instead of norm.mgz I use aseg.mgz:
mri_ca_label -align -nobigventricles -write-probs aseg.mgz transforms/talairach.m3z /Applications/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz
Freesurfer then tells me: "writing label probabilities to aseg.mgz" - so I assume that is a success.
Now in order to extract a white matter mask, I have tried both mri_extract_label and mri_binarize (although the point of this one is to binarize) to extract these probability values of the white matter areas from aseg.mgz. Unfortunately, I am not getting any probability values in the mask, neither in the form of 0-255 nor 0-1.
I've tried searching for another command I can use to create masks, such as mri_wmfilter but I think that one is outdated since it looks to a specific directory called "brain" within the subject folder. Is there another command I can use to extract masks with probability values? Or do I need to run the remaining pipeline of commands after mri_ca_label in order to achieve this?
Your help is greatly appreciated.
Thanks,
Vanessa Palzes Staff Research Associate Brain Imaging & EEG Lab San Francisco VA Medical Center 4150 Clement Street San Francisco, CA 94121 Tel: 415-221-4810 ext. 6155
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Thursday, March 01, 2012 9:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 97, Issue 1
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