Hi Vanessa, what exactly are you trying to do? Write out a volume with the voxel values having the posterior probability of white matter? Then do what with it?
cheers Bruce On Thu, 1 Mar 2012, Palzes, Vanessa wrote: > 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 as mri_wmfilter but I think that one is outdated since it looks to a 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-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of > freesurfer-requ...@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 > > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of Freesurfer digest..." > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
