what is a noise ROI? Do you mean for fMRI analysis? You can probably achieve the same thing by eroding the white matter labels once. Everything that is left will almost certainly have p>.9
cheers Bruce On Thu, 1 Mar 2012, Palzes, Vanessa wrote: > Instead of getting binary values in a mask of the white matter, I would > like to get probability values of each voxel being a part of the white > matter, and only include voxels that have a high probability (.9+). > We've been using the wm masks to create noise ROIs. > > 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: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Thursday, March 01, 2012 10:02 AM > To: Palzes, Vanessa > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Probabilistic white matter mask > > 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 as mri_wmfilter but I think that one is outdated since it looks to a 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 >> >> >> > > > 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. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
