Hi Vanessa, my point is that I don't think you need the posterior probabilities. Just get the hard wm segmentation and erode it once or twice, and you will be left with voxels that are almost exclusively (and certainly) white matter.
cheers Bruce On Thu, 1 Mar 2012, Palzes, Vanessa wrote: > Hi Bruce, > > Yes, this is what I want to do - to form white matter ROIs, the white > matter partial volume maps are thresholded at a partial volume fraction > of 0.99 and then eroded by two voxels in each direction to further > minimize partial voluming with gray matter". > > So my question was that if there is a way to get a range of values from > the wm masks instead of 0s and 1s. > > Thanks again, > > 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 10:39 AM > To: Palzes, Vanessa > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] Probabilistic white matter mask > > Hi Vanessa, > > I'm saying if you extract the white matter segmentation, then erode it > once the remaining voxels will almost all be unpartial-volumed white > matter. Note that a threshold on the p-value isn't the same as finding > unpartial-volumed voxels (which I think is really what you want). > > cheers > Bruce > > > On Thu, 1 Mar 2012, Palzes, > Vanessa wrote: > >> Yes, noise ROIs for fMRI analysis. So are you saying when I extract wm >> masks, then the probabilities of those voxels being a part of white >> matter should be >.9? Is there no way of specifying a threshold? >> >> 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 10:21 AM >> To: Palzes, Vanessa >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] Probabilistic white matter mask >> >> 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. 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