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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