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:fischl@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:fischl@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:fischl@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-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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