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I've tried searching for another command I can use to create masks, such as mri_wmfilter but I think that one is outdated since it looks to a specific directory called "brain" within the subject folder.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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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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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
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
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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.
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
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@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.
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
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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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.
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
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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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.
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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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: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
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
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You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
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"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
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properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Palzes, Vanessa