Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang
Hi Thang,
putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look?
Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote:
Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang
Thang,
As Bruce said, there should be something called "Left-Putamen" "Right-Putamen" "Left-Caudate" "Right-Caudate" that should NOT have zero values. There is something in that file called "Left-Caudate/Putamen" and "Right-Caudate/Putamen" that will have a zero value has there is nothing in the aseg that is labeled as that.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, July 27, 2006 9:05 PM To: Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] caudate/putamen values for mri_segstats
Hi Thang,
putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look?
Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote:
Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use or have not been in use yet. Is there a way of manually getting values for these regions? Thank you for all the help, -Thang
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Jenni, those were the regions to which I was referring. Are there any plans for those zero-value regions to be labeled? We're interested in investigating the insula, Left-Caudate/Putamen, and Right-Caudate/Putamen and would like to know if there are any plans for these regions to be labeled. Thank you for your time, -Thang
-----Original Message----- From: Jenni Pacheco [mailto:jpacheco@nmr.mgh.harvard.edu] Sent: Thursday, July 27, 2006 6:13 PM To: 'Bruce Fischl'; Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] caudate/putamen values for mri_segstats
Thang,
As Bruce said, there should be something called "Left-Putamen" "Right-Putamen" "Left-Caudate" "Right-Caudate" that should NOT have zero values. There is something in that file called "Left-Caudate/Putamen" and "Right-Caudate/Putamen" that will have a zero value has there is nothing in the aseg that is labeled as that.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, July 27, 2006 9:05 PM To: Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] caudate/putamen values for mri_segstats
Hi Thang,
putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look?
Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote:
Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use
or
have not been in use yet. Is there a way of manually getting values
for
these regions? Thank you for all the help, -Thang
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Thang,
we do label the caudate and the putamen. Did you look at your aseg volume to see if they are there?
Bruce
On Fri, 28 Jul 2006, Nguyen, Thang Q wrote:
Thank you Jenni, those were the regions to which I was referring. Are there any plans for those zero-value regions to be labeled? We're interested in investigating the insula, Left-Caudate/Putamen, and Right-Caudate/Putamen and would like to know if there are any plans for these regions to be labeled. Thank you for your time, -Thang
-----Original Message----- From: Jenni Pacheco [mailto:jpacheco@nmr.mgh.harvard.edu] Sent: Thursday, July 27, 2006 6:13 PM To: 'Bruce Fischl'; Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] caudate/putamen values for mri_segstats
Thang,
As Bruce said, there should be something called "Left-Putamen" "Right-Putamen" "Left-Caudate" "Right-Caudate" that should NOT have zero values. There is something in that file called "Left-Caudate/Putamen" and "Right-Caudate/Putamen" that will have a zero value has there is nothing in the aseg that is labeled as that.
Jenni
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Thursday, July 27, 2006 9:05 PM To: Nguyen, Thang Q Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] caudate/putamen values for mri_segstats
Hi Thang,
putamen and caudate should definitely *not* be 0. Did you look at the aseg volume in tkmedit? How does it look?
Bruce On Thu, 27 Jul 2006, Nguyen, Thang Q wrote:
Hello all, I used mri_segstats to get subcortical volumes my subjects. However, for some of the regions like the putamen and caudate, I get values of zero. I have been told that these values are either no longer in use
or
have not been in use yet. Is there a way of manually getting values
for
these regions? Thank you for all the help, -Thang
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Thang,
The Caudate and the Putamen are labeled. They should be in your aseg.stats file as "Left-Putamen" "Right-Putamen" "Left-Caudate" and "Right-Caudate". If they are not there then there is likely something wrong with your aseg.
the label that is specifically called "Left-Caudate/Putamen" and "Right-Caudate/Putamen" is not something that corresponds to a label in our aseg, and there are no plans to change the current labels.
You should be using the values from "Left-Putamen" "Right-Putamen" "Left-Caudate" and "Right-Caudate".
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jenni Pacheco -
Nguyen, Thang Q