Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared
You can get the WM from our white matter segmentation (wmparc.mgz and stats table wmparc.stats). You'd need to pick the cortical labels that you want to define as the "frontal lobes". You should create a binary mask with mri_binarize, passing the indices of the segments you want to use with the --match option, then load the mask in tkmedit to see whether it is what you expect. You can do a similar thing with the gray matter, but you can get the volumes from the ?h.aparc.astats
doug
Jared Price wrote:
Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with an atlas of the lobes (that covers WM and GM) for that kind of job
roberto
On Tue, Aug 18, 2009 at 9:24 PM, Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can get the WM from our white matter segmentation (wmparc.mgz and stats table wmparc.stats). You'd need to pick the cortical labels that you want to define as the "frontal lobes". You should create a binary mask with mri_binarize, passing the indices of the segments you want to use with the --match option, then load the mask in tkmedit to see whether it is what you expect. You can do a similar thing with the gray matter, but you can get the volumes from the ?h.aparc.astats
doug
Jared Price wrote:
Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
actually, Doug's wm parcellation tool should be able to parcel out the frontal white matter from a lobar segmentation.
cheers Bruce On Wed, 19 Aug 2009, roberto toro wrote:
That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with an atlas of the lobes (that covers WM and GM) for that kind of job
roberto
On Tue, Aug 18, 2009 at 9:24 PM, Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can get the WM from our white matter segmentation (wmparc.mgz and stats table wmparc.stats). You'd need to pick the cortical labels that you want to define as the "frontal lobes". You should create a binary mask with mri_binarize, passing the indices of the segments you want to use with the --match option, then load the mask in tkmedit to see whether it is what you expect. You can do a similar thing with the gray matter, but you can get the volumes from the ?h.aparc.astats
doug
Jared Price wrote:
Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
fantastic! I didn't know of that feature :) thanks, roberto
On Wed, Aug 19, 2009 at 4:07 PM, Bruce Fischlfischl@nmr.mgh.harvard.edu wrote:
actually, Doug's wm parcellation tool should be able to parcel out the frontal white matter from a lobar segmentation.
cheers Bruce On Wed, 19 Aug 2009, roberto toro wrote:
That will not be able to separate the only frontal WM from the rest of the WM, isn't it? I have used FSL (a mix of bet,flirt and fnirt) with an atlas of the lobes (that covers WM and GM) for that kind of job
roberto
On Tue, Aug 18, 2009 at 9:24 PM, Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can get the WM from our white matter segmentation (wmparc.mgz and stats table wmparc.stats). You'd need to pick the cortical labels that you want to define as the "frontal lobes". You should create a binary mask with mri_binarize, passing the indices of the segments you want to use with the --match option, then load the mask in tkmedit to see whether it is what you expect. You can do a similar thing with the gray matter, but you can get the volumes from the ?h.aparc.astats
doug
Jared Price wrote:
Hi freesurfer gurus, We are doing some freesurfer processing for a collaborating lab and the PI has asked us for a measure of gray matter volume and a measure of white matter volume, both of which need to be specific to just the frontal lobes. Does anyone know of a simple, and accurate, way of acquiring these measures from freesurfer? Thanks. Jared
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Jared Price -
roberto toro