Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface?
Thanks a lot,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823
It will certainly do cortex. We do not have a segmentation for subarachnoid spaces. Or are you just talking about extra cerebral CSF? We do have a segmentation for xCSF, but it is not the most beautiful thing in the world. For WM, the GTM will give you a PVC corrected value for the entire lh and rh cerebral WM (and cerebellar) segments. Is that all you need?
On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface?
Thanks a lot,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes I need the lh and rh cerebral WM for sure, but not just the values, also an image. And I need also a corrected image for the extra cerebral CSF. How can I get that?
Thank you very much,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, May 21, 2020 10:32 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question on partial volume correction
It will certainly do cortex. We do not have a segmentation for subarachnoid spaces. Or are you just talking about extra cerebral CSF? We do have a segmentation for xCSF, but it is not the most beautiful thing in the world. For WM, the GTM will give you a PVC corrected value for the entire lh and rh cerebral WM (and cerebellar) segments. Is that all you need?
On 5/19/2020 11:36 AM, Barletta, Valeria wrote: Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface?
Thanks a lot,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You can try using --rbv. In theory, you can use mueller-gaertner (--mgx), but I don't have it set up to look at WM or CSF. And be careful because the extracerebral CSF segmentation is often not very good.
On 5/21/2020 1:07 PM, Barletta, Valeria wrote:
Yes I need the lh and rh cerebral WM for sure, but not just the values, also an image. And I need also a corrected image for the extra cerebral CSF. How can I get that?
Thank you very much,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Thursday, May 21, 2020 10:32 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] question on partial volume correction It will certainly do cortex. We do not have a segmentation for subarachnoid spaces. Or are you just talking about extra cerebral CSF? We do have a segmentation for xCSF, but it is not the most beautiful thing in the world. For WM, the GTM will give you a PVC corrected value for the entire lh and rh cerebral WM (and cerebellar) segments. Is that all you need?
On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers, We need to analyze PET data after correcting for partial volume effect in the cortex, white matter and subarachnoid space. Is Freesurfer's partial volume correction working on all these areas or only the grey matter volume and surface? Is there a way to use gtmseg on the white matter and outside the pial surface?
Thanks a lot,
Valeria Barletta, MD Massachusetts General Hospital 149 13th Street, Charlestown MA 02129 (617)-724-8823
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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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Barletta, Valeria -
Douglas N. Greve