Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016).
1) Is the choroid plexus included in the binarized then 3mm eroded segmentation to find the mean ventricular CSF signal?
2) Is there a way to input my own estimation of ventricular CSF signal to mri_gtmpvc?
Thanks! Adam
What do you mean? You have your own CSF segmentation and you want to use that instead of the one created by gtmseg?
On 10/20/2016 11:32 AM, Adam Martersteck wrote:
Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016).
- Is the choroid plexus included in the binarized then 3mm eroded
segmentation to find the mean ventricular CSF signal?
- Is there a way to input my own estimation of ventricular CSF signal
to mri_gtmpvc?
Thanks! Adam
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for replying Doug,
Yes, I would like to use my own mask if the choroid plexus is included but *only* for Tau PET. There is high off-target binding of the new tau PET ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid that high signal when estimating CSF.
I think choroid plexus being included for all the other types of PET I plan on using (FDG or amyloid PET) is great -- because it bridges the ventricles at the septum pellucidum (intended or not) -- and makes the erosion of 3mm much less 'harsh' because it's eroding from a connected mass of 1 segmentation instead of two independent segmentations (left and right ventricles).
if choroid plexus is not included -- then no worries, I'll continue using it for AV1451 Tau PET just like for amyloid and FDG PET as planned. If it is -- is there a way to expose the CSF estimation in the script so that I could input my own estimation (just the ventricles)?
Thanks! Adam
On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
What do you mean? You have your own CSF segmentation and you want to use that instead of the one created by gtmseg?
On 10/20/2016 11:32 AM, Adam Martersteck wrote:
Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016).
- Is the choroid plexus included in the binarized then 3mm eroded
segmentation to find the mean ventricular CSF signal?
- Is there a way to input my own estimation of ventricular CSF signal
to mri_gtmpvc?
Thanks! Adam
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
Hi,
Just want to bump this to the top now that the weekend is over!
Thanks for any insights about the CSF estimation, Adam
On Fri, Oct 21, 2016 at 1:03 PM, Adam Martersteck acmarter@gmail.com wrote:
Thanks for replying Doug,
Yes, I would like to use my own mask if the choroid plexus is included but *only* for Tau PET. There is high off-target binding of the new tau PET ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid that high signal when estimating CSF.
I think choroid plexus being included for all the other types of PET I plan on using (FDG or amyloid PET) is great -- because it bridges the ventricles at the septum pellucidum (intended or not) -- and makes the erosion of 3mm much less 'harsh' because it's eroding from a connected mass of 1 segmentation instead of two independent segmentations (left and right ventricles).
if choroid plexus is not included -- then no worries, I'll continue using it for AV1451 Tau PET just like for amyloid and FDG PET as planned. If it is -- is there a way to expose the CSF estimation in the script so that I could input my own estimation (just the ventricles)?
Thanks! Adam
On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
What do you mean? You have your own CSF segmentation and you want to use that instead of the one created by gtmseg?
On 10/20/2016 11:32 AM, Adam Martersteck wrote:
Hi FreeSurfer team,
Hopefully Doug or someone familiar with the new PET PVC implementation can answer a few things I can't seem to find on http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer or either of Doug's PVC publications (2013 or 2016).
- Is the choroid plexus included in the binarized then 3mm eroded
segmentation to find the mean ventricular CSF signal?
- Is there a way to input my own estimation of ventricular CSF signal
to mri_gtmpvc?
Thanks! Adam
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
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 Adam, it might depend on which version you are running. I've been working on it over the last year and made some changes related to choroid plexus. The version that I have now does not merge CP with CSF. You can check in your analysis by running
cd gtmdir/aux
mri_binarize --i seg.nii.gz --match 31 --count count.dat
mri_binarize --i seg.nii.gz --match 63 --count count.dat
If you see something like
Found 675 values in range
then the CP is represented as a separate ROI (left and right, 31 and 63 from FreeSurferColorLUT.txt)
doug
On 10/21/2016 02:03 PM, Adam Martersteck wrote:
Thanks for replying Doug,
Yes, I would like to use my own mask if the choroid plexus is included but /only/ for Tau PET. There is high off-target binding of the new tau PET ligand AV1451 (formerly called T807) in choroid plexus. I wanted to avoid that high signal when estimating CSF.
I think choroid plexus being included for all the other types of PET I plan on using (FDG or amyloid PET) is great -- because it bridges the ventricles at the septum pellucidum (intended or not) -- and makes the erosion of 3mm much less 'harsh' because it's eroding from a connected mass of 1 segmentation instead of two independent segmentations (left and right ventricles).
if choroid plexus is not included -- then no worries, I'll continue using it for AV1451 Tau PET just like for amyloid and FDG PET as planned. If it is -- is there a way to expose the CSF estimation in the script so that I could input my own estimation (just the ventricles)?
Thanks! Adam
On Thu, Oct 20, 2016 at 3:24 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What do you mean? You have your own CSF segmentation and you want to use that instead of the one created by gtmseg? On 10/20/2016 11:32 AM, Adam Martersteck wrote: > Hi FreeSurfer team, > > Hopefully Doug or someone familiar with the new PET PVC implementation > can answer a few things I can't seem to find on > http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer <http://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer> or either of Doug's > PVC publications (2013 or 2016). > > 1) Is the choroid plexus included in the binarized then 3mm eroded > segmentation to find the mean ventricular CSF signal? > > 2) Is there a way to input my own estimation of ventricular CSF signal > to mri_gtmpvc? > > Thanks! > Adam > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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Douglas N Greve