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).
>
> 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
> 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.