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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