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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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. > > > > > _______________________________________________ > 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 gr...@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
