Hi Ping - The total number of paths that were sampled doesn't enter the picture. Of these sampled paths, some get rejected and some get accepted. The latter are added up to get an estimate of the posterior probability distribution of the path (that's path.pd.nii.gz). You can normalize to a total sum of 1 by diving that volume with its total sum.
The default threshold is 20% of the maximum value, to get rid of the tails of the distribution (which would need more total samples to converge than the center of the distribution anyway). You can of course find your own averages at a different threshold from path.pd.nii.gz if you wish. Hope this helps, a.y On Fri, 14 Dec 2012, Ping-Hong Yeh wrote: > Hi Anastasia, > Just follow up on this thread.. > If 5000 samples were used for each voxel, how can I normalize the > intensity of path.pd volumes to a sum of 1 ? > Also what thresholding value was chosen to calculate the tract volume, > shown in the pathstats.overall.txt ? > > Thanks. > ping > > > > On Fri, Nov 9, 2012 at 10:56 AM, Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Jon - The path.pd volumes are indeed the posterior probability >> distributions of each pathway. They are not normalized to a sum of 1 >> though b/c they're estimated by a sampling algorithm (drawing sample paths >> from this unknown distribution and adding up the sample paths, instead of >> estimating the distribution directly). >> >> Hope this helps, >> a.y >> >> On Fri, 9 Nov 2012, Jon Clayden wrote: >> >>> Dear all, >>> I understand that the various "path.pd" image files that are created by >>> TRACULA represent a posterior >>> distribution over the corresponding tract location, but I was wondering if >>> someone could explain to me >>> exactly what the values in these images mean. I assume that they are not >>> probabilities as such, since they >>> have values ranging up to several hundreds. >>> >>> Thanks in advance, >>> Jon >>> >>> >> _______________________________________________ >> 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. >> > _______________________________________________ > Freesurfer mailing list > 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
