Sorry for not being clear. I meant how to calculate path length based on path.pd.nii.gz, and the Center and Weight Average of the scalar images? Thanks.
On Fri, Dec 21, 2012 at 3:45 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Ping - Are you asking how you can produced the stats? You could use > fslstats with path.pd.nii.gz as the mask, and redirect the outputs to a file > that looks like pathstats.overall.txt. You could either keep the same names > for the measures or edit the tractstats2table script to change the names > that it allows. Hope I answered your questions. > > a.y > > > On Fri, 21 Dec 2012, Ping-Hong Yeh wrote: > >> Hi Anastasia, >> >> Thank you the answers. >> One more question, if I'd like to use the scalar images created by >> other methods, e.g. non-linear fitting, how can I feed this images to >> output the stats like the pathstats? I knew the "tractstats2table" >> will do the jobs, but it is binarized and hard-coded. >> >> ping >> On Thu, Dec 20, 2012 at 5:30 PM, Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> >>> 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
