Path length: that's independent of any external scalar images. Weighted average: you multiply with the actual value in path.pd.nii.gz, then average. Center average: you average only over the voxels in path.map.nii.gz.
On Fri, 21 Dec 2012, Ping-Hong Yeh wrote: > 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
