Hi Vincent - That is correct. The average values of FA/MD/RD/AD in pathstats.byvoxel.txt are averaged over all the sampled paths for that subject at equivalent positions along the trajectory of the path. Roughly speaking, if 0<=s<=1 is the arc length along the path, where s=0 is the starting point and s=1 is the ending point of the path, the values are averaged at a set number of arc lengths, s = [0, ds, 2*ds, ... 1] along the paths. The corresponding position is established among all sampled paths for a subject and the FA/MD/RD/AD are averaged at that position for all sampled paths. So it's esentially an average value at a given cross-section of the pathway.
Hope this helps, a.y On Mon, 9 Dec 2013, Vincent Brunsch wrote: > Hi Anastasia, > Thanks for the new features! The first one helps me a lot!! When looking > at 2., I realized I had not understood the Avg values in pathstats.byvoxel. > The non-Avg values are just the measures at each of these voxels on the > MAP, ok. But then it says > " The last four entries are the axial diffusivity, radial diffusivity, > mean diffusivity, and fractional anisotropy at the same position, > averaged over all sampled paths. " > "Same position" refers to e.g. the first position of a sampled path that > could be located at a different voxel than stated in that row (x,y,z) in > the beginning, right? > I understand that this is an equivalent to the weighted Average values > in pathstats.overall as all sampled paths are considered, even if a > voxel would be hit more than once by the MCMC algorithm. > If this is correct, it also seems that every sampled path for one > subject comprises the same number of voxels? This only differs BETWEEN > subjects as is pointed out later by your new feature? > Best, > Vincent > > > Am 12/9/2013 9:23 AM, schrieb Anastasia Yendiki: >> Hi all - I have just posted a tracula software update. This update adds >> some new functionality without any changes to any existing functionality, >> so you can use it with any analyses you have already done in 5.3. >> >> What's new: >> 1. Compute measures of head motion, as in our recent paper: >> http://www.sciencedirect.com/science/article/pii/S1053811913011312 >> >> 2. Makes it easier to perform "along-the-tract" type analyses by combining >> the FA/MD/etc values from multiple subjects by position along each tract. >> >> 3. Gradient vector tables can now be different for each scan, they can be >> formatted in columns or rows, and blank lines at the end of the table >> should not pose a problem. >> >> 4. Fixed a small scripting bug that was causing the longitudinal stream >> not to run at all on certain platforms. >> >> You can get the update here: >> http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates >> >> Download the file for the appropriate platform (same as your freesurfer >> 5.3 distribution), unzip it, and copy the files directly into your >> $FREESURFER_HOME/bin. >> >> The trac-all wiki page has been updated, with the new command-line >> options shown in red: >> http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Arguments >> >> The tracula tutorials have also been updated with info on how to use these >> new features. Specifically: >> >> 1. For measures of head motion, see "Outputs from quality assessment" in: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaOutputs >> >> 2. For along-the-tract analyses, see "Anisotropy and diffusivity along the >> trajectory of a pathway" in: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics >> >> 3. For new options for specifying gradient tables, see "Specify the >> diffusion-encoding gradient table" in: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >> >> Enjoy and thank you for your feedback, >> a.y >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > --- > This email is free from viruses and malware because avast! Antivirus > protection is active. > http://www.avast.com > > _______________________________________________ > 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 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.
