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

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