How to calculate the FA value of a tract when given tractometry profile?

Dear All,

Richie-Halford A, Cieslak M, Ai L, Caffarra S, Covitz S, Franco AR, et al. An analysis-ready and quality controlled resource for pediatric brain white-matter research. Sci Data. 2022;9(1):616

This paper shared tractometry profiles of 24 tracts using pyAFQ. See below for specific methodologies.

Each streamline was resampled to 100 nodes and the robust mean at each location was calculated by estimating the 3D covariance of the location of each node and excluding streamlines that are more than 5 standard deviations from the mean location in any node. Finally, a bundle profile of tissue properties in each bundle was created by interpolating the value of MRI maps of these tissue properties to the location of the nodes of the resampled streamlines designated to each bundle. In each of 100 nodes, the values were summed across streamlines, weighting the contribution of each streamline by the inverse of the Mahalanobis distance of the node from the average of that node across streamlines. Bundle profiles of mean diffusivity (MD) and fractional anisotropy (FA) from the diffusional kurtosis imaging (DKI) model , implemented in DIPY

Can I take the average of 100 nodes of a tract as the FA value of the tract? Or how to calculate the FA value of a tract when given such tractometry profile?

Any help is greatly appreciated!

Hi @fullcream ,

Often times you see groups sample the middle 80 nodes because you get lots of noise/partial volume effects from branching that happens at the ends of tracts.

You can also use something like tcksample from MRtrix:

tcksample track.tck fa.nii.gz fa_vals.txt -stat_tck mean -precise


Thanks for your reply! @Steven.

Indeed, I get a csv file that all 24 tracts and their corresponding FA values of 100 nodes. So I can just calculate the average of the middle 80 nodes just like you suggested.

Can you give me with some references on these? I would like to study them in depth

Often times you see groups sample the middle 80 nodes

Thanks again for your help!

We excluded the first and last 10 nodes because they are susceptible to crossing with U-fibers and partial voluming with gray matter. Although the results of the remaining 80 nodes are plotted as tract profiles (Figs. 3, 4), we averaged the data of 80 nodes to obtain a single-number summary of each metric per subject for statistical comparisons. For the dMRI metrics, we report the average results of the two runs.

FA was computed based on a standard tensor model
(Basser and Pierpaoli, 1996) to index white-matter coherence
for each tract. Each tract’s FA profile was computed across
each tract in each hemisphere and subject and then averaged
across the middle 50% portion of each tract’s profile to index
coherence (Figure 1C; Supplemental Information).

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@Steven Thank you very much! And thank you for finding out those papers! I’ll read it in depth.