# How to calculate AFD after SIFT2

Hi,

I would like to calculate AFD values for several tracts. I know there are a lot of discussion on the forum already, but I was hoping someone could tell me specifically how to calculate AFD, as I am still not 100% sure about this. I ran the intensity normalisation across subjects, did the bias field corrections and calculated a group average response function. My questions is after running tcksift2, what exactly do I then do to get the AFD values? Do I just sum the cross-section multipliers for each streamline that are in the output textile or do I add them up and then divide by streamline length?

Cheers, Lena

Hi @Lena13,

At that point, just summing of the weights does the job (or just track counting in case of SIFT1; those all have the same weight in that case). The crucial insight to gain is that the streamline length is, at that point, not weighting the result itself (and hence should not be divided by any more). SIFT(2) makes the streamline counts/weights match the underlying AFD, but thereâ€™s only 1 streamline/weight per streamline, however short or long that streamline is. The streamline, after SIFTing, tries to fit, on average the underlying AFDs; not the sum of them along the streamline length.

Not sure if thatâ€™s a clear explanationâ€¦ @rsmith may be able to explain it from other points of view.

Cheers,
Thijs

Great, thatâ€™s all I needed to know. Thanks for clarifying this!

@ThijsDhollander got it, but just a warning on nomenclature: AFD is a measure of fibre volume, whereas the streamlines count after SIFT / sum of streamline weights after SIFT2 is a measure of fibre cross-sectional area. This factoring out of the streamlines length is important from both physical and biological perspectives, and also in the way the result is described; i.e. I would not refer to such a quantity as â€śThe AFD of the tractâ€ť, since that statement would imply a volume measurement. â€śConnection densityâ€ť probably suffices, unless we can come up with something better: â€śIntra-cellular cross-sectional areaâ€ť doesnâ€™t really roll off the tongueâ€¦

I know what youâ€™re referring to of course, but I must say that Iâ€™ve found even this terminology has been causing quite a bit of confusion lately (in the way it also pops up in e.g. the description of the `afdconnectivity` command: â€śa measure that is more related to the cross-sectional volume of the tractâ€ť).

This confusion, I have found, seems to arise from the (â€śclash withâ€ť) terminology we use for (fixel-)based analysis of fibre density (FD), fibre cross-section (FC) and the combined metric FDC. The way â€ścross-sectional volume (or area) of the tractâ€ť is mentioned in a SIFT / SIFT2 / `afdconnectivity` context, seems to refer to FC (because it sounds like it), but its â€śequivalentâ€ť is actually (much closer to) FDC; but then on average for the whole tract; i.e., SIFT(2) factors in both the â€śFDâ€ť per voxel that it (aims to) fit, as well as the â€świdthâ€ť (cross-sectional area on a macroscopic scale) of the bundle. Both reductions (at some point along a given tract) of FD and/or FC would cause a reduction of the â€śconnection densityâ€ť probability that is the output from SIFT(2) for that given tract.

So as the terminology is maturing, Iâ€™d personally try to aim for something that sounds a bit more like, or at least drives usersâ€™ intuition towards, the â€śFDCâ€ť concept, rather than sounding too much purely like the â€śFCâ€ť one. Or in other words, reserve the terminology of â€śfibre cross-section(al area) (FC)â€ť for the pure macroscopic effect: this is actually what weâ€™ve been doing now in some recent submissions and publications if we were facing the challenge of describing â€śFBA of FD and FCâ€ť in more general terms for the sake of an abstract (of a paper): using terminology like â€śmicroscopicâ€ť and â€śmacroscopicâ€ť to refer to the specific nature of the 2 separate properties we can extract and compare.

cross-sectional volume

Self-contradiction in 2 words Letâ€™s not base too much off of that descriptionâ€¦

This confusion, I have found, seems to arise from the (â€śclash withâ€ť) terminology we use for (fixel-)based analysis of fibre density (FD), fibre cross-section (FC) and the combined metric FDC.

The issue in my eyes is actually the FC metric. This isnâ€™t a â€śfibre cross-sectionâ€ť, but a â€śchange in fibre cross-sectionâ€ť. Iâ€™ve tried to clarify this where I can, and would have preferred if it were part of the â€śofficial definitionâ€ť of the term partly for this reason, but a compromise was needed so as not to bloat the FBA terminology.

So as the terminology is maturing, Iâ€™d personally try to aim for something that sounds a bit more like, or at least drives usersâ€™ intuition towards, the â€śFDCâ€ť concept, rather than sounding too much purely like the â€śFCâ€ť one.

Iâ€™d hesitate about explicitly comparing it with FDC, since the similarity is incomplete and would be of little use to anyone doing connectomics but not FBA. If you have a good understanding of both concepts, then absolutely itâ€™s closest to FDC; but Iâ€™m not sure if drawing the parallels helps or hinders education of the concept.

The important points to convey are that with tractography we get a total fibre connection density (as opposed to a cross-sectional change), of the pathway (as opposed to individual fixels), and that this quantity is proportional to fibre cross-sectional area rather than volume (as opposed to FC, which is a change in cross-sectional area that modulates a volume) and is therefore invariant to changes in length.

And all preferably in four words or less.

â€¦ Does the forum have a voting feature?

1 Like

I wouldnâ€™t really let this evolve based on a popularity vote. For those interested, Iâ€™ve created a GitHub â€śissueâ€ť about this. Itâ€™d be good to get some constructive discussion going, but this thread was probably not the ideal place to kick it offâ€¦ (my bad ).