Deterministic Tractography Error (FACT)

1

Hi all,

I am following Andy’s Brain Book MRtrix tutorial #7: Streamlines (MRtrix Tutorial #7: Streamlines — Andy's Brain Book 1.0 documentation)
and was trying to do a deterministic tractography by FACT algorithm.

I couldn’t find a standard explanation on conducting deterministic tractography,
I got stuck on a problem that streamlines are not connected like the following picture.

Screen Shot 2021-09-03 at 8.06.02 PM
Screen Shot 2021-09-03 at 8.06.02 PM686×503 119 KB

original code:
tckgen -act 5tt_coreg.mif -backtrack -seed_gmwmi gmwmSeed_coreg.mif -nthreads 8 -maxlength 250 -cutoff 0.06 -select 10000000 wmfod_norm.mif tracks_10M.tck

the code I wrote:
tckgen -act 5tt_coreg.mif -seed_gmwmi gmwmSeed_coreg.mif -nthreads 8 -maxlength 250 -cutoff 0.06 -select 10000000 wmfod_norm.mif tracks_10M_det.tck -algorithm FACT

Was there anything wrong(perhaps maxlength or cutoff…?) with the code above?
Can you tell me the general settings of deterministic tractography?
I want to find out what I had missed, but cannot find the right answer.

Thank you so much for your help!
Hope you have a great day.

Best wishes,
Sujin.

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2

Hi @Suzan_Park Sujin,

I think you may also want to swap the diffusion gradient directions. Also, changing polarity. Sometimes I also get unusual tractography. Best wishes.

Suren

3

FACT requires vector fields rather than FODs as input.

What happens is that the spherical harmonic coefficients of the FODs are interpreted as vector fields resulting in nonsensical fiber tracks.

So your FODs are probably fine (no need to swap gradient directions or anything) , but you need to stick to tracking algorithms that operate on FODs.

4

Thanks for your reply! We tried another algorithm SD_STREAM and got much better result! We would have been in trouble for so long without your help :rofl:
Hope you have a nice day :slight_smile:

1 Like