Whole brain fibers shorter than expected

1

Hi to mrtrixers!
I am working on 2 human groups’ brain tractography. But the .tck files seem weird because the fiber lengths are much shorter than what I expected.

My DWI data for both subject groups underwent eddy only. As single-shell data, I ran:

  1. dwi2response tournier -shells 1000,0 -nthreads 8
    and averaged responses within groups (responsemean command).

  2. FODs were calculated via:
    dwi2fod -shells 1000 msmt_csd dwi_eddy_prepro.nii common_mean_res.txt “$fod_file” -mask dwi_eddy_prepro_mask.nii.

  3. 5ttgen T1_raw.mif 5tt_nocoreg.mif

  4. flirt T1_raw.nii mean_b0_dwi_eddy_prepro.mif -dof 6 -omat diff2struct_fsl.mat

  5. transformconvert diff2struct_fsl.mat mean_b0_dwi_eddy_prepro.mif T1_raw.mif flirt_import diff2struct_mrtrix.txt

  6. Coregistered T1_coreg.mif and 5tt_coreg.mif via:
    mrtransform -linear diff2struct_mrtrix.txt -inverse.

  7. Generated GM-WM interface mask:
    5tt2gmwmi 5tt_coreg.mif gmwmSeed_coreg.mif.

  8. Executed tractography:
    tckgen -act 5tt_coreg.mif -backtrack -seed_gmwmi gmwmSeed_coreg.mif -select 10000 wmfod_norm.mif tracks_10k.tck.

Questions:

  1. Are my parameters and steps reasonable?
  2. Are abnormally short whole-brain tracts (see fig.1) caused by inadequate preprocessing (e.g., missing bias field correction)?
    fig.1 tck&t1
    fig.1 tck&t11210×773 242 KB

Many thanks
Yaqin

2

Hi Yaqin.

I am not an MRtrix expert. It seems you are missing some preprocessing steps (see for some information and links: Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging | Nature Protocols, Questions about FOD abnormalities and bias correction in single-shell FBA pipeline - #2 by WilliamFCB)

Also, when using single shell data you should use Single-Shell 3-Tissue CSD (SS3T-CSD) and not MSMT-CSD.

Cheers
William

3

HI William，
Thanks for your comments.
I think the MSMT-CSD can be used with single-shell data, according to Fibre density and cross-section - Single-tissue CSD — MRtrix3 3.0 documentation, specifically subsection 9 supports it. But I am not sure whether using SS3T-CSD will output better results or not.

I can only doubt that there is a problem with the preprocessing steps. Referring to the paper you mentioned, I found that my previous misunderstanding was that the denoising and Gibbs ringing processes are optional rather than necessary. It seems that eddy correction alone is still not sufficient. Next, I plan to start from the denoising step, reprocess the data, and then proceed with tractography.

Many thanks
Yaqin