Tracking pipeline for data without EPI distortion correction?

Thanks all for your time,
I have a huge dataset without reversed phase data, my pipeline is as below:

  1. eddy current raw DWI data
  2. using freesurfer recon-all processing T1;(it’s already done, so I can’t use the registered T1)
  3. mrresize DWI from 2mm to 1mm, then using fnirt to register T1 to DWI, considering the frontal distortion I choose non-linear registration
  4. using 5ttgen to process non-linear registered T1
  5. using ACT to build tracts

tckgen ./odf_tournier.mif ./3_Tractography/tournier_Randseed20_WM_act_SDstream.tck -algorithm SD_STREAM -mask mask_erode_2.mif -seed_random_per_voxel …/1_T1Proc/5tt_WM.mif 20 -act …/1_T1Proc/5tt2dwispace.nii.gz

  1. using fnirt register atlas generated from Freesurfer with resized DWI, then using tck2connectome to extract tracts belong to atlas

Please give me some suggestions for improve my pipeline

Hi,

I don’t think there is anything wrong with that pipeline, however I don’t think the non-rigid registration will be as accurate as you need for this. My feeling is that the 5TT won’t be well aligned with your diffusion data, and neither the labels from freesurfer. I would use an atlas similar to the AAL for this case and without ACT. But you could try your approach and see if the results are good enough.

Best regards,

Manuel

Hi,

I can’t change my atlas :cold_sweat:, but I think I can perform tckgen without ACT and to see if the result is better than with ACT.
for suggestions on EPI distortion correction you gave before, I think they non-rigid register the DWI to T1 which firstly rigid transforming to DWI, I wonder if this transformation would affect the bvec?

Hi,

Yes, this is one way to do it. From my understanding, you have to constrain the registration to the phase encoding direction (see here), but I’ve seen some works when they don’t constrain this transformation (or at least, they don’t say it). A version of this approach is implemented in fmriprep and sdcflows.

If I’m correct, the non-rigid transformation from the B0 to the rigidly registered T1w doesn’t affect to the bvecs. I hope this helps.

Best regards,

Manuel