Tracts normalization with fsl warps

1

Dear experts
I am trying to normalize tracts to MNI. I was wondering if my procedure is correct (especially regarding the 3rd step). Warps were generated in fsl (TBSS).

  1. invwarp --ref=subj_FA.nii.gz --warp=subj_FA_to_target_warp.nii.gz --out=MNI_2_subj_warp.nii.gz
  2. warpinit FMRIB58_FA_1mm.nii.gz identity_warp1.nii
  3. applywarp --ref=subj_FA.nii.gz (or FMRIB58_FA_1mm.nii.gz ??) --in=identity_warp1.nii --warp=MNI_2_subj_warp.nii.gz --out=tracts_subj_2_MNI_warp.nii --interp=nn
  4. warpcorrect tracts_subj_2_MNI_warp.nii.gz tracts_subj_2_MNI_warp_corr.mif
  5. tcknormalise tracks_1M.tck tracts_subj_2_MNI_warp_corr.mif
    tracks_1M_MNI.tck

Thanks,
H

2

Hi Hamed,

I was wandering if you found the solution for the problem. I am in a very similar situation, and the code that you wrote here work for me.

Regards,

Manuel

3

Hi Manuel
I just saw your reply. Happy to see it worked for you too. :slight_smile:
Cheers,
Hamed