Registration based distortion correction

Forums Forums BrainSuite Diffusion Pipeline (BDP) Registration based distortion correction

This topic contains 5 replies, has 4 voices, and was last updated by  divarada 1 year, 7 months ago.

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  • #70

    cbhushan
    Moderator
    I want to use BDP to run registration based distortion correction for my 4D dti 
    image, but I don't find any flag to enter image T1. Could you please explain me 
    how to use it? Many thanks.
    
    • This topic was modified 4 years, 5 months ago by  cbhushan.
  • #73

    Kim
    Participant

    Hi Bhushan,

    Thank you so much for your reply. So <prefix_filename>.dwi.RAS.bvec and <prefix_filename>.dwi.RAS.correct.nii.gz are my new bvec rotated and dti with epi distprtion corrected? Thanks.

    Best regard,
    Kim

    • #74

      cbhushan
      Moderator

      Yes, <prefix_filename>.dwi.RAS.correct.nii.gz is distortion corrected diffusion-weighted images and <prefix_filename>.dwi.RAS.bvec is corresponding bvec file.

  • #1332

    farzanforoosh
    Participant

    Hello , I am wondering whether “bdp” tool in BtrainSuite can correct for motion artifact in diffusion data or not !

  • #1364

    divarada
    Participant

    Hi, currently we do not support motion correction. One way you can correct for motion is by rigid registration of all diffusion weighted images with one reference image (like a b=0 image). You can use our affine registration addon tool to achieve this – https://neuroimage.usc.edu/neuro/Resources/BDPAddons#affineReg

  • #71

    cbhushan
    Moderator

    T1w image is the first argument to BDP on command line. See below for usage. This file should be the bias-field corrected output from BrainSuite in nifti-1 format.

    bdp.sh <BFC FILE> [OPTIONAL FLAGS] --nii <NIFTI FILE> --bvec <GRADIENT FILE> --bval <B-VALUE>

    More usage details can be found here: http://brainsuite.org/processing/diffusion/pipeline/

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