distortion correction based on T1w (minimal correction found)

Forums Forums BrainSuite Diffusion Pipeline (BDP) distortion correction based on T1w (minimal correction found)

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    • #99
      jgonicor
      Participant

      We have run the distortion correction of dwi data based on T1w on the test dataset (as provided with Brain Suite) and also on one subject (dwi + T1w) collected at our institution. In both cases, when overlaying the dwi.nii.gz file with the dwi.RAS.correct.nii.gz, we have observed that the distortion correction applied is minimal. Is there anything we could possibly not doing correctly? For the test dataset we are simply running:

      “bdp.sh 2467264.bfc.nii.gz –nii 2467264.dwi.nii.gz -g 2467264.dwi.bvec -b 2467264.dwi.bval”

      Please let us know if we should proceed with any further test or change any parameter in the call to bdp.sh.

      Kind regards,

      Joaquin

    • #100
      cbhushan
      Moderator

      Hi Joaquin, Defining a brain mask for diffusion data, using –dwi-mask, can substantially improve the correction. can you show some images (screenshots) which shows inadequate correction?

    • #747
      jottino
      Participant

      Hi!

      I’m starting with BS too because of the possibility of correcting EPI distortions with T1-weighted images.

      I used both the –dwi-mask and –t1-mask in order to improve the correction following your advice, but the outcome was pretty the same. In fact, the outcome was even worse when I used one (–dwi-mask) or both masks (dwi+t1) than when I did not use any of them.

      Maybe without a fieldmap and only a T1 little correction could be made? Don’t get me wrong, I’m quite glad with correcting at least a little of such distortions than leave my DWI volumes with such disturbances.

      Regards,
      Jonatan

    • #782
      divarada
      Participant

      Can you check if the phase encode direction (–dir) that you gave as input is correct ?

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