Error in find_bounding_box

Forums Forums BrainSuite Diffusion Pipeline (BDP) Error in find_bounding_box

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    • #1152
      jtanedo
      Participant

      Hello,

      Would I be able to get some guidance on which files to check for addressing the error below?

      Thank you!

      Best,

      Rigid registration done.

      Setting up data for non-rigid registration based distortion correction…
      Correcting intensity non-uniformity in b=0 image…Index exceeds matrix dimensions.
      Error in find_bounding_box (line 16)

      Error in EPI_correct_files_registration_INVERSION>trim_msk_PED (line 513)

      Error in EPI_correct_files_registration_INVERSION (line 271)

      Error in coregister_diffusion_mprage_pipeline (line 219)

      Error in BrainSuite_Diffusion_pipeline (line 26)

    • #1153
      divarada
      Participant

      This issue generally happens when the masking code fails in BDP – since this is a heuristic approach it is possible that it fails for certain cases. Can you try specifying the brain mask file diffusion data ? Use –dwi-mask flag for specifying the mask file.

    • #1154
      divarada
      Participant

      typo : –dwi-mask (there are two hyphens)

    • #1155
      jtanedo
      Participant

      Thank you divarada.

      I actually do specify the dwi-mask. In fact, here is my call

      bdp.sh t1.bfc.nii.gz –nii dwi.nii.gz -g encoding.bvec -b encoding.bval –t1-mask t1_mask.bfc.nii.gz –dwi-mask dwi_mask.nii.gz

    • #1156
      divarada
      Participant

      Can you try without giving the dwi-mask and/or t1-mask then ?

      Generally we have seen this when the mask is creating some issues. I am not sure if its the same reason in your case, so we will have to try a few things.

    • #1157
      jtanedo
      Participant

      I’ve just tried removing both the masks and I am encountering the same issue.

    • #1166
      divarada
      Participant

      Can you share the dwi mask file (dropbox ?)? This is most likely a corner case related to the masking file specified and debugging this issue is specific to the particular images that you are using.

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