March 6, 2018 at 2:43 pm #1152
Would I be able to get some guidance on which files to check for addressing the error below?
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)
March 6, 2018 at 2:50 pm #1153
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.
March 6, 2018 at 2:51 pm #1154
typo : –dwi-mask (there are two hyphens)
March 6, 2018 at 3:35 pm #1155
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
March 7, 2018 at 12:04 pm #1156
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.
March 7, 2018 at 3:20 pm #1157
I’ve just tried removing both the masks and I am encountering the same issue.
March 16, 2018 at 2:32 pm #1166
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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