BDP error

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    • #112
      bokkyuki@usc.edu
      Participant

      Hello,

      I got an error during BDP process. The below is the error message:

      Warning: The KEYBOARD function cannot be used in compiled applications.
      > In keyboard at 4
      In register_volumes_affine>my_normalized_mutual_information at 595
      In register_volumes_affine>error_affine_reg at 484
      In register_volumes_affine>error_grad_affine_reg at 453
      In register_volumes_affine>error_grad_affine_reg at 466
      In register_volumes_affine>@(x)error_grad_affine_reg(x,scale,Imoving_small,Ist
      atic_small,mask_moving_small,mask_static_small,reg_options) at 393
      In gradient_descent_backtrack at 62
      In register_volumes_affine at 393
      In register_files_affine at 448
      In EPI_correct_files_registration_INVERSION at 108
      In coregister_diffusion_mprage_pipeline at 219
      In BrainSuite_Diffusion_pipeline at 27

      Saving output files…

      Rigid registration done.

      Setting up data for non-rigid registration based distortion correction…Attempt
      ed to access I1_m(1); index out of bounds because numel(I1_m)=0.

      Error in normalize_intensity (line 17)

      Error in EPI_correct_files_registration_INVERSION (line 168)

      Error in coregister_diffusion_mprage_pipeline (line 219)

      Error in BrainSuite_Diffusion_pipeline (line 27)

      MATLAB:badsubscript

      —————————————————–

      Thank you,

    • #113
      cbhushan
      Moderator

      This error is most likely related to incorrect estimation of diffusion brain mask. Can you please check the file <fileprefix>.dwi.RSA.mask.nii.gz and see if looks like reasonable mask for diffusion data (<fileprefix>.dwi.RSA.nii.gz)? I am guessing that it would be highly incorrect.

      If that is the case, then please edit the mask manually in BrainSuite to cover brain-area reasonably in diffusion data. Then you should use this mask as input in BDP via –dwi-mask flag.

      • #172
        bokkyuki@usc.edu
        Participant

        Hello!

        It is working if I edit the mask manually, but it took a lot of time to edit the mask manually. I ran this process with earlier version of BDP (14a), and it generated correct dwi mask. So I wonder if the wrong dwi mask from the new version of BDP is a kind of an error.

      • #173
        cbhushan
        Moderator

        Hi, couple of things regarding this:

        First, the algorithm of BDP for automatic masking did change in 15a as compared to 14a, which was also based on feedback from BDP users. We tried to make it more robust to variety to datasets in our test-sets. However, it is possible that the performance for your dataset is not optimal with this change. If you can send us a sample dataset, on our support email address, then we can include it in our test-set.

        Having said that, if you have masks from 14a run then you can directly use the generated masks with any version of BDP. It should work without any problem.

        Also, in case you are editing masks manually, you do not need to make very precise masks. You can just use thresholding in mask-tool – just make sure you are not missing big chunks of brain.

    • #683
      carnico
      Participant

      Hi to all,

      I think I’ve the same problem.

      The <fileprefix>.dwi.RSA.nii.gz to me looks reasonable. (https://www.dropbox.com/s/fdhhn9l1futgst9/Screen%20Shot%202017-04-08%20at%2010.22.02.png?dl=0)mask

      I try to run the command line with a mask defined by me:

      /Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-mask dti_brain_mask.nii.gz –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

      and changing the dwi masking method:

      /Applications/BrainSuite16a1/bdp/bdp.sh t1.bfc.nii.gz –dwi-masking-method intensity –tensor –FRT –FRACT –nii dti.nii -g dti.bvec -b dti.bval

      but same error appear.

      This is the outputlog link:

      log

      Do you have any suggestion?

      Best Regards

      Nicolò

    • #693
      divarada
      Participant

      Hi Nicolò,

      Sorry for the late response.
      This looks like a mask issue, even though your mask inputs are reasonable there could be processing steps changing the mask.
      Here are a few things I can think of
      1. Can you check if your t1.mask.nii.gz looks reasonable ?
      2. Since the program crashed, can you check if BDP created a temporary mask file called epi_mask.nii.gz. BDP deletes these files but may be in this case it stopped before deleting. If you do find such a file, how does it look?
      4. Run BDP to save intermediate png files using the flag –png-out or –p. This will save snapshots of the masks prior to this failure. Can you check the output <name>.approx_align.png. I have to warn you that this is a very memory intensive process.

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