Process Diffusion Data with BDP

Forums Forums BrainSuite Diffusion Pipeline (BDP) Process Diffusion Data with BDP

Viewing 11 reply threads
  • Author
    Posts
    • #1351
      wy
      Participant

      Hi,

      I am getting this error when i run the dti script provided on the website.
      All the flags and files are fine.
      “/Applications/BrainSuite18a/bdp/bdp.sh A01.bfc.nii.gz –tensor –FRT –FRACT –nii /Users/BS_SPGR/A01/data.nii -g bvec -b bval”

      Any help?

      ================================================================================
      Setting up dataset and inputs
      ================================================================================
      Reading input flags…

      ***************************************
      * *
      * Error running BDP *
      * *
      * A MANDATORY INPUT IS NOT DEFINED *
      * *
      ***************************************

      Error message:
      Diffusion data is a mandatory input. –nii flag must be used to define input
      diffusion data.

      Error help/resolution:
      BDP could not find any flag defining a mandatory input. Please refer to error
      message above. You can visit the BrainSuite website at following url for
      documentation of BDP Usage:
      http://brainsuite.org/processing/diffusion/flags/

    • #1354
      yeunkim
      Participant

      Hi,

      Could you try putting two dashes in front of nii? i.e. --nii

      So the command line would be:
      /Applications/BrainSuite18a/bdp/bdp.sh A01.bfc.nii.gz –tensor –FRT –FRACT –nii /Users/BS_SPGR/A01/data.nii -g bvec -b bval

    • #1362
      wy
      Participant

      Hi, thanks.
      But i am getting the same error!

      BDP Version: 18a (build #0073), released 2018-02-14

      ================================================================================
      Setting up dataset and inputs
      ================================================================================
      Reading input flags…

      ***************************************
      * *
      * Error running BDP *
      * *
      * A MANDATORY INPUT IS NOT DEFINED *
      * *
      ***************************************

      Error message:
      Diffusion data is a mandatory input. –nii flag must be used to define input
      diffusion data.

      Error help/resolution:
      BDP could not find any flag defining a mandatory input. Please refer to error
      message above. You can visit the BrainSuite website at following url for
      documentation of BDP Usage:
      http://brainsuite.org/processing/diffusion/flags/

    • #1363
      wy
      Participant

      Oh sorry even though it appears that i am using a single dash, i am actually using 2 (- – )!
      It is only when i paste it here does it look like that!
      I think you had the same problems when you pasted. Check your reply.
      Any other thing that might be wrong for this to work?

    • #1365
      divarada
      Participant

      There must be a BDPSummary.txt generated. It will have details of the command that was used such as this one:

      COMMAND USED:

      bdp.exe 2523412.bfc.nii.gz
      –nii 2523412.DTI64.nii.gz
      –bval 2523412.DTI64.bval
      –bvec 2523412.DTI64.bvec
      –tensors
      –frt
      –fract

      Approximate processing time: 19.82 minutes

      Can you please copy the text from there ?

    • #1366
      wy
      Participant

      Hello again,

      Thank you for your comment. There is no BDPSummary.txt anywhere!

    • #1372
      wy
      Participant

      Could you possibly let me know where should this txt file be?

    • #1384
      divarada
      Participant

      BDPsummary should have been generated in the same folder as the bfc file but since in your case it did not generate then most likely BDP exited before that step.

      I repeated your command with a dataset I had :
      bdp.exe 2523412\2523412.bfc.nii.gz –tensor –fract –frt –nii 2523412\2523412.DTI64.nii -b 2523412\2523412.DTI64.bval -g 2523412\2523412.DTI64.bvec

      and it was able to find my file and went beyond the step that is crashing for you. So looks to be a syntax issue.

      Even though I am not sure, here are quick pointers that might help you:
      – check if all files exist and are accessible to bdp
      – check space, double dashes
      – remove fract and frt, just run tensor
      – try a different input dataset

    • #1388
      wy
      Participant

      Ok, thank you for your answer. That did solve the problem. I was copy pasting the command directly from the website, which has only one dash before each flag. Once, i added t dashes it worked.

      The command ran but i still have a problem which was later one. Here is the error i got.
      I searched online, but the only solution is to replace the NaNs with zeros!

    • #1389
      wy
      Participant

      Here is the Error:

      Matching resolution of the images…Error using eig
      Input to EIG must not contain NaN or Inf.

      Error in get_original_grid_data (line 44)

      Error in register_files_affine (line 313)

      Error in EPI_correct_files_registration_INVERSION (line 109)

      Error in coregister_diffusion_mprage_pipeline (line 219)

      Error in BrainSuite_Diffusion_pipeline (line 26)

    • #1396
      wy
      Participant

      Any help on this error?

    • #1397
      divarada
      Participant

      Can you try adding masks for structural and diffusion data and try running the BDP command.

      There are two flags I want you to add and let me know if the error still persists:
      1. –dwi-mask <filename.nii.gz> : Specifies the filename of the brain-mask file for diffusion data.
      2. –t1-mask <filename.nii.gz> : Specifies the filename of the brain-mask file for input T1-weighted image.This mask can be same as the brain mask generated during BrainSuite extraction sequence.

      More details of flags can be found at http://brainsuite.org/processing/diffusion/flags/

Viewing 11 reply threads
  • You must be logged in to reply to this topic.