Process Diffusion Data with BDP

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

This topic contains 11 replies, has 3 voices, and was last updated by  divarada 1 year, 6 months ago.

  • 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/

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