question for BDP installation and usage

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    • #4760
      Ycc
      Participant

      I have installed MATLAB runtime 2019b and BrainSuite21a package, I have some problems when I using BDP on windows. Here is the error:

      C:\Users\Ycc\Documents\temp\DTI_BDP>”C:\Program Files\BrainSuite21a\bdp\bdp.exe” 2523412.bfc.nii.gz –tensor –-nii 2523412.dwi.nii.gz –g 2523412.dwi.bvec –b 2523412.dwi.bval

      BDP Version: 21a (build #0081), released 2021-05-05

      ================================================================================
      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:

      BDP: Flags

      I don’t know how can I fix that. I really like the pipeline, it can help me a lot. Any answer is appreciate.

    • #4761
      David Shattuck
      Keymaster

      hello –

      Our forum software changes how hyphens appear, so it can be difficult to tell exactly what you wrote. I think you have two hyphens before g and b, but these should only have one. Try running this:

      "C:\Program Files\BrainSuite21a\bdp\bdp.exe" 2523412.bfc.nii.gz --tensor –-nii 2523412.dwi.nii.gz -g 2523412.dwi.bvec -b 2523412.dwi.bval

      and see if that fixes the problem.

      thanks,
      David

    • #4778
      Ycc
      Participant

      I have done what you said, but it still didn’t work. I don’t know how to fix it.

      C:\Users\Ycc>cd C:\Users\Ycc\Downloads\BrainSuiteTutorialDWI
      
      C:\Users\Ycc\Downloads\BrainSuiteTutorialDWI>"C:\Program Files\BrainSuite21a\bdp\bdp.exe" 2523412.bfc.nii.gz --tensor --nii 2523412.dwi.nii.gz -g 2523412.dwi.bvec -b 2523412.dwi.bval
      
      BDP Version: 21a (build #0081), released 2021-05-05
      
      ================================================================================
                               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:
      
      BDP: Flags
      ***************************************
      • This reply was modified 1 year, 1 month ago by Ycc.
      • This reply was modified 1 year, 1 month ago by David Shattuck. Reason: changed code to pre
      • #4780
        Ycc
        Participant

        Two hyphens before tensor and nii, and one hyphens before g and b.

      • #4781
        David Shattuck
        Keymaster

        If you enclose your text with pre tags, it should show it as you wrote it. [code] doesn’t work, unfortunately. pre uses angle brackets rather than square brackets.

    • #4784
      David Shattuck
      Keymaster

      I am not near a Windows machine at the moment, but I just tried this on Linux using the data from https://brainsuite.org/tutorials/dtiexercise/ and it started. I copied the arguments from your post.

      I will try it on Windows later today and get back to you.

      BrainSuiteTutorialDWI>/opt/BrainSuite21a/bdp/bdp.sh 2523412.bfc.nii.gz --tensor --nii 2523412.dwi.nii.gz -g 2523412.dwi.bvec -b 2523412.dwi.bval
      
      BDP Version: 21a (build #0081), released 2021-05-05
      
      ================================================================================
                               Setting up dataset and inputs
      ================================================================================
      Reading input flags...
      
      Checking input files...
      
      .mask.nii.gz file found: 2523412.mask.nii.gz
      BDP will use this file as brain mask. You can specify a custom brain mask by
      using flag --t1-mask . The custom mask must overlay correctly
      with input BFC image in BrainSuite.
      
      Processing data with fileprefix:
      	2523412
      
      ================================================================================
                         Co-registration and Distortion Correction
      ================================================================================
      Reading the input parameters for co-registration...
      Total memory (physical+swap) found: 126.53GB
      
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