[Ycc]

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.

[David Shattuck]

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

[Ycc]

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 11 months, 2 weeks ago by Ycc.
• This reply was modified 11 months, 2 weeks ago by David Shattuck. Reason: changed code to pre

[Ycc]

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

[David Shattuck]

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.

• This reply was modified 11 months, 2 weeks ago by David Shattuck.

[David Shattuck]

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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