[wy]

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/

[yeunkim]

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

[wy]

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/

[wy]

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?

[divarada]

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 ?

[wy]

Hello again,

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

[wy]

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

[divarada]

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

[wy]

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!

[wy]

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)

[wy]

Any help on this error?

[divarada]

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/

[Author]

Posts