[leonidastra86]

I try to run BDP for the first time and I have some problems. I run macOS Sierra, give in Terminal the appropriate path and receive the following message:

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

I am sure I am missing something, a space between the letter or so but everything I tried didn’t really work.

The path that I give is:

/Applications/BrainSuite16a1/bdp/bdp.sh /Users/leonidastra86/Desktop/Diffusion/ o20170124_183359lalalas008a1001.bfc.nii — nii /Users/leonidastra86/Desktop/Diffusion/lalala.nii
-g /Users/leonidastra86/Desktop/Diffusion/lalala.bvec
-b /Users/leonidastra86/Desktop/Diffusion/lalala.bval

For any help I would be really gracious.

[sychoi]

you had an extra space: “- nii” instead of “–nii”
also make sure the command is all in one line with no returns.

/Applications/BrainSuite16a1/bdp/bdp.sh /Users/leonidastra86/Desktop/Diffusion/ o20170124_183359lalalas008a1001.bfc.nii –nii /Users/leonidastra86/Desktop/Diffusion/lalala.nii -g /Users/leonidastra86/Desktop/Diffusion/lalala.bvec -b /Users/leonidastra86/Desktop/Diffusion/lalala.bval

[sychoi]

the forum is not posting the dashes correctly. there should be 2 dashes before nii
you can find an examples here
http://brainsuite.org/processing/diffusion/pipeline/

[leonidastra86]

After changing some things (careful with microsoft word, it automatically changes the dashes and the spaces) it worked.
Thank you so much!
Could you please tell me what the Threshold in connectivity means? Is it qualitative or could I somehow find the size of the fibres?
The tractography is deterministic?

[leonidastra86]

In addition to my questions above, I have already the next problem in the next 2 patients. I get the following message:

Error message:
Number of volumes in NIfTI file does not equal the number of b-matrices.
Total number of images found: 2
Total number of bmatrices: 1

Error help/resolution:
Check to make sure that bvec/bval or bmat file have correct number of entries
corresponding to the diffusion scan file. Check to make sure gradient file
contains “0, 0, 0” row(s)/col(s) for b=0 images.

I tried to transform the Dicoms with dcm2niigui and the newer mricron but I always get the same results. What do I do false? The .bvec file has values:
0
0
0
and the .bval just 0.

[Anonymous]

Here is what is wrong:

Total number of images found: 2
Total number of bmatrices: 1

In other words, there are two diffusion weighted images but bval/bvec files only specify scan parameters for one image. You should have two rows/cols in both bval and bvec file.

Another note: Your data, with only two diffusion images, will not have enough information to obtain a good diffusion model like DTI, ODF etc and BDP may actually fail computing them. Other things like distortion correction and registration should still work as expected.

[leonidastra86]

It was actually a bundle that included 2 series of 22 images. I had more but I thought it wouldn’t work. My images are all in dicom and I must transform them everytime. The program to transform them is in my opinion the issue. dcm2niigui is the simplest but I am not really sure about the results. I usually receive many files and I don’t know which of them I should include in the path that I use.

Do you have an example for me?

Or should I have one .bvec and one .bval file only?

[sychoi]

Sorry for the late response. From dcm2nii you should be getting a nifti file, bvec and bval file for each series. If you are using a philips scanner with their stock sequences, you will have a dummy volume at the end and dcm2nii will output 6 files for each series. the 3 files mentioned and the same 3 files but starting with “x” where the dummy sequence is removed which is what you want to use.

You can find example files here: http://brainsuite.org/WebTutorialData/DWI_Feb15.zip
and explanations of file formats here: http://brainsuite.org/processing/diffusion/file-formats/

[leonidastra86]

The issue is resolved but thank you for your response anyway.
I have to admit, sometimes come Nifti from dcm2nii with the wrong number of bvals und bvecs and I need to do it again or download the dcom files again.

Anyway, now it works and I learn the program and its issues every day a little more. Thank you very much for your support.

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