Hi team, I have encountered a problem. During working with dti data in sct, the bvec and bval cannot be found, and they seem to be required for process. What the problem might arise from? Do you have any suggestion to solve it? I work with nifti files, and expected to have bvec and bvals, but seems they are hidden, or not available. appreciate in advance.
Thank you for your question! If I’m understanding correctly, your dataset contains the DTI image files, but does not contain the corresponding bvals and bvecs files?
To answer your question, I’ll share two quotes from this helpful DTI Preprocessing page:
The .bval and .bvec files should be created from the raw dicom headers by whichever method you used to create the raw dwi NIFTI file in the previous section. Some methods (e.g., dinifti, dicomToNifti.m) do not create these files for you. If you don’t have those files (and you can’t create them yourself (no easy task)) you should talk to the person who programmed your DWI sequence and get the files that are specific to your use case.
- Use dcm2nii to create the nifti file from the raw data.
- This process will return three files: (1) A file with the .nii.gz extension (2) a file with a .bval extension and (3) a file with a .bvec extension.
For a description of what the bvals and bvecs files should look like, please visit this page.
If you have any other questions, please let us know!
yes I used this method and it did not make .bvec and .bval extentions. Thank you for the quick response. will look more closely on it to see if I can find any clue. Will let you know, if I could.
@Lilian , dcm2nii is deprecated (see the red part in here), and it could be the reason you didn’t see bvals/bvecs (recent MR pulse sequences might have not been recognized). Could you try with dcm2niix instead?
Of course, will try this. Appreciate it.