DWI configuration file with different bvalue

Hello,

I’m experiencing an issue while attempting to use DCM2BIDS for my DWI images. The data I have was recorded by Philips, and I have two DWI images, each accompanied by its respective .bval and .bvec files, which I have attached. One of the images contains only B0 (with 5 bval=0). I’m curious to know how I can concatenate these images or how to configure the DWI files so that I can incorporate both of them. Essentially, I would like to understand the correct naming convention to consider the bval number, such as “sub-001_ses-t0_dwi.bval”.

1- bvals : 0 0 0 0 0
2- bvals : 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

I need an image with bval like this: 0 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000

Thank you.
Hengameh

I am going to assume that these two series have the same phase encoding polarity (e.g. this pair was not intended for spatial undistortion with TOPUP). Many clinical sequences only acquire a single b=0 volume, but it is often useful to have a few b=0 volumes as these images form the denominator for several derived diffusion metrics. Ideally, these should be interspersed within a series. If you do acquire b=0 series in a separate series, you need to be very careful as some scanners will optimize parameters - check the JSON files to make sure the echo time and bandwidth match.

If your data meets these assumptions, you can concatenate your data. Use fslmerge for the image files and paste (a bash command) for the bvals/bvecs.

2 Likes

Thank you for your response.
Before proceeding with the analysis, I would like to confirm if the following format is correct for each series that I include:

{
“criteria”: {
“SeriesDescription”: “DTI 30dirs 1T2 b1000”
},
“dataType”: “dwi”,
“modalityLabel”: “dwi”,
“customLabels”: “b-1000”
}

Based on this format, the filename for a DWI image with a b-value of 0 will be “sub-001_ses-t0_dwi_b-0.nii.gz”. Similarly, for a DWI image with a b-value of 1000, the generated filename will be “sub-001_ses-t0_dwi_b-1000.nii.gz”.

Regards
Hengameh

The b label is not valid, so it will not make your data BIDS valid. File paths must be named something like:
sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>][_part-<mag|phase|real|imag>]_dwi.nii[.gz].

dcm2bids will automate ses and run, but anything else would need to be custom added.

Best,
Steven