How to preprocess diffusion MRI?

Dear SITK-users

How to preprocess diffusion MRI DICOM images? So far we have been using publicly available processed DWI nifti file and the given .bvec and .bval files. Now, we would like to do preprocessing from DICOM file. However, there are number of questions.

We used dcm2niix library to convert DICOM image into nifti file as the first step. We checked both DTI and DWI images. One of the DTI files was showing 4 dimension while DWI images were all 3 dimensional. During the processing, it generated nifti file along with .bval and .bvec files. However, the .bval and .bvec files were containing only zero instead of gradient directions. Are we looking at the correct dMRI file? We are still in confusion whether we have to look for DTI or DWI file.

We also looked for the tags (0018, 9087) Diffusion b-value, (0018, 9089) Diffusion Gradient Orientation where all values were 0 in DTI file. Could you please guide us which is the appropriate DICOM file to look into which can provide us the required .bvec and .bval values. Is there any other tag we should look for to generate these files?

Beside what are the other important steps to complete the preprocessing before we start generating the fiber tracts?

I would really appreciate forum Simple ITK members for been so helpful.

Thanks you so much.

Best Regards,

Hello @Sunita_Patel,

This is not a SimpleITK related question, so this is not the relevant forum for this question.

Possibly this is related to converting from DICOM to the Brain Imaging Data Structure (BIDS) structure. Take a look at this tutorial which may be relevant.

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Thanks Ziv for your response. We got a clue to solve the problem. Most probably it is an anonymization problem which is replacing .bvec and .bval with 0.

Best regards,

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