This article serves as a brief introduction to DWMRI processing.

Tools and files used in this article:

dwmri.dcm is a 32 direction, 1000 b-value DWMRI dicom file, dcm2niix is a commonly used DICOM to NIFTI converter, nifti_utils is a library to work with NIFTIs in MATLAB, dwmri_visualizer is a visualization tool for diffusion images in MATLAB, and FSL is a powerful and commonly used medical image processing library.

A very common pipeline for dwmri processing is:

- The first consideration is to determine which acquisition parameters to use; this is application dependent. For example, if diffusion tensor imaging (DTI) is desired, then an acquisition with 32 gradient directions and a b-value of 1000 can be used. For high angular resolution diffusion imaging (HARDI), 60 gradient directions and a b-value of 2000 or greater can be used. Regardless of the desired application, I would recommend acquiring data which makes use of FSL‘s preprocessing tools:
**topup**and**eddy**. The bare minimum requirement to use both of these tools is to acquire an additional reverse phase-encoded B0 along with your acquisition. - and 3. Typically, the output from a diffusion scan is a DICOM file. This format is generally used within a PACs to send data from a scanner to some storage archive. DICOMs typically aren’t used directly in image processing. Instead, NIFTIs are a commonly used. To convert the DICOM in this tutorial to a NIFTI you can use the dcm2niix tool:
mkdir dwmri_nifti dcm2niix -f dwmri -o dwmri_nifti/ dwmri.dcm

Be sure to use the most updated version of

`dcm2niix`

. It is actively maintained and new patches are released frequently. The outputs are:`dwmri_ADC.nii, dwmri.bval, dwmri.bvec, and dwmri.nii`

. The DICOM in this tutorial came from a Philips scanner which synthesizes an ADC image which is not useful, so we can go ahead and remove`dwmri_ADC.nii`

. The`bvec`

and`bval`

files are metadata containing the gradient directions and diffusion weighting. You can perform some preliminary checks to make sure outputs look correct:cat dwmri_nifti/dwmri.bval cat dwmri_nifti/dwmri.bval | tr '\t' '\n' | wc -l fslhd dwmri_nifti/dwmri.nii | grep dim[0-9] | grep -v pix

You can also view the data in an image viewer like MIPAV or directly in MATLAB.

One important aspect of

`dcm2niix`

is that it outputs the NIFTI and b-vectors in a way which are compatible with FSL. The way it does this is by doing two things: 1) The output NIFTI should have “RADIOLOGICAL” orientation and 2) the b-vectors should be in “RADIOLOGICAL voxel convention“. A NIFTI is in “RADIOLOGICAL” convention if the determinant of its`sform`

/`qform`

is negative (this essentially means it uses a left-handed coordinate system). b-vectors are in “RADIOLOGICAL voxel convention” if, after the NIFTI has been loaded into “RADIOLOGICAL” convention, the b-vectors are oriented with respect to the voxels. This is super confusing, but suffice it say two things for now: 1) if you use`dcm2niix`

your NIFTI and b-vectors will be compatible with FSL and 2) your b-vectors will be oriented with respect to the voxels. Anyway, you can check the NIFTI by using:fslorient dwmri_nifti/dwmri.nii

The output should be

`RADIOLOGICAL`

. Checking if the b-vectors are in “RADIOLOGICAL voxel convention” is done easiest by fitting a diffusion tensor and plotting the primary eigenvector direction (done in step 5). - Preprocessing is pretty involved. There are three main sources of distortions in DWMRI: 1) susceptibility distortions, 2) eddy current distortions and 3) patient movement. The current state of the art is to use FSL’s
`topup`

and`eddy`

which corrects for all three of these things. Prior to this, corrections for eddy currents and patient movement were done using 12-DOF affine registrations (FSL’s`eddy_correct`

, which is now deprecated) while susceptibility distortion was corrected by using a field map. Because`topup`

/`eddy`

are somewhat complicated, I’ve written an entire article for it. If you are following along and eager to start processing, then just use the raw data for now. - Processing! This is the fun part! There are two approaches I’d like to take here: 1) A simple command-line DTI fit and 2) A MATLAB script to perform a DTI fit. DTI is a good way to get introduced to DWMRI processing because it’s a simple model that requires solving linear equations. The b-vector based diffusion equation for DTI is:
Where S is the intensity value at a voxel for a given b-vector and b-value,

**g**is the b-vector, b is the b-value, and**D**is the diffusion tensor. We have S(**g**,b), S(**0**,0), b, and**g**. We just need to obtain**D**. If you divide by S(**0**,0), take the natural log, divide by -b, then solve for the components of**D**, you will obtain a linear set of equations which you can get the least squares solution to.Anyway, to get the diffusion tensor fit with FSL, do the following:

fslroi dwmri_nifti/dwmri.nii dwmri_nifti/b0.nii 0 1 bet dwmri_nifti/b0.nii dwmri_nifti/mask.nii -m mkdir fsl_dtifit dtifit -k dwmri_nifti/dwmri.nii -o fsl_dtifit/dti -m dwmri_nifti/mask_mask.nii.gz -r dwmri_nifti/dwmri.bvec -b dwmri_nifti/dwmri.bval fslview fsl_dtifit/dti_FA.nii.gz fsl_dtifit/dti_V1.nii.gz

The outputs should be like the following (after changing DTI display options to “Lines RGB”):

Checking the fibre orientations along the corpus collosum is a standard check to make sure everything is “ok” (or at least not egregiously wrong).

Ok, so doing this from the command-line is cool, but doing it in MATLAB is more powerful. The following will fit the diffusion tensor, compute the main eigenvector (V1) and the fractional anisotropy (FA):

%% Set environment addpath(genpath('nifti_utils')); addpath(genpath('dwmri_visualizer')); %% Fit diffusion tensor dwmri_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile('dwmri_nifti','dwmri.nii'),'double'); bvecs = dlmread(fullfile('dwmri_nifti','dwmri.bvec')); bvals = dlmread(fullfile('dwmri_nifti','dwmri.bval')); mask_vol = nifti_utils.load_untouch_nii_vol_scaled(fullfile('dwmri_nifti','mask_mask.nii.gz'),'logical'); % Split into B0 and DWI b0_vol = dwmri_vol(:,:,:,bvals == 0); dwi_vol = dwmri_vol(:,:,:,bvals ~= 0); bvecs_dwi = bvecs(:,bvals ~= 0); bvals_dwi = bvals(bvals ~= 0); % Make output directory mkdir('matlab_dtifit'); % Loop over and compute diffusion tensor, V1, and FA V1_vol = zeros(size(dwmri_vol,1),size(dwmri_vol,2),size(dwmri_vol,3),3); FA_vol = zeros(size(dwmri_vol,1),size(dwmri_vol,2),size(dwmri_vol,3)); for i = 1:size(dwmri_vol,1) for j = 1:size(dwmri_vol,2) for k = 1:size(dwmri_vol,3) if mask_vol(i,j,k) % Compute A: -b*g*g' gx = bvecs_dwi(1,:)'; gy = bvecs_dwi(2,:)'; gz = bvecs_dwi(3,:)'; A = -bsxfun(@times,bvals_dwi',[gx.^2 2*gx.*gy 2*gx.*gz gy.^2 2*gy.*gz gz.^2]); % Fit using linear least squares DT = mldivide(A,squeeze(log(abs(dwi_vol(i,j,k,:)./b0_vol(i,j,k))))); DT_mat = zeros(3,3); % Reshape to matrix DT_mat(1,1:3) = DT(1:3); DT_mat(2,2:3) = DT(4:5); DT_mat(3,3) = DT(6); DT_mat(2,1) = DT_mat(1,2); DT_mat(3,1:2) = DT_mat(1:2,3)'; if all(isfinite(DT_mat(:))) % Get eigenvectors and eigenvalues [V,D] = eig(DT_mat); % Sort by size [D,I] = sort(diag(D),'descend'); V = V(:, I); % Store V1 V1_vol(i,j,k,:) = V(:,1); % Compute FA FA_vol(i,j,k) = sqrt(1/2)*sqrt((D(1)-D(2))^2 + (D(2)-D(3))^2 + (D(3)-D(1))^2)/sqrt(D(1)^2+D(2)^2+D(3)^2); end end end end end %% Save output template_nii = load_untouch_nii(fullfile('dwmri_nifti','dwmri.nii')); % V1 template_nii.img = V1_vol; nifti_utils.save_untouch_nii_using_scaled_img_info(fullfile('matlab_dtifit','dti_V1.nii.gz'),template_nii,'double'); % FA template_nii.img = FA_vol; nifti_utils.save_untouch_nii_using_scaled_img_info(fullfile('matlab_dtifit','dti_FA.nii.gz'),template_nii,'double'); %% Plot % Get visualizer xform_RAS = nifti_utils.get_voxel_RAS_xform(fullfile('dwmri_nifti','dwmri.nii')); dv = dwmri_visualizer({V1_vol,FA_vol}, ... [], ... FA_vol, ... xform_RAS, ... 'colorized_FA', ... {'w',1}); % Plot dv.plot_slice(47,'coronal','top-centroid',1); axis image dv.plot_slice(26,'axial','top-centroid',0.8); axis image

The outputs look very similar to the FSL outputs (a good thing):

A few things:

*Your MATLAB code looks interesting, do you have an article on how to work with NIFTIs in MATLAB?*

*Why was I able to load the NIFTI untouched and the b-vectors directly and compute the V1 in the correct orientation?*

I was able to do this because `dcm2niix`

will output b-vectors with respect to the voxels, which is what my code assumes.

*Is the way FSL deals with b-vectors confusing to anyone else?*

Yes. In fact, this resulted in a software bug in the MRtrix package. It most likely went unnoticed for a while because most people use `dcm2niix`

and do not have DWMRI NIFTIs in “NEUROLOGICAL” convention, so it was * probably * assumed that FSL b-vectors were always with respect to voxels, which is only true if the NIFTI is in “RADIOLOGICAL” convention.

*Why does FSL do this!?*

I believe it’s because FSL wants to insure a left-handed coordinate system for all NIFTIs loaded into FSL. This would insure something like a 6-DOF registration can always be achieved with a rotation and translation. If anyone else knows a better or more correct reason then they can leave a response in the comments.