Visualization toolbox for DWMRI related processing, including: DTI, spherical harmonics, etc...
If you use this tool in your research, please cite with:
- Install FSL
- (optional - only if plotting PASMRI) Install camino
- Download repos and (optional) example data:
git clone https://github.com/justinblaber/nifti_utils.git
git clone https://github.com/justinblaber/dwmri_visualizer.git
# Optionally download example data (note this is quite large... sorry)
wget https://justinblaber.org/downloads/github/dwmri_visualizer/data.zip
unzip data.zip
- In MATLAB:
>> addpath(genpath('nifti_utils'));
>> addpath(genpath('dwmri_visualizer'));
>> data_path = 'data';
If you've downloaded the example data, then run specific cells in each script:
>> edit test_dwmri_visualizer.m
>> edit test_dwmri_plot.m
Select cells from test_dwmri_visualizer.m
and test_dwmri_plot.m
are shown below:
%% Directions test - bedpostX
% Load data
dyads1_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dyads1.nii.gz'),'double');
dyads2_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dyads2.nii.gz'),'double');
mean_f1samples_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'mean_f1samples.nii.gz'),'double');
mean_f2samples_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'mean_f2samples.nii.gz'),'double');
mean_fsumsamples_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'mean_fsumsamples.nii.gz'),'double');
mask_vol = nifti_utils.load_untouch_nii_vol_scaled(fullfile(data_path,'mask.nii.gz'),'logical');
xform_RAS = nifti_utils.get_voxel_RAS_xform(fullfile(data_path,'dwmri.nii.gz'));
% Get visualizer
dv = dwmri_visualizer({dyads1_vol,dyads2_vol; ...
ones(size(mask_vol)),mean_f2samples_vol}, ...
mean_fsumsamples_vol, ...
mask_vol, ...
xform_RAS, ...
'directions', ...
{'r','b'; ...
0.25,0.25; ...
1,0.05});
% Make a plot
dv.plot_slice(47,'coronal','boundingbox');
axis image
%% DTI - colorized by v1 direction
% Load data
dwmri_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dwmri.nii.gz'),'double');
bvals = dlmread(fullfile(data_path,'dwmri.bval'));
dt_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dt.nii.gz'),'double');
v1_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'v1.nii.gz'),'double');
fa_vol = nifti_utils.load_untouch_nii_vol_scaled(fullfile(data_path,'fa.nii.gz'),'double');
xform_RAS = nifti_utils.get_voxel_RAS_xform(fullfile(data_path,'dwmri.nii.gz'));
% Get visualizer
dv = dwmri_visualizer({dt_vol(:,:,:,3:end),v1_vol}, ...
mean(dwmri_vol(:,:,:,bvals == max(bvals)),4)-0.25, ...
fa_vol*1.75, ...
xform_RAS, ...
'DT', ...
{40,1});
% Make a plot
dv.plot_slice(26,'axial','boundingbox');
axis image
light('Position', [5, 5, 5], 'Style', 'infinite')
%% sh_coefs test - MT_SCSD
% Load data
dwmri_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dwmri.nii.gz'),'double');
bvals = dlmread(fullfile(data_path,'dwmri.bval'));
sh_coefs_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'mt_scsd_sh_coefs.nii.gz'),'double');
fa_vol = nifti_utils.load_untouch_nii_vol_scaled(fullfile(data_path,'fa.nii.gz'),'double');
xform_RAS = nifti_utils.get_voxel_RAS_xform(fullfile(data_path,'dwmri.nii.gz'));
% Get visualizer
dv = dwmri_visualizer(sh_coefs_vol, ...
mean(dwmri_vol(:,:,:,bvals == max(bvals)),4)-0.25, ...
fa_vol*2, ...
xform_RAS, ...
'sh_coefs', ...
{8,60,true});
% Make a plot
dv.plot_slice(47,'coronal','top-centroid',1);
axis image
light('Position', [5, 5, 5], 'Style', 'infinite')
%% sh_coefs test - MT_SCSD
% Load data
dwmri_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'dwmri.nii.gz'),'double');
bvals = dlmread(fullfile(data_path,'dwmri.bval'));
sh_coefs_vol = nifti_utils.load_untouch_nii4D_vol_scaled(fullfile(data_path,'mt_scsd_sh_coefs.nii.gz'),'double');
fa_vol = nifti_utils.load_untouch_nii_vol_scaled(fullfile(data_path,'fa.nii.gz'),'double');
xform_RAS = nifti_utils.get_voxel_RAS_xform(fullfile(data_path,'dwmri.nii.gz'));
% Get visualizer
dv = dwmri_visualizer(sh_coefs_vol, ...
mean(dwmri_vol(:,:,:,bvals == max(bvals)),4)-0.25, ...
fa_vol*2, ...
xform_RAS, ...
'sh_coefs', ...
{8,60,true});
% Make the plot
dwmri_hdr = load_untouch_header_only(fullfile(data_path,'dwmri.nii.gz'));
f = dwmri_axial_coronal_plot(dv, ...
{'MT_SCSD', ...
[' B-values: ' num2str(unique(bvals)) '; lmax: 8; mrtrix path: ~/mrtrix3'], ...
[' Gradient Directions: ' num2str(length(find(bvals ~= 0)))], ...
[' Slice Dimensions: ' num2str(dwmri_hdr.dime.dim(2)) ',' num2str(dwmri_hdr.dime.dim(3))], ...
[' Slices: ' num2str(dwmri_hdr.dime.dim(4))], ...
[' Voxel Resolution: ' num2str(round(dwmri_hdr.dime.pixdim(2),1)) ' x ' num2str(round(dwmri_hdr.dime.pixdim(3),1)) ' x ' num2str(round(dwmri_hdr.dime.pixdim(4),1))], ...
'Justin Blaber', ...
'justin.blaber@vanderbilt.edu', ...
'Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data (Tournier et al 2014)', ...
'N/A', ...
'MT_SCSD_v1_1_0'});
% Apply light to axes
all_axes = findall(f,'type','axes');
for i = 1:length(all_axes)
light(all_axes(i), 'Position', [5, 5, 5], 'Style', 'infinite');
end