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FAQs

1. Where can I download example data?

We provide a group of test data to test the software, and the data was also used in [11] .

2. Why images and fibers are not properly aligned in my case?

This typically happens when nifti image headers are modified before generating fiber.

In DiffusionKit, a command named bninfo is provided to print out the header information inside a NIfTI image. To check whether an NIfTI data is canonical:

$ bninfo data.nii.gz

you would get:

...
qform_i_orientation = 'Left-to-Right'
qform_j_orientation = 'Posterior-to-Anterior'
qform_k_orientation = 'Inferior-to-Superior'
...

This indicate that you are lucky. And the matrix that transforms voxels coordinates (I/J/K) to physical locations (X/Y/Z) is orthogonal. However, it doesn't matter if this isn't true, the image can be converted with bnconvert. With --reorient argument, it transforms the input image into orthogonal one with head information modified as well.

$ bnconvert data_brain.nii.gz data_brain_r.nii.gz -r

Warning

However, there would be problems if bnconvert converts a 4D vector image, e.g. tensor data, ODF/FOD data etc.

Usually, the reorient step should be taken when DICOM image is converted to NIFTI image, with argument -r y.

For more information, we recommand reading FSL's Orientation Explained and Docs on qform and sform to get a good understanding of orientation layout within NIfTI data format.

3. How to extract the gradient table if the dcm2nii/MRIcron fails?

The dcm2nii/MRIcron are useful to extract the gradient table for the DWI data. Occasionally, they fails to get the gradient table, though it indeed get the NIFTI data from the DICOM images. Herein we provide a temporary solution by calling the MATLAB/dicominfo which depends on a specified keyword dictionary.

function findGrad(dcmfile)
% This script is special to locate the individual grad directions
% for each DICOM file, if the dicom2nii tool failed to extract them.
% by NMZUO, Sept. 12, 2014

% Change the following if still fails
%prestr = 'DiffusionGradientOrientation';
prestr = 'DiffusionGradient';

myhdr = dicominfo(dcmfile);
myfind = fieldnamesr(myhdr, prestr);
iLen = length(myfind);
iCount = 0;

for i=1:iLen
   mystr = myfind{i};
   if strfind(mystr, prestr)
       iCount = iCount + 1;
       disp(['Field containing ' prestr ': ' num2str(iCount) ]);
       disp(mystr);

       % to extract the grad directions
       eval(strcat('myhdr.', mystr))
   end
end
end

Please download the two files fieldnamesr.m and findGrad.m . The first one is to generate the full string of the keyword dictionary and second is to find the locations. If your problem remains unsolved, please send us your data (only one 2D/3D DICOM image is enough) and then we will update our DICOM dictionary.