The Diffusional Kurtosis Estimator (DKE) is software for processing Diffusional Kurtosis Imaging (DKI) data.
DKI Protocols & Data Processing
DKE is written primarily in MATLAB. It can be run either from executables or from source code. An advantage of running DKE from executables is that it can be run under the free MATLAB Compiler Runtime (MCR) R2012a (or R2013b for OS X), whereas MATLAB is needed for running DKE from source code. An advantage of running DKE from source code is that you can modify your copy of the source code to suit your own purposes.
The DKE executables for 32- and 64-bit Windows, 64-bit Linux, and 64-bit macOS are available from our DKE project pages on NITRC.
The source code can be downloaded from this site using either the Downloads menu or via "git clone" (if you have a git client installed). If you download DKE via "git clone", you can later update to the latest version on this site with "git pull".
In order to run DKE from source code, you need to have MATLAB. The files dke_preprocess_bruker.m, dke_preprocess_dicom.m, and map_interpolate.m make calls to SPM. So if your image files are in Bruker format or DICOM format, or if you interpolate the parametric maps, you will need SPM to be installed and in your MATLAB path.
Most of the source code for DKE is in the mfiles subdirectory, which should be added to your MATLAB path. The subdirectory that has the gradient vectors file that you use should be added to your MATLAB path, or else the full path name of the gradient vectors file used should be specified in the fn_gradients parameter in the input parameter file.
DKE makes use of MEX files (MATLAB executable files) for speed. Previously-compiled MEX files are in the subdirectories that end in "*mex". To use these files, add the appropriate subdirectory to your MATLAB path. For example, if you want to run DKE in MATLAB on macOS:
>> addpath /path/to/mfiles
>> addpath /path/to/gradientVectors
>> addpath /path/to/mac64mex
>> dke /path/to/DKEParameters.dat
Note that the previously-compiled MEX files might not work on your computer, depending on the specific version of the operating system that you are using. In that case, you need to recompile the MEX files yourself with MATLAB Coder.
You can create MEX files for augment_constraints, compute_rd, and compute_rf by opening the corresponding .prj files in MATLAB. These files are in separate directories alongside the mfiles directory. MATLAB Coder will convert the .m files into C code and compile the C code into MEX files.
You can also create the MEX file for mlsei using MATLAB Coder. The source code is in C (converted from Fortran). Instructions are in mexlsei_setup.m in the mlsei/mfiles directory, but some of the steps have been done. Make the f2c library, move it to the "c" directory, and then create the MEX file. For example, on a 64-bit Linux computer (computer type = glnxa64), in MATLAB:
>> pwd
ans =
/home/username/src/dke/mlsei/c/libf2c
>> !make -f makefile.lx64
cc -c f77vers.c
cc -c i77vers.c
cc -c -DSkip_f2c_Undefs -O -DNON_UNIX_STDIO -fPIC main.c
...
ar: creating libf2cx64.a
ranlib libf2cx64.a
>> !mv libf2cx64.a ..
>> cd ../..
>> pwd
ans =
/home/username/src/dke/mlsei
>> mex -L "./c" -lf2cx64 -outdir . -v ./c/mexlsei.c ./c/dlsei.c
...
The MEX files can then be moved to the appropriate directory ending in "mex", for example linux64mex if you are using 64-bit Linux.
Added:
- DTI fib file output. If the flag output DTI tracks is on it will automatically output the DTI.fib file to. The gaussian dODF is used to visualize the ODFs but there is commented code in there to change it to the elipsoid. The directions in the fib file for tractography is the first eigenvector.
Changed:
- Updated DKE version and date-time strings
Removed:
- None