Dependencies

1. CMake (min version 3.15)
2. gcc-8 or newer
3. libzip
4. QT5 or newer
5. VTK7 or newer (installed with QT support)
6. ACVD (https://github.com/valette/ACVD/tree/83f7c05a7b3ccf0445708cea918b4b11325fb229)
7. Trekker (https://github.com/dmritrekker/trekker)

Important notes on dependency installation:

• First, make sure that you have QT5 or QT6 installed. If you decide to install QT from source, you may need to install WebEngine, WebChannel, WebSockets, WebView, Positioning.
• For VTK, you will need an installation with QT support. Some operating systems have readily available packages for this. For example, in Debian (or Ubuntu), you can just install "libvtk*-qt" (* indicates the VTK version).
• If you are going to install VTK from source, make sure to set VTK_USE_QT to ON.
• You will then need to install ACVD from source. ACVD recently went through an update and the latest update is not yet supported by real-time tractogram visualizer. Please use the above link when installing ACVD (commit #83f7c05).
• Lastly, compile Trekker.

Installation of rttvis

Edit and run the build.sh file. This will make a clean install by replacing the existing build folder.

Executable will be generated under the build/bin directory.

How to use rttvis

Provide the four necessary input images listed below. Make sure that all images are in the same RASMM space based on the NIFTI sform convention.

1. T1: T1-weighted MRI image of the subject
2. Mask: Brain mask image. For example the mask generated by FSL eddy during the diffusion MRI preprocessing step can be used.
3. FOD: Fiber orientation distribution image. Trekker accepts for example MRtrix generated FODs. More information on the FOD format can be found here.
4. ACT: rttvis performs anatomically constraint tractography using Trekker's pathway rules. With this, generated streamlines: (i) do not end inside the white-matter, and (ii) they do not cross corticospinal fluid. Currently there is no option to disable this and an ACT image has to be provided. The ACT image basically consists of only 4 numbers. There are -1, 0, 1 and 2. Outside the brain is -1. Corticospinal fluid is 0. White matter is 1. Gray matter is 2. If you had run the Freesurfer pipeline and have an aparc+aseg image, you can use the Python tool here to obtain the ACT image.

Different processing pipelines might have different conventions for FOD directions. You can use the Order Of Direction option to vary the direction as you wish. By default XYZ is assumed (no change). A lower case can be used to switch the direction, e.g., xYZ switches the sign of the first component. The order of components can be changed as well, e.g., yXz switches the sign of the second component while replacing it with the first, at the same time the sign of the last component is also changed.

By default spherical harmonics coefficients are converted to a discretized spherical function to increase the tracking speed. If desired this can be turned off.

Tractography parameters are explained in Trekker's web-site.

ENJOY!

Please contact by e-mail for questions.

Contact

Dogu Baran Aydogan, PhD | ([email protected])
-Research Director (Assist. Prof.) @ A.I. Virtanen Inst. for Molecular Sciences, Uni. of Eastern Finland (UEF)
-Research Fellow @ Dept. of Neuroscience and Biomedical Eng., Aalto Uni.