Spinal cord tractography tools of software

Hello everyone, I watched the recent workshop video. In the part about dMRI, I didn’t see how to display the results of DTI and tractography. I don’t know what tools and software you use for tractography.Can you introduce me to the best visualization software and tools currently available for spinal cord tractography?

Hi @DeshengKong,

Thank you for reaching out. SCT does not do tractography, but only does the pre-processing of the DWI data, so that they can then be inputted into a third party tractography software. Examples of such software include:

  1. FSL (FMRIB Software Library): A comprehensive library of analysis tools for FMRI, MRI, and DTI brain imaging data. It includes modules for diffusion tractography.
  2. MRtrix3: A set of tools for the analysis of diffusion MRI data, known for its advanced tractography algorithms and visualization capabilities.
  3. TrackVis and Diffusion Toolkit: TrackVis is a software tool that visualizes and analyzes fiber track data from diffusion MRI datasets. It often works in conjunction with the Diffusion Toolkit, which is used for processing diffusion-weighted MR images.
  4. DTI-TK (Diffusion Tensor Imaging - Tensor Toolkit): This is a toolkit specifically designed for the spatial normalization and analysis of diffusion tensor images.
  5. 3D Slicer: An open-source software platform that is widely used for medical image informatics, image processing, and three-dimensional visualization. It has modules for diffusion MRI and tractography.
  6. Dipy (Diffusion Imaging in Python): This is a free and open-source software project focusing on the analysis of diffusion MRI data, particularly diffusion tractography, using Python.
  7. Camino: An open-source software toolkit for the analysis and visualization of diffusion MRI data, including tractography.
  8. BrainSuite: A collection of image analysis tools designed to process magnetic resonance images (MRI) of the human brain, including diffusion MRI tractography.
  9. ExploreDTI: A graphical toolbox for processing, analyzing, and visualizing diffusion MR data.
  10. MRTrix: An older version of MRtrix, still used in some research contexts for diffusion MRI data analysis.

Thank you for your reply. Are all of these software suitable for cervical spinal cord tractography? Or based on your experience, is there any software among these that is most suitable for the tractography of cervical spinal cord with intramedullary tumor?

Based on my experience, I would advise against tractography. Some arguments taken from Cohen-Adad J. Microstructural imaging in the spinal cord and validation strategies. Neuroimage. 2018 Nov 15;182:169–83.

Another approach for extracting metrics within specific spinal tracts relies on diffusion tractography. The basic idea is to perform diffusion experiments (e.g., DTI), run tractography, and then isolate tracts based on their location within the cross-sectional plane of the cord (which could be done manually or using existing atlases, as presented above). These tracts are then transformed into ROIs (1 inside the tract, 0 outside) that are used to average metrics. Like for atlas based approaches, this approach suffers from potential mis-registration between diffusion and other metrics. Also, this approach suffers from circularity problem: DWI data are used to generate tractography-based ROIs, however if there is a lesion or strong compression that affects DWI data, this will hamper the reliability of the tractography and subsequently bias the metric quanti- fication. Moreover, diffusion images can suffer from strong image dis- tortions, which could also affect the quality of tractography. Nevertheless, this approach has been successfully used in (Ciccarelli et al., 2007; Van Hecke et al., 2008) and showed good reproducibility in (Smith et al., 2010).

Additional resource:

  • McLachlin S, Leung J, Sivan V, Quirion PO, Wilkie P, Cohen-Adad J, Whyne CM, Hardisty MR. Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation. Neuroradiology. 2021 Mar;63(3):373–80.

Thank you very much for your reply. I will consider this issue carefully. Currently, there are many papers on the application of tractography in the research of DTI in spinal cord tumors or brainstem tumors. I don’t know what your opinion is. If it is not recommended, tractography, do you have any good suggestions for DTI research related to spinal cord tumors,For example, cervical spinal ependymoma or astrocytoma?

There are indeed many papers on the application of tractography in spinal cord tumors. It is always possible to run tractography in patients with tumors, observe that some tracts are deviated and/or interrupted, make a few figures showing the tractography results (tractography papers are very “photogenic”), and publish the paper. My concern is about the interpretability of these studies. Again, tractography is non specific. The white matter could be “intact” and the tractography bundles could be interrupted due to other reasons (eg, susceptibility distortion, low SNR, crossing fibers, partial volume effect). Similarly, the actual white matter tracts could be completely disrupted, but the tractography bundles would show no disruption, due to other reasons (eg, scaring tissue with anisotropic diffusion properties, yielding high FA and no interruption in the bundles).

I would return the question and ask what the tractography would be used for? For example, if the goal is to assess the integrity of white matter along the tracts possibly affected by the presence of a tumour, another approach would be to rely on an atlas to then extract DWI metrics (it could be DTI, or it could be other DWI models such as NODDI, etc.) within specific tracts, while making sure to exclude a region close to the tumor that could cause spurious results. That would provide a more controlled and non-binary (ie: tract interrupted: yes/no) output of the study. There are many ways data can/should be analysed. I cannot provide one-fit-all analysis approach, as the best approach depends on the goal of the study, the underlying hypotheses, the type of data being acquired, the quality of the data, etc.

Yes, Our purpose is not to pursue good-looking pictures, although we previously thought that tractography might be a good research method. The purpose of our research is to observe the integrity of the spinal cord in patients with spinal cord tumors such as ependymoma or astrocytoma. Generating tractography is not the purpose of our research. The purpose of our research is The degree of damage to the spinal cord caused by tumors, and trying to find some characteristics that can guide surgery or predict patient prognosis. We have DTI data, maybe extract DWI metrics is possible. Do you have other suggestions?

Yes, extracting DWI metrics sounds like a reasonable approach. If it makes sense with your hypotheses, I would do it in regions not affected by the tumor (eg, above/below the tumor), to be able to use probabilistic atlases and a more reliable mapping of the various spinal white matter tracts.

Thank you very much for your patient answer. We will re-examine our research methods and content to find the best solution.