I currently have track files of diffusion tensor imaging (DTI) data generated from FSL's probtrackX tractography tool. What is the best software to visualize the streamlines from FSL in 3D?
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$\begingroup$ I encounter the same problem in visualizing the tractography generated by FSL. I wanna ask do you find an appropriate way to solve the problem. I will appreciate that if you can give me a hint about this. Thank you so much. $\endgroup$– ShiAug 2, 2019 at 14:10
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$\begingroup$ It doesn't generate streamline object as far as I know. I think the best way to visualize them would be to take the fdt_paths.nii file and threshold appropriately. Those are the voxels that streamlines traverse through. $\endgroup$– SabCoSep 9, 2019 at 23:14
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I must say I am not an expert, but the following sources look helpful:
- Gao et al. (2013) write
The voxel value in the resulting dataset represents the number of streamline samples passing through this voxel times the expected length of these samples. The probabilistic-tractography-derived DDM was generated by keeping the values of those voxels located at the WGM interface and setting the remaining voxels to zero. Again, the DDMs were rendered on the 3D WGM interface in DTI space.
- The FDT Userguide discusses tractography and PROBTRACKX in section 2.6.3;
- Catani & Thiebaut de Schotten (2008) discuss how diffusion tensor imaging (DTI) tractography can be used to virtually dissect white matter pathways in the living human brain;
- This presentation contains a lot of references;
- Specialist fora like this one may be of help.
References
- Catani & Thiebaut de Schotten, Cortex (2008); 44(8):1105-32
- Gao et al., PLoS ONE (2013); 8(10): e75065