I am using MRtrix to perform probabilistic and deterministic whole-brain tractography on a large, high resolution dataset. I am encountering issues with space and runtime constraints. I appreciate that the tractography should take a lot of time and space, but I want to reach out in the off-chance that there is a way to compress the track files during/after runtime or to speed up the process.
I am doing single shell diffusion imagery with the Tournier algorithm for dwi2response and CSD for the FOD generation. The goal is to produce a complete and thorough set of tracts for the entire brain.
For probabilistic tractography, I am using the following command:
tckgen fod_S66971.mif -seed_random_per_voxel mask.mif 50 -minlength 0.5 -maxlength 800 -cutoff 0.1 -angle 45 ~/out_prob_whole_brain_P1.tck -algorithm ifod2
For deterministic tractography, I am using this command:
tckgen fod_S66971.mif -seed_random_per_voxel mask.mif 50 -minlength 0.5 -maxlength 800 -cutoff 0.1 -angle 45 ~/out_det_whole_brain_P1.tck -algorithm sd_stream
I am running MRtrix on a desktop computer with the following specifications:
OS: Mac OS X 10.11.6
Processor: 3.5 GHz 6-Core Intel Xeon E5
RAM: 64 GB 1866 MHz DDR3 ECC
Some specific things that I am wondering are:
- Is there a more efficient way of running tckgen, perhaps if I alter the preceding steps?
- Is 50 a valid choice for “-seed_random_per_voxel” given the objective of making a thorough set of tracts? / Which parameters can I adjust to improve runtime, and how much effect would they have?
- Where would the computational bottleneck likely be? (We can move the process onto a computing cluster if necessary)
I appreciate any help and insight you can provide! Thank you so much!