Dear MRtrix experts,
I’m writing to ask if it’s better to interpolate first and then use isotropic voxels to run ACT, or I should put the size of voxels in the header information. Does the MRtrix3 automatically do interpolation for you in that way?
Thank you in advance,
The size of the (anisotropic) voxels should already be in the image header based on however the data were initially obtained.
The tractography code in MRtrix3 all operates in “scanner space” / “real space”, acquiring interpolated values from any input images. So having a 5TT image with anisotropic voxels should work seamlessly, and hence there shouldn’t be any reasonable justification for resampling the data onto an isotropic grid first.
Thank you for the reply.
You mentioned that I should use the 5TT image for tckgen, I would like to ask if I -include, -seed, and -mask [white matter mask], will that be similar to input 5TT image? I know in the case of 5TT image, the seed will then be generated from the WM/GM interface, instead of randomly sampled from the white matter mask. I’m wondering if there are any other differences that I should be aware of (e.g., the fiber tracking will be restricted to white matter).
I would like to ask if I -include, -seed, and -mask [white matter mask], will that be similar to input 5TT image?
These are generally best considered as separate mechanisms for separate purposes. ACT is for improving the plausibility of all streamlines regardless of interest in specific pathways; ROIs are for extraction of said specific pathways.
Having said that, within certain specific experiments, if you were to generate appropriate binary masks, it’s possible that you could generate a result using ROIs alone that would be comparable to what you would get with a combination of ACT and ROIs, notwithstanding the grid artefacts that would be more prevalent with the former due to binarisation of tissue masks. To do so may however require a certain degree of familiarity with the nuances of how the tractography code operates / substantial experimentation to get the desired outcome. To describe precisely how these differences would play out would however take a lot of text.
I know in the case of 5TT image, the seed will then be generated from the WM/GM interface, instead of randomly sampled from the white matter mask.
There are again two separate concepts being conflated here: the use of ACT for imposing anatomical constraints, and the mechanism used for streamline seeding. While a 5TT image is requisite for the GM-WM interface seeding mechanism to be used, providing a 5TT image does not force streamlines to be seeded from the interface; other mechanisms (e.g. seeding throughout the white matter) can still be used. The list of available seeding mechanisms is presented in the command’s help page.