MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
I believe it had been suggested at some point by @maxpietsch that use of the CSF ODFs for registration / template construction could be detrimental. However there are circumstances in which having a three-tissue-decomposition template could be beneficial. One approach is to simply use the WM and GM ODFs for registration / template construction, save the non-linear warps, and then apply those non-linear warps to the CSF ODFS and average in template space.
An alternative approach would be to include the CSF ODFs as input to population-template, but give that contrast a weight close to zero. However this means that these data will nevertheless be included in computations by mrregister.
Ideally, population_template would catch the special case where a particular contrast is given a weight of zero. it would then:
Omit that contrast from any mrregister calls
If -nocleanup, still execute any transformation calls to produce intermediate template images with that contrast
Generate the user-specified output template image for that contrast
I believe it had been suggested at some point by @maxpietsch that use of the CSF ODFs for registration / template construction could be detrimental. However there are circumstances in which having a three-tissue-decomposition template could be beneficial. One approach is to simply use the WM and GM ODFs for registration / template construction, save the non-linear warps, and then apply those non-linear warps to the CSF ODFS and average in template space.
An alternative approach would be to include the CSF ODFs as input to
population-template, but give that contrast a weight close to zero. However this means that these data will nevertheless be included in computations bymrregister.Ideally,
population_templatewould catch the special case where a particular contrast is given a weight of zero. it would then:mrregistercalls-nocleanup, still execute any transformation calls to produce intermediate template images with that contrast