I know that this topic has been extensively discussed on the forum but I seem to still have unanswered questions. I am going to summarise the steps that I think should be carried out and the rational behind them (mostly). I would appreciate any one of you could confirm / refute my thoughts. Note that I have not run all the analysis yet so I cannot provide images (as yet).
As a background, I will assume that the tutorial on https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html has been followed up to point 13 " Warp FOD images to template space"
I am also going to refer to comments in this thread (How to restrict fixelcfestats to subset of tracts).
So at this point we would have a population template FOD and individual FODs in template space. We also have a fixel mask from the tutorial command:
fod2fixel -mask ../template/template_mask.mif -fmls_peak_value 0.06 ../template/wmfod_template.mif ../template/template_fixel_mask_dir
I also plan to generate three tracts from three ROIs (basically pairwise connectivity). I would think that the best way to do this would be on the population template.
My first question is: do the densities of these tracts matter - i.e. should we go down the route of computing a whole brain tractogram, doing SIFT(2) then extracting the streamlines, or would simple seed-target tracking suffice?
I will assume that we can do seed-target tracking and we can concatenate the results using
tckedit. I will call the resultant file
Following Dave’s suggestion (from this thread), I will run this command:
tck2fixel network.tck template_fixel_mask_dir template_fixel_mask_dir network_TDI.mif
Then follow the rest of Dave’s suggestions, ie:
mrthresold -abs 1 template_fixel_mask_dir/network_TDI.mif template_fixel_mask_dir/network_mask.mif
Would it then simply be a matter of running step 14 but replacing the mask with the network mask? ie:
foreach * : fod2fixel -mask ../template/network_mask.mif IN/fod_in_template_space_NOT_REORIENTED.mif IN/fixel_in_template_space_NOT_REORIENTED -afd fd.mif
Then continue down the tutorial.
Does that sound right?