I´m trying to do my analysis following these steps:
A visitation (streamline) map or tractogram was constructed for each individual (all streamlines starting from a specific seed). In order to allow comparison of these maps between participants, the tractograms were normalized by log transforming the data and then dividing each voxel’s value by that of the maximum value in the map yielding voxel values between 0 and 1 ( Mars et al., 2016). Then, Targets were drawn as 3 × 3 × 3 voxel regions of interest. The average of all voxel´s values was calculated for each target. Permutation testing was then used to test for a difference between each target
I am unsure how to transfer this to mrtrix:
- If I use tckgen with the -seed_image option, i get streamlines that start in the seed and go to the rest of the brain, but SIFT cannot be applied.
- If I do tckgen with the -seed_image option anyway, I can use the tckmap command with the -vox option in order to get the visitation map.
- However I am not sure about the next two steps: log-transforming the data and getting the maximum value in the map in order to divide all other voxels by this value.
I know, doing a log-transfrom on your data needs to be thought through thorougly, however as I read through a lot of FAQs on this forum (and Mars et al. 2016, who are doing the same statistical analysis as me), I feel like it´s the right choice, as I want to do tract-wise permutation tests.
Thanks in advance!
(reference: Mars, R. B., Foxley, S., Verhagen, L., Jbabdi, S., Sallet, J., Noonan, M. P., … & Rushworth, M. F. (2016). The extreme capsule fiber complex in humans and macaque monkeys: a comparative diffusion MRI tractography study. Brain Structure and Function , 221 , 4059-4071.)