If I am processing multiple sessions for one subject, should I treat each session independently and perform the analysis as usual? What to do with the connectome results, compared to fsl or freesurfer glm)? Is there any paper to recommend?
Thank you so much!
I think for both questions, it depends on your research question:
If you are only interested in changes in diffusion data between timepoints, and expect the T1w image to remain unchanged, then technically the intrinsic scan-rescan variance of the connectome data can be reduced if you combine your T1w images, obtain a single tissue segmentation / parcellation, and use that segmentation / parcellation in conjunction with each DWI dataset separately (see Appendix). Note however that that particular experiment linked was a conceptual demonstration, not my advocating that that’s how the tools should be used. If the data are considered independent, then they should be treated independently.
Assuming that your hypothesis is of a consistent change between time points across individuals, then what you have is a paired t-test. The FSL GLM wiki page is still the first port of call; the MRtrix3 interface for performing such is the
-errors ise option, explanation for the naming of such is in Anderson Winkler’s 2014 GLM paper.