Hello,
I am very new to MRtrix and stuck on trying to extract mean FD/FC/FDC values from specific parts of a tract.
In my analysis, I performed FBA and looked at the correlation between fixel metrics (FD, logFC, FDC) and scores on a cognitive outcome measure. I specifically focussed on the superior longitudinal fasciculus (SLF), extracted using TractSeg. I started by analysing all 3 branches separately, and found significant findings across all 3 metrics and SLF branches.
However, to reduce the number of comparisons across metrics/measures/tracts, the reviewer has asked that we simplify our analysis by performing one GLM across the whole SLF tract for each fixel metric, “mapping” significant results to the specific branches (i.e., SLF I - III), and extract each subject’s mean within the significant fixels mapped to that tract for further visualisation.
I have been able to “map” the significant fixels from the whole SLF to each branch using fixel2tsf for visualisation:
fixel2tsf fwe_pvalue.mif …/tractseg_output/TOM_trackings/SLF_I_overall.tck fwe_pvalue_SLF_I.tsf
fixel2tsf fwe_pvalue.mif …/tractseg_output/TOM_trackings/SLF_II_overall.tck fwe_pvalue_SLF_II.tsf
fixel2tsf fwe_pvalue.mif …/tractseg_output/TOM_trackings/SLF_III_overall.tck fwe_pvalue_SLF_III.tsf
This seems to have worked, and now I can visualise exactly what branch of the SLF each of these significant fixels belong to - great!
The problem is, I cannot work out how to extract the mean of the significant fixels within each of these tracts.
I would think I need to be able to create a mask of the significant fixels in each of the .tsf files and run mrstats - but alas, it seems this is not possible.
Any advice here?
Thank you!
Jake.