sungoku / fba_paper

A repository of code used in Shannon Kelley's paper "Age-related differences in white matter: Understanding tensor-based results using fixel-based analysis"

fba_paper

A repository of code used in Shannon Kelley's paper "Age-related differences in white matter: Understanding tensor-based results using fixel-based analysis"

Whole Brain FBA

• Scripts showing how Fixel_based analysis was done
• Run in order from run_mtrix 1 to run_mrtrix5
• Also shows how PVE mask was created

Tract Specific Analysis

• Examples of commands used for Tract Specific analysis
• Subject's mean value is calculated in Tract_to_Values
• Compile.m shows how values for each subject for each tract are compiled
• Permutation.m shows the script for permutation testing
• Cohen.m shows how Cohen's D was found for a tract
• Visualize shows the commands used to visualize tracts for the figures

FA-CX Correction

• Functions/scripts for FA-CX correlation correction
• pregress1.m corrects for correlations across subjects;
• pregress2.m then corrects for correlations across voxels.
• The "looper" scripts loop through all subjects to perform the corrections.
• Be sure to input the folders where the FA, CX, and output files are stored.

Other MrTrix Commands

• Contains a page of other commands used during analysis
• How to get FA files, CX files, Visualization, whole brain VBA, etc.