A set of MATLAB scripts to perform Sholl analysis on tractography images in left and right sides. Run this after you have your fdt_paths.nii.gz files in the directory structure specified below.
Alternatively, it isn't too hard to change the script to fit your own directory structure. All that's needed is to change how the loops work in the run_*.m files.
Make sure your directory structure matches this:
(root)
└───(subject)
│ └───SHOLL
│ └───L
│ └───fdt_paths.nii.gz
│ └───R
│ └───fdt_paths.nii.gz
└───(subject)
│ └───(same as above)
└───(subject)
│ └───(same as above)
...
It doesn't matter what naming scheme you choose for the individual (subject) directory, as long as they are all in the same root directory, both have a L and R subdirectory (for left and right side), and have fdt_paths.nii.gz in each L and R directory. You can also name your (root) directory whatever you want.
Create a seed.txt in the same directory as each fdt_paths.nii.gz containing the desired xyz seed coordinates separated by spaces, e.g. if your desired origin for the Sholl analysis was the voxel at (20, 40, 3), your seed file would look like:
20 40 3
Such that your directory structure is now:
(root)
└───(subject)
│ └───SHOLL
│ └───L
│ └───fdt_paths.nii.gz
│ └───seed.txt
│ └───R
│ └───fdt_paths.nii.gz
│ └───seed.txt
└───(subject)
│ └───(same as above)
└───(subject)
│ └───(same as above)
...
Place all MATLAB .m script files in the same directory. Then run run_sholl_analysis.m, choosing your (root) directory when prompted.
This will generate sholl_output.mat in each L and R directory containing the results of the Sholl analysis for each tractography image. The variables in the sholl_output.mat file are dists and conns, representing an array of distances in mm and the number of connections at that distance, respectively.
Once you've finished the previous step and have your sholl_output.mat files in each folder, run run_sholl_plots.m, choosing your (root) directory and desired bin size (in millimeters) when prompted. A common choice for bin size is 2.
This will generate bin_output.mat in each L and R directory containing the binned Sholl outputs bins, conns_bins, representing an array of the bin endpoints and connections in each bin, respectively. It will also generate a sholl.fig figure in each L and R directory based on these binned outputs.
Right now sholl_analysis.m uses a hashmap to tally connections per distance. This seems to experience loss of precision in the calculated Euclidean distance despite all of the values being multiples of 0.5. This is mostly a non-issue due to the binning performed before generating the plots but if anyone knows a more sane way of mapping Euclidean distance to sum of connections in MATLAB please let me know.
This script uses Paul's textprogressbar in order to display progress during sholl_analysis.m.