Dear FSL experts,
I've run probtrackX for 2 pathways (let's say A,B) and would like to now the % of voxels that overlap between them. I'd appreciate if you could help me to figure out the right way to do it.
The steps to get the % of overlapping Vx between A & B would be:
1) Since I did probtrackX in 2 directions in order to get the average for each pathway, I should first calculate the average fdt_path for each tract. The command for this would be something like this
fslmaths fdt_paths_A_dir1.nii.gz -add fdt_paths_A_dir1.nii.gz -div 2
2) Binarize the average fdt_paths. How can I determine the threshold to use for this?
3) Find the % of overlapping Vx between the average_fdt_pathsA and the average_fdt_pathsB. If I multiply the average_fdt_pathsA by average_fdt_pathsB, I expect to have as an output an image with the overlap between the 2, right? Is there any way to count for the number of Vx within this binarized image using FSL commands so that I can express the overlap as a %?
Thank you in advance for your assistance.
Best wishes,
Noelia
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