Hi Noelia,
see below.
> On 8 Dec 2017, at 14:57, Noelia Martinez Molina <[log in to unmask]> wrote:
>
> 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
Rather than using the raw streamline counts from the fdt_paths files, you should first divide both of them by their respective waytotal. This way, you get probabilities values in each voxel that you can then average using the same command you posted above.
>
> 2) Binarize the average fdt_paths. How can I determine the threshold to use for this?
I don’t know which tracts you are testing specifically, but usually 0.01 (after division by the waytotal) is a good starting point. You can adjust the threshold by visually inspecting the tract shape in fsleyes.
>
> 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 %?
Once you have multiplied the binarised tract masks using fslmaths, you can use:
fslstats intersection_volume -V
The first value will be the number on non-zero voxels that are common between the two masks.
Hope this helps, cheers,
Matteo
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