FSL

### proj_thresh

proj_thresh is a command line utility that provides an alternative way of expressing connection probability in connectivity-based segmentation. It is run on the output of probtrackx when classification targets are used.

The output of Connectivity-based seed classification is a single volume for each target mask, named seeds_to_{target} where {target} is replaced by the file name of the relevant target mask. In these output images, the value of each voxel within the seed mask is the number of samples seeded from that voxel reaching the target mask.
proj_thresh is run as follows:

proj_thresh list_of_volumes threshold

Where the list of volumes is the outputs of Connectivity-based seed classification (i.e., files named seeds_to_target1 etc etc) and threshold is expressed as a number of samples
For each voxel in the seeds mask that has a value above threshold for at least one target mask, proj_thresh calculates the number of samples reaching each target mask as a proportion of the total number of samples reaching any target mask. The output of proj_thresh is a single volume for each target mask.