splitclustercoords
no way to compare when less than two revisions
Differences
This shows you the differences between two versions of the page.
— | splitclustercoords [2010/07/04 16:08] (current) – created jochen | ||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ====== splitclustercoords ====== | ||
+ | ===== Motivation ===== | ||
+ | Whenever clusters are reported in tables, it frequently happens that distinct areas are //grouped// into one cluster, e.g. due to the fact that the selected threshold simply makes them appear // | ||
+ | |||
+ | Instead of having to manually alter the threshold (and thus enforce the peak locations to be associated with or grouped into separate clusters), this function allows to search within any given cluster for local maxima/ | ||
+ | |||
+ | ===== Function reference ('help splitclustercoords' | ||
+ | < | ||
+ | |||
+ | FORMAT: | ||
+ | |||
+ | Input fields: | ||
+ | |||
+ | c | ||
+ | v | ||
+ | k size threshold for sub-clusters (default: 3) | ||
+ | d | ||
+ | |||
+ | Output fields: | ||
+ | |||
+ | cs list of cluster sizes | ||
+ | cv Cx1 cell array with lists of values | ||
+ | cl Vx4 lister of cluster voxels | ||
+ | cc Cx1 cell array with lists of coordinates</ | ||
+ | |||
+ | ===== Arguments ===== | ||
+ | ==== c ==== | ||
+ | This is a list of coordinates ('' | ||
+ | |||
+ | ==== v ==== | ||
+ | Associated values (same order, naturally). These values must be given as absolute values (sorting will occur from highest to lowest!) | ||
+ | |||
+ | ==== k ==== | ||
+ | If given, this overrides the default, whereby identified sub-compartments must have at least this number of associated voxels. **This parameter was introduced to avoid finding peaks at the edge of a mask, where values might be increasing again towards the edge**. | ||
+ | |||
+ | ==== d ==== | ||
+ | If given, this overrides the default, which means that also (in the default case) second-degree neighbors (neighbors of neighbors) are considered; this is to avoid that remaining noise in the map leads to virtual (but practically meaningless) sub-clustering. | ||
+ | |||
+ | ===== Outputs ===== | ||
+ | //The outputs have been parallelized with the output of [[clustercoordsc]], | ||
+ | |||
+ | ==== cs ==== | ||
+ | This is simply a list of cluster sizes, whereas the first number always represents the cluster with the highest value (main peak). | ||
+ | |||
+ | ==== cv ==== | ||
+ | This is a '' | ||
+ | |||
+ | ==== cl ==== | ||
+ | This is a combined list of cluster coordinates and sub-cluster index values (by extending the '' | ||
+ | |||
+ | ==== cc ==== | ||
+ | As an alternative, | ||
+ | |||
+ | ===== Algorithm ===== | ||
+ | The algorithm works as follows: | ||
+ | |||
+ | * all voxel values within the given cluster coordinates are sorted from highest to lowest | ||
+ | * the highest voxel coordinate is marked as " | ||
+ | * beginning with the next highest voxel value, each voxel is, in turn, tested for whether it is linked to one of the subclusters (by determining the minimal distance to voxels that are already marked); this means all voxels directly connected without interruption are marked belonging to the same subcluster -- in case one voxel is connected to several subclusters (where sub-clusters meet), it picks the subcluster with the direct neighbor that has the highest value | ||
+ | * this continues (step three) until all voxels are marked | ||
+ | * finally the **// | ||
+ | |||
+ | The last step is done to remove " | ||
+ | |||
+ | **While the size of any given subcluster gives an indication about how big of a " | ||
+ | |||
+ | A suggested wording for a manuscript would be: | ||
+ | |||
+ | < | ||
+ | (statistic value above threshold for all considered voxels, minimum | ||
+ | clustersize in voxels). Local maxima (activation or correlation peaks) | ||
+ | are given whenever values within a cluster were were found to be not | ||
+ | connected to the already considered (central) mass in a higher-values-first | ||
+ | watershed searching algorithm.</ | ||
+ | |||
+ | //Note: This last term, " |
splitclustercoords.txt · Last modified: 2010/07/04 16:08 by jochen