To do this you need to have Matlab R2013b installed in your computer. Slightly older versions of Matlab will also work. Newer versions do not work, because of incompatibility with some of the graphical functions used in idTracker.
Download idTracker's source code from
http://www.idtracker.es/code and copy it to some folder in your hard drive (make sure it's a folder where you have full write permissions).
Go to Matlab, and make that folder your working directory (that's the path you see right on top of command window)
In command window, type idTracker and press enter. This will execute idTracker, exactly in the same way as the compiled version. From here you can track a video normally. But you can also do the following:
Once idTracker starts, choose the first video you want to process. idTracker will open it. Tune all idTracker's parameters for that video. Once you are done, instead of pressing "Start", press "S&E". This will save the parameters and exit idTracker. Now ther should be a subfolder in the same folder as the video, called "segm". Inside this subfolder, there should be a file called "datosegm".
You can repeat this procedure for all the videos you want to track, so that all of them have the adequate paremeters. If you have many videos that you want to track with the same parameters, you can click on "import tracking parameters", and use the parameters you tuned for another video.
Now, go to the "segm" subfolder of one of your videos. Drag & drop the file "datosegm" on Matlab's command window. Matlab will auto-generate a line that starts as load(.....). This loads the contents of the file, which consist of a single variable called "variable". It contains idTracker's parameters.
Now, type
variable.empezarsinmas=1;
This will tell idTracker to not wait for you to press "start", but start the tracking immediately. Then, type
idTracker(variable)
This will start idTracker once again. But this time it already has everything it needs to do the tracking. You only need to wait until it finishes.
You can create a simple Matlab script which looks like this:
load(.....)
variable.empezarsinmas=1;
idTracker(variable)
load(.....)
variable.empezarsinmas=1;
idTracker(variable)
load(.....)
variable.empezarsinmas=1;
idTracker(variable)
...
...
where each "load" line loads a different "datosegm" file, corresponding to a different video. In this way, idTracker will track one video after another on its own.