Hi there -- I just spent some time trying to figure this out myself (using MouseTracker as well) and I cobbled together a batch script that appears to work. Writing DOS scripts seems to be a lost art...
Code:
rem **read in first line from ML text file and store in subj variable
set /p subj=<C:\MediaLab\CurrentSubjectInfo.txt
rem **split first line into two tokens; subj# is second token
for /f "tokens=1,2 delims= " %%a in ("%subj%") do set s1=%%a&set s2=%%b
rem **run MTracker (or whatever program) using current ML subject number
C:\MouseTracker\runner.exe -s %s2% -f C:\MouseTracker\sample\fruit-veggies.csv
Copy and paste that code into a text file (Notepad works). When you save the file, be sure to select "All files" under the "Save as type" dropdown. Give the file a .bat extension (e.g., MT.bat). You can save this .bat file in the same folder where your .exp and .que MediaLab files are located, and you can run the .bat file within a .que using the Executable item type.
The only red flag here is that the paths within the .bat file are NOT relative, so you will need to update the paths to the MediaLab folder and your MouseTracker .csv files to reflect their locations on the specific computer running the .bat file.
Hope that helps!
Kurt