Merging all files in a folder with an avidemux batch file
Ok I have found a solution using ffmpeg instead of avidemux. I made the following batch file. In this case, I had to know the folder where the ffmpeg executable was, and also i managed to convert the resolution to a different one
for %%f in (*.mp4) do (
    echo file %%f &gt;&gt; list.txt
)
F:\ffmpeg\bin\ffmpeg.exe -f concat -safe 0 -i list.txt -vf scale=320:240 output.avi
del list.txt

This did the trick!