I am trying to run this command from command-line prompt:
\"D:\\\\fiji\\\\fiji.exe -macro D:\\\\fiji\\\\macros\\\\FFTBatch.ijm --headless\"
You don't have to run cmd.exe, just create ProcessStartInfo object and pass the command with its parameters to it. Like this:
System.Diagnostics.ProcessStartInfo info = new System.Diagnostics.ProcessStartInfo("your command", "parameters");
Here is an example that shows you how to do it:
System.Diagnostics.ProcessStartInfo info = new System.Diagnostics.ProcessStartInfo("tree.com", "/f /a");
System.Diagnostics.Process p = new System.Diagnostics.Process();
p.StartInfo = info;
p.Start();
p.WaitForExit();
So in your case, this is your command: "D:\\fiji\\fiji.exe" and this is your command parameters or arguments: @"-macro D:\\fiji\\macros\\FFTBatch.ijm --headless"