I couldn't find a way to load and process the Nikon 12-bit RAW files from the D3100 directly with MATLAB.  So, I found a way from MATLAB to kick off the NX-D software and perform the conversion.

First, to run the program, I had to use a .bat file.  This could be created in MATLAB, then executed.  The main idea is to have the Capture NX-D program open with the required file highlighted.  Also, you need to have run NX-D before to set all the settings (output directory, 16-bit TIFF, etc.).

cd \
cd "Program Files"
cd Nikon
cd "Capture NX-D"
cd Module
start "" "CaptureNX-D.exe" C:\path_to_file\DSC_5097.NEF"
exit

Once NX-D is running, then you can use the Java robot to send the keys to start.  Here is the MATLAB code to run the .bat file, and then kick off the conversion.

%% Code
% Raise the Nikon Capture NX-D program with a specified filename, and kick
% off a capture

close all
clear

% Raise Nikon Capture NX-D program with the correct file highlighted (see
% test.bat)
status = system('test.bat &');

% Create active x server
h = actxserver('WScript.Shell');

% Get the java robot
import java.awt.Robot
import java.awt.event.*
my_robot = Robot;

% Bring the window to the foreground
temp = h.AppActivate('Capture NX-D');
% Check to see that the window came up
if temp == 1
    % Kick off the conversion, i.e., CTRL-E
    pause(0.1);
    my_robot.keyPress(17);
    pause(0.1);
    my_robot.keyPress(69);
    pause(0.1);
    my_robot.keyRelease(69);
    pause(0.1);
    my_robot.keyRelease(17);
    % Let window raise
    pause(0.5);
    % Press enter (assumes TIFF 16 bit already selected)
    my_robot.keyPress(10);
    pause(0.1);
    my_robot.keyRelease(10);
end