Parsing Raw ADC Data into Voltage Levels
The problem has been solved. 

function X = ReadTiAdcData(filename,N)
fid = fopen(filename,'r');
X = fread(fid,'int16');
fclose(fid);
X = X-2^(N-1);
X = X./2^(N-1);


Jim B's post explains the HSDC's binary file encoding and how to convert from it. N = 12. Turns out the full scale voltage didn't matter because we just needed the scaled voltage level relative to full scale, which was already encoded in the binary file, "full scale" being 4096.

I hope this is helpful for those who are struggling with converting raw ADC data using the TI HSDC.