Minchul,

Thank you for your question. Can you tell me what the scale is in your subtract.jpg? Are we talking about a 1% difference or a 10% difference (positive or negative) ? 

Changing the dti_method.dti_flag to 1 in dkeparameters will output an FA map calculated using the DTI method (calculating D without estimating the W term). You can use this map and compare it to the FSL output. 

dti_method.dti_flag = 0; % whether (1) or not (0) to estimate DTI parametric maps based on the DTI (in addition to DKI) signal model (default: 0)

Best, 
Emilie