Hello, thank you for your efforts!

I've been using MRI_reface for an HN dataset and encountered several issues where the tool did not perform as expected. I've detailed these instances in the uploaded document. (I used about 150 HN cases from TCIA but only about 40 were successful. I've tried using both DICOM and Nifti images, cropping the images to include only the head, and changing -altReg to 1 for failed cases.)

Could you also provide more details about the registration methods:

1. 
   

   Your manuscript mentioned that MRI_reface uses ANTs symmetric non-linear registration. What alternative registration method is used when -altReg is set to 1?

   
   
   
2. 
   

   The description of -altReg states "Internally, coreg runs with two different masks, then the one with the lowest cost function is used." Which two masks are referred to here?

   
   
   
3. 
   

   Will MRI_reface return outputs in the original image space when I apply manual external registration and provide the registration file?

   
   
   

Thank you for your time and assistance.