Hi Juan,

Thank you for your quick reply. I am not using the rigid registration option because it is disabled after I input my brainmask in Step 1 and I did not check the automatic skullstripping option. My brainmask is registered to my T1 image and the skullstripped image looks good. 

The _labels_EMS.nrrd file looks good too, I see that it has segmented my image. I think even the MID0 files in the FinalMasking folder look ok, but not sure why I don't see anything in the QCistern file. 

I am copying a link here with more files https://drive.google.com/file/d/1CRu7RxD...

Thank you again!

Best wishes,
Jane