I am analyzing the resting state data. As previous studies did, I wanted to get the timecourse of WM and CSF as the nuisance signal. I used fast to segment 1*1*1 structure image and got the binary mask of WM and CSF (also some questions I mention in last letter, hoping to get your reply). 

Because my resting state data is 2*2*2, I used flirt for the registration: 

flirt -in binary_mask.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -output std_mask.nii.gz. 

But I found the std_mask.nii.gz was not binary. So I can not use it as the mask to extract timecourse.  I could not understand it and checked. Yes, binary_mask.nii.gz is a binary image and std_mask.nii.gz is not. What should I do? 

I have an extra question: should I do the registration on the structure images firstly and then use fast to segment them?

Thanks!

Mingxia Zhang