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Dear FSL experts,

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