Hi Mingxia - the default interpolation method for flirt will combine signal from adjacent volumes, including those with zero values. Use nearest neighbour interpolation to avoid this, like so:
flirt -in binary_mask.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain -output std_mask.nii.gz -interp nearestneighbour
Cheers - John
----- Original Message -----
From: "zhang mingxia" <[log in to unmask]>
To: [log in to unmask]
Sent: Thursday, April 11, 2013 1:30:58 PM
Subject: [FSL] binary mask is "flirt" into a non-binary image?
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?