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Hi Mark, Thanks so much. There are three more questions when I tried: fsl_motion_outliers -i raw.nii.gz --fd -s FD.txt -o output.txt. (1) There is a column of value in FD.txt (the first is 0). These are FDs of all timepoint, right? (2) Which script can delete some volumes of the 4D files? For example, there are 200 volumes of raw.nii.gz. I want to delete first 5 volumes and then calculate FD of every timepoint. (3)You said the output.txt is the "locations of the identified outliers (it will not be created if there are no outliers)." I took a look at the output.txt and found the amount of columns was not the same with different subjects (e.g., 5 columns in one subject and 9 in another). Sorry I didn't understand what every column stood for and why the amount of columns was different in different subjects. Thanks again for your always helpful answers. Mingxia Zhang On Thu, Apr 4, 2013 at 11:52 AM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > You need to use the -s option if you want to get the metric values (in > this case the metric is FD). The output from -o is the locations of the > identified outliers (it will not be created if there are no outliers). > Note that you currently must specify the -o option even if you don't want > this output. > > All the best, > Mark > > > On 4 Apr 2013, at 12:37, zhang mingxia <[log in to unmask]> > wrote: > > > Dear FSL experts, > > > > For reviewers' suggestion, I am trying to get framewise displacement for > my analysis. I found the script of fsl_motion_outliers could do that. > Following the instruction (if I understand correctly), I used the script as > below: > > > > fsl_motion_outliers -i raw.nii.gz --fd -o try.txt > > > > I expected there was a column in try.txt which should be the framewise > displacement. But there was a column of zero. What's wrong with my use of > this script? > > > > Thanks! > > > > Mingxia Zhang >