Hello,
	  Thank you for your upload. I cannot reproduce your error locally on OSX - the values I obtain for fd/fdrms are different, both to each other and those in the files you sent. Additionally the values obtained do not seem inconsistent for this kind of data set. Can you rerun just to confirm that you get identical output files for rsfMRI_4D.nii?

Kind Regards
Matthew

> Dear Matthew,
> 
> Thank you very much for your help. I uploaded the following files:
> rsfMRI_4D.nii
> FD.txt
> FDrms.txt
> Best,
> 
> Jun
> 
> 2016/02/09 9:00、FSL automatic digest system <[log in to unmask]> のメール：
> 
>> 差出人: Matthew Webster <[log in to unmask]>
>> 件名: Re: framewise displacement
>> 日付: 2016年2月8日 20:41:09 JST
>> 
>> 
>> Hello Jun,
>>                        Can you upload your input data file to:
>> 
>> https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
>> 
>> Kind Regards
>> Matthew
>> 
>>> Dear Mark,
>>> 
>>> Thank you very much for your response. Not only the mean but each time point data is too small (please find attached --fd file of a subject). More strangely, --fd and --fdrms create the same output (please see --fdrms file). This may be due to my environment (Mac), as my colleague could calculate FD and FDrms correctly using fsl_motion_outliers (he runs FSL on virtual machine (probably Linux) on Windows).
>>> I also tried DPABI to calculate FD (Power) and FDrms (Jenkinson), and it seems successfully (Please see the attached excel file). They are larger than those from fsl_motion_outliers and seems reasonable.
>>> Is it possible that there is Mac-specific bug in fsl_motion_outliers?
>>> Best,
>>> 
>>> Jun
>>> 
>>> 
>>>> 差出人: Mark Jenkinson <[log in to unmask]>
>>>> 件名: Re: framewise displacement
>>>> 日付: 2016年2月3日 0:20:50 JST
>>>> 
>>>> 
>>>> Hi,
>>>> 
>>>> I agree that this is small, though remember that it is an average, so peak values in a mcflirt report might be downweighted a lot by a majority of smaller values.  That being said, I'm still surprised at how small these values are, but I've double-checked the scripts and everything should be in mm.  Is the motion correction actually having a noticeable impact on the images?
>>>> 
>>>> All the best,
>>>> Mark
>>>> 
>>>> 
>>>> 
>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jun Miyata <[log in to unmask]>
>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>> Date: Tuesday, 2 February 2016 03:29
>>>> To: "[log in to unmask]" <[log in to unmask]>
>>>> Subject: Re: [FSL] framewise displacement
>>>> 
>>>> And I found results were the same when I tried FSL 5.0.9.
>>>> Best,
>>>> 
>>>> Jun
>>>> 
>>>> 2016/02/02 12:06、Jun Miyata <[log in to unmask]> のメール：
>>>> 
>>>> Dear Mark,
>>>> Thanks, then my output (--fd file) seems too small. I'm planning to use mean FD for group matching and as a nuisance covariate. The group mean of mean FD is 0.0046 mm for patients and 0.0043 for healthy controls. Is this true for subjects, some of whose absolute displacement calculated from MCFLIRT are around 2-3 mm?
>>>> I used following command:
>>>> fsl_motion_outliers -i <raw fMRI volume> -o <output name> -s --fd
>>>> I confirmed that the input data is raw data, not preprocessed data. FSL version is 5.0.5, on OSX Mavericks. I appreciate your advice.
>>>> Best,
>>>> Jun
>>>> 差出人: Mark Jenkinson <[log in to unmask]>
>>>> 件名: Re: framewise displacement
>>>> 日付: 2016年1月29日 18:37:34 JST
>>>> Hi,
>>>> Yes, it is mm.
>>>> All the best,
>>>> Mark
>>>> From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Jun Miyata <[log in to unmask]>
>>>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>>>> Date: Friday, 29 January 2016 09:31
>>>> To: "[log in to unmask]" <[log in to unmask]>
>>>> Subject: [FSL] framewise displacement
>>>> Dear FSL experts,
>>>> I calculated framewise displacement using fsl_motion_outliers. What is the unit of it? Is it mm just like Power et al, 2012?
>>>> Thanks in advance,
>>>> Jun
>>>> 
>>>> 
>>> <--fd><--fdrms>
>>