fsl_motion_outliers user here (not official FSL person!).
I've found this happens if you have NaNs in your imaging data matrices. Replacing these with zeroes does the trick for me. Might be worth checking your files.
If this is the source of the issue, you can easily fix with:
fslmaths yourfile.nii -nan yourfile_withoutNaNs.nii
On Wed, 23 Aug 2017, Adi Maron-Katz wrote:
> I am running fsl_motion_outliers using the instructions in https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers
> The input file that I give is a 4D nii of the mni motion residuals, and the command seems to be running (no error is produced).
> However, no result file is generated in the designated result file path.
> The command that I used was:
> fsl_motion_outliers -i <full path my input 4d nii with no suffix> -o <full path of my output file no suffix> --fd --thresh=0.5
> Any advice would be highly appreciated.
> Many thanks
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