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Have you tried something to distinguish your input file names from your output file name? Maybe one of these: fslmerge -t output4D.nii.gz ???.nii.gz fslmerge -t output4D.nii.gz c*.nii.gz d*.nii.gz Kathy Pearson ----------------------------------------------------------- Hi, I'm trying to merge 26 nifti files. When I write ls in the command line (I am located in the folder where the images I want to merge are) I get this: ls *.nii.gz c01.nii.gz c11.nii.gz d08.nii.gz c02.nii.gz c12.nii.gz d09.nii.gz c03.nii.gz c13.nii.gz d10.nii.gz c04.nii.gz d01.nii.gz d11.nii.gz c05.nii.gz d02.nii.gz d12.nii.gz c06.nii.gz d03.nii.gz d13.nii.gz c07.nii.gz d04.nii.gz c08.nii.gz d05.nii.gz c09.nii.gz d06.nii.gz c10.nii.gz d07.nii.gz And that is the order in which I want to merge them. Then I write fslmerge -t output4D.nii.gz *.nii.gz And I check the output in fslview. Volume 0 to 10 correspond to c01-c11. Which is fine. Then volume 11 is c5 again, volume 12 is c6... etc. I don't understand what's going on and what I'm doing wrong? The weird thing is that if I concatenate only c01.nii.gz to c10.nii.gz it does it fine. But once I add one more file, then it get's crazy and repeats randomly one of the previous files. Thank you in advance!