help > RE: Got Multiple Output files after conversion (dcm to nii), which one do I use?
Feb 8, 2019  06:02 AM | Chris Rorden
RE: Got Multiple Output files after conversion (dcm to nii), which one do I use?
With the old dcm2nii it would convert a 3D acquisition (e.g. 't1.nii') and then losslessly apply orthogonal rotations so the image slices are roughly axial ('o') and then apply a crop ('co') to remove excess neck. The 'co' opften worked better with the contemporary SPM8 and FSL's BET. 

You can get a similar cropped image if you use dcm2niix's '-x y' option. However, recent FSL BET with the "robust" (-r) option and SPM12's clever built-in spm_maff8 function tend to be much more robust to excess neck signal. I doubt this is required for modern tools

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TitleAuthorDate
Luie Wang Feb 5, 2019
Chris Rorden Feb 6, 2019
Luie Wang Feb 7, 2019
RE: Got Multiple Output files after conversion (dcm to nii), which one do I use?
Chris Rorden Feb 8, 2019
Luie Wang Feb 11, 2019