dcm2niix -m default

[lamaresh]

the default value for -m argument in dcm2niix is 2 and possible values are 0,1,2,y,n where 0=, 1=y and 2 is described as auto and is an intermediate behaviour so images are not split only on the base of series instance UID (https://github.com/rordenlab/dcm2niix/blob/master/console/main_console.cpp)

in nipype the corresponding merge_imgs input trait is a boolean. I think it should be update to an Enum to maintain the same behaviour of the command line program, something like this for Dcm2niixInputSpec:

merge_imgs = traits.Enum(
        "2",
        "1",
        "0",
        argstr="-m %s",
        usedefault=True,
        desc="merge 2D slices from same series regardless of echo, exposure, etc. - [0=no, 1=yes, 2=auto]")

[effigies]

We need to preserve backwards compatibility. Fortunately, True == 1 and False == 0, so we could still use an enum:

merge_imgs = traits.Enum(0, 1, 2, argstr='-m %d')

We cannot change the default to 2, though, as that would break tools relying on the default being False.

[lamaresh]

maybe you could skip the argument if not specified by the user, so dcm2niix will use it's own version default?