help message problems when partial values are given

[KrisThielemans]

If a command line is incomplete, the executables print a usage message. However, confusingly it says that current values are default. Example

$ pvc_rl -x 10 -y 16 -z 9 --iter 1  blur.nii.gz 

Option outputfile is required but not defined
 Command tags: 
   -x < X > 
      = The full-width at half maximum in mm along x-axis
        With: X (Default = 10)
   -y < Y > 
      = The full-width at half maximum in mm along y-axis
        With: Y (Default = 16)
   -z < Z > 
      = The full-width at half maximum in mm along z-axis
        With: Z (Default = 9)
   [ -i --iter [ Val ] ]
      = Number of iterations
        With: Val (Default = 1)
   [ -d --debug ]
      = Prints debug information
 Command fields: 
   < petfile > 
      = PET filename
        With: petfile (Default = blur.nii.gz)
   < outputfile > 
      = output filename

Actually the default number of iterations is 10, and x,y,z and petfile do not have defaults (i.e. are required)

[bathomas]

I seem to remember this being a feature of ITK's metaCommand. In an ideal world, I think the command line parsing should either be replaced or custom written. I've never really liked the images without switches but have been reluctant to change as it would break the the nipype wrapper.

[KrisThielemans]

ok. We have control over this, so cannot fix this either. We will therefore leave this issue open as a warning for others.