AFNI: prefix and suffix

[chrisgorgo]

I was just looking through the AFNI code. I found two weird things:

1. There are a lot of output_file inputs which correspond to output prefixes - is this correct?
2. There are many suffix inputs which due to lack of argstr are not functional.

[satra]

some pointers please :)

[chrisgorgo]

https://github.com/nipy/nipype/blob/master/nipype/interfaces/afni/preprocess.py#L29

https://github.com/nipy/nipype/blob/master/nipype/interfaces/afni/preprocess.py#L130

[satra]

thanks.

do you remember what happens when argstr is missing? does it crash? otherwise the second example looks ok,
except the default value should be in the traits definition itself.

@ssikka: could you please join this discussion and answer question 1 and also point it to brian. chris: brian is trying to clean up the out_file inputs with abspath.

[ssikka]

HI all,

1. I see its inconsistent, I will make inputs.out_file and outputs.out_file as consistent i/p and o/p output file names in all the interfaces.
2. I havent used suffix myself, so I need to cross verify this. May be its better to use argstr and make sure it works.

Thanks!

[chrisgorgo]

I had a proper look at this and the current implementation is correct. Sorry for the confusion:

1. What AFNI calls a "--prefix" is treated as full output filename if a given string has an extension (I was not aware of that and thought it works as a normal prefix).

2. I thought suffix was meant to be a command line option and was a copy-and-paste kind of mistake. It is in fact used for generating filenames in the interface methods.