ENH: More nipype style documentation for easier end use

[ostanley]

Re: our Jan 21 meeting here are two examples of the atlas brex documentation. I think the piece that is missing is a listing of the actual params, and roughly what they do, and a default setting. Everything I added for this I grabbed from either the AtlasBrex class or the bash script itself.

Current:

inputnode:
restore_T1: preprocessed (debiased/denoised) T1 file name
restore_T1: preprocessed (debiased/denoised)T2 file name

arguments:
params_template: dictionary of info about template
params: dictionary of node sub-parameters (from a json file)
name: pipeline name (default = “extract_pipe”)

Outputs:
smooth_mask.out_file: Computed mask (after some smoothing)

Proposed:

inputnode:

• restore_T1: preprocessed (debiased/denoised) T1 file name
• restore_T1: preprocessed (debiased/denoised)T2 file name

arguments:

• params_template: dictionary of info about template
  • template_head: Atlas with skull default: NMT
  • template_brain: Atlas with skull removed, default NMT_SS
• params: dictionary of node sub-parameters (from a json file)
  • f: initial BET fraction, default 0.5
  • reg: method of template registration, default 1
    0 = FNIRT w/ bending
    1 (default) = FNIRT membrane-energy regularization
    2 = ANTs/SyN w/ N4Bias
    3 = w/o N4Bias
  • w: warp resolution, default 10,10,10
  • msk: mask binarization threshold (in %) for fslmaths default a,0,0
• name: pipeline name (default = “extract_pipe”)

Outputs:

• smooth_mask.out_file: Computed mask (after some smoothing)