Refactor more

[tsalo]

Closes #265.

Changes proposed in this pull request

• Rename init_cbf_compt_wf to init_compute_cbf_wf.
• Rename init_gecbf_compt_wf to init_compute_cbf_ge_wf.
• Rename init_asl_confs_wf to init_asl_confounds_wf.
• Rename init_asl_geref_wf to init_asl_reference_ge_wf.
• Rename init_asl_gereg_wf to init_asl_reg_ge_wf.
• Rename init_asl_t1_getrans_wf to init_asl_t1_trans_ge_wf.
• Rename init_asl_gestd_trans_wf to init_asl_std_trans_ge_wf.
  • There are enough similarities between the GE and non-GE versions that I think I can combine them. The GE version needs to skip HMC and SDC, it accepts 4D ASL files instead of split 3D volumes, and it doesn't create a final reference image.
    • Allow HMC and SDC transforms to be "identity" when they're not used. Then we don't need to count the transforms or have "use_hmc" or "use_fieldwarp" parameters.
    • Set hmc_xforms and fieldwarp to identity in GE workflow.
    • Split ASL files for GE workflows.
    • Add flag that will skip the final reference image generation for GE data.
• Document the steps in init_asl_preproc_wf in greater detail, with an eye toward highlighting the differences between init_asl_preproc_wf and init_asl_preproc_wf.
• Reorder steps in init_asl_preproc_wf to be as linear as possible.
• Create a new identity node in init_asl_preproc_wf to wrangle multi-echo vs. single-echo data.
• Whenever possible, loop over the various CBF connections between workflows, rather than having separate connection assignments. This reduces the amount of code, and only increases the complexity a little bit.
• Remove unused outputnode from init_cbfplot_wf and init_gecbfplot_wf.

Documentation that should be reviewed