Remove QSIPrep-specific parameters and Config elements

[tsalo]

Closes #16.

Changes proposed in this pull request

• Remove the following CLI parameters and their associated config attributes:
  • --skip-bids-validation
  • --anat-only / workflow.anat_only
  • --ignore / workflow.ignore
  • --skip-anat-based-spatial-normalization / execution.skip_anat_based_spatial_normalization
  • --anat-modality / workflow.anat_modality
  • --dwi-denoise-window / workflow.dwi_denoise_window
  • --denoise-method / workflow.denoise_method
  • --unringing-method / workflow.unringing_method
  • --dwi-no-biascorr / workflow.dwi_no_biascorr
  • --b1-biascorrect-stage / workflow.b1_biascorrect_stage
  • --no-b0-harmonization / workflow.no_b0_harmonization
  • --denoise-after-combining / workflow.denoise_after_combining
  • --separate-all-dwis / workflow.separate_all_dwis
  • --distortion-group-merge / workflow.distortion_group_merge
  • --anatomical-template / workflow.anatomical_template
  • --b0-to-t1w-transform / workflow.b0_to_t1w_transform
  • --intramodal-template-iters / workflow.intramodal_template_iters
  • --intramodal-template-transform / workflow.intramodal_template_transform
  • --b0-motion-corr-to / workflow.b0_motion_corr_to
  • --hmc-transform / workflow.hmc_transform
  • --hmc-model / workflow.hmc_model
  • --eddy-config / workflow.eddy_config
  • --shoreline-iters / workflow.shoreline_iters
  • --pepolar-method / workflow.pepolar_method
  • --fmap-bspline / workflow.fmap_bspline
  • --fmap-no-demean / workflow.fmap_demean
  • --use-syn-sdc / workflow.use_syn_sdc
  • --force-syn / workflow.force_syn
  • --recon-only / execution.recon_only
  • --recon-input / execution.recon_input
• Remove the following config attributes:
  • execution.output_layout
  • execution.qsirecon_dir
  • execution.run_preproc_and_recon
  • execution.task_id
  • workflow.cifti_output
  • workflow.do_reconall
  • workflow.dwi_only
• Initially remove but then add back in:
  • --b0-threshold / workflow.b0_threshold
  • --skip-odf-reports / execution.skip_odf_reports
  • --output-resolution / workflow.output_resolution