Remove QSIPrep-specific parameters and Config elements #6
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mattcieslak
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Aug 12, 2024
| b1_biascorrect_stage = None | ||
| """The stage of processing at which to apply B1 bias correction. Either "final" (after | ||
| resampling), "none" (skipped entirely) or "legacy" (before concatenation).""" | ||
| cifti_output = None |
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I could see a ScalarMapper writing to cifti sometime in the future
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I'm hoping that, by that time, we'll have CIFTIs defined in --output-spaces instead.
mattcieslak
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Aug 13, 2024
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--------- Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>
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Aug 14, 2024
* Remove dwi, anatomical, and fieldmap workflows. * Remove lots of unused interfaces. * Update __init__.py * Remove more. * Do more. * Update __init__.py * Add init_output_grid_wf back in. * Remove QSIPrep-specific parameters and Config elements (#6) --------- Co-authored-by: Matt Cieslak <mattcieslak@gmail.com> --------- Co-authored-by: Matt Cieslak <mattcieslak@gmail.com>
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Closes #16.
Changes proposed in this pull request
--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_inputexecution.output_layoutexecution.qsirecon_direxecution.run_preproc_and_reconexecution.task_idworkflow.cifti_outputworkflow.do_reconallworkflow.dwi_only--b0-threshold/workflow.b0_threshold--skip-odf-reports/execution.skip_odf_reports--output-resolution/workflow.output_resolution