Files in UNCDEPENdLab/fmri.pipeline

Analysis of fMRI Data on HPC clusters

NEWS.md R/R_batch_job.R R/RcppExports.R R/afni_3dclusterize.R R/afni_3dclustsim.R R/afni_3dfwhmx.R R/afni_3dfwhmx_list.R R/afni_3dttest.R R/afni_whereami.R R/backproject_medusa.R R/bids_tools.R R/build_design_matrix.R R/build_fwe_correction.R R/build_l1_models.R R/build_l2_models.R R/cluster_job_submit.R R/deconvolve_nlreg_resample.R R/event_lock_timeseries.R R/extract_glm_betas_in_mask.R R/fill_atlas_with_stats.R R/finalize_pipeline_configuration.R R/fmri.pipeline-package.R R/fmri_ts.R R/fmri_utility_fx.R R/fsl_generate_fsf_contrast_syntax.R R/fsl_generate_fsf_ev_syntax.R R/fsl_generate_fsf_lvl1_ev_syntax.R R/fsl_helper_functions.R R/fsl_l1_model.R R/fsl_l2_model.R R/fsl_l3_model.R R/generate_mask_diagnostics.R R/get_l1_confounds.R R/get_output_directory.R R/glm_helper_functions.R R/job_tracking_functions.R R/l1_helper_functions.R R/lookup_nifti_inputs.R R/meta_mixed_by.R R/mixed_by.R R/populate_l1_from_yaml.R R/ptfce_spec.R R/rle_dt.R R/run_feat_sepjobs.R R/run_glm_pipeline.R R/setup_glm_pipeline.R R/setup_l1_models.R R/setup_l2_models.R R/setup_l3_models.R R/specify_contrasts.R R/spm_funcs.R R/spm_sceptic_model.R R/sqlite_functions.R R/summary_functions.R R/truncate_runs.R R/ui_helpers.R R/voxelwise_deconvolution.R R/wait_for_job.R R/yaml_outputs.R README.md inst/Rscript/ROI_TempCorr.R inst/Rscript/feat_lvl1_to_afni.R inst/Rscript/feat_lvl2_to_afni.R inst/bin/ptfce_zstat.R inst/bin/upd_job_status.R local/combine_brms.R local/decon_alignment.R local/decon_compression.R local/deconvolve_funcs.R local/extract_sceptic_atlas_deconvolved.R local/extract_sceptic_map_betas.R local/fwe_tests.R local/get_mmy3_trial_df.R local/rt_prediction_meta_analysis.R local/run_glm_betas_atlas.R local/run_pe_models.R local/test_backproject.R local/test_batch.R local/test_batch_local.R local/test_glm_pipeline.R local/test_glm_pipeline_clean.R local/test_meta_mixed_by.R man/R_batch_job.Rd man/R_batch_sequence.Rd man/add_baseline_regressors.Rd man/add_custom_feat_syntax.Rd man/add_tracked_job_parent.Rd man/afni_3dclusterize.Rd man/afni_3dclustsim.Rd man/afni_3dclustsim_list.Rd man/afni_3dfwhmx.Rd man/afni_3dfwhmx_list.Rd man/afni_whereami.Rd man/as.character.formula.Rd man/as_dhms.Rd man/bl1_build_events.Rd man/bl1_build_models.Rd man/bl1_build_signals.Rd man/bl1_get_cols.Rd man/build_3dclustsim_permutation.Rd man/build_beta_extraction.Rd man/build_design_matrix.Rd man/build_fwe_correction.Rd man/build_l1_models.Rd man/build_l2_models.Rd man/build_l3_models.Rd man/calculate_subject_exclusions.Rd man/check_nums.Rd man/choose_glm_models.Rd man/choose_glm_set.Rd man/cleanup_glm_pipeline.Rd man/cleanup_regressor.Rd man/cluster_job_submit.Rd man/cluster_submit_shell_jobs.Rd man/combine_feat_l3_to_afni.Rd man/compress_mts_pca.Rd man/compute_spike_regressors.Rd man/concat_design_runs.Rd man/convolve_cpp.Rd man/convolve_dcv_hrf.Rd man/convolve_double_gamma.Rd man/convolve_regressor.Rd man/create_fwe_spec.Rd man/create_new_hi_model.Rd man/create_tracking_db.Rd man/deconvolve_nlreg.Rd man/deconvolve_nlreg_resample.Rd man/detrendts.Rd man/dhms.Rd man/do_convolve.Rd man/dsigmoid.Rd man/enforce_glms_complete.Rd man/event_lock_ts.Rd man/evt_align_decon_files.Rd man/export_glm_config.Rd man/extract_bids_info.Rd man/extract_fsl_betas.Rd man/extract_glm_betas_in_mask.Rd man/feat_stats_to_brik.Rd man/fields_from_spec.Rd man/file_ext.Rd man/file_sans_ext.Rd man/fill_atlas_with_stats.Rd man/finalize_confound_settings.Rd man/finalize_pipeline_configuration.Rd man/fir1Bandpass.Rd man/fmri.design.Rd man/fmri.pipeline-package.Rd man/fmri.stimulus.Rd man/fmri_ts.Rd man/fsl_generate_fsf_contrast_syntax.Rd man/fsl_generate_fsf_ev_syntax.Rd man/fsl_generate_fsf_lvl1_ev_syntax.Rd man/fsl_l1_model.Rd man/fsl_l2_model.Rd man/fsl_l3_model.Rd man/fwe_spec.Rd man/generate_feature.Rd man/generate_feature_armadillo.Rd man/generate_mask_diagnostics.Rd man/generate_motion_regressors.Rd man/generate_run_data_from_bids.Rd man/generate_subject_data_from_bids.Rd man/generate_trial_data_from_bids.Rd man/get_collin_events.Rd man/get_contrasts_from_spec.Rd man/get_feat_status.Rd man/get_l1_config.Rd man/get_l1_confounds.Rd man/get_l2_config.Rd man/get_l3_config.Rd man/get_medusa_compression_score.Rd man/get_medusa_interpolated_ts.Rd man/get_mr_abspath.Rd man/get_output_directory.Rd man/get_tracked_job_status.Rd man/hours_to_dhms.Rd man/insert_df_sqlite.Rd man/insert_tracked_job.Rd man/interpolate_fmri_epochs.Rd man/lookup_dim.Rd man/lookup_nifti_inputs.Rd man/lookup_nvoxels.Rd man/lookup_run_volumes.Rd man/meta_mixed_by.Rd man/mixed_by.Rd man/mobj_fit_lm.Rd man/mobj_refit_lm.Rd man/names_to_internal.Rd man/ol_mean_min_max.Rd man/ol_unique.Rd man/path_sanitize.Rd man/pca_motion.Rd man/place_dmat_on_time_grid.Rd man/populate_defaults.Rd man/populate_last_events.Rd man/ptfce_spec.Rd man/read_df_sqlite.Rd man/read_feat_dir.Rd man/read_feat_inputs.Rd man/read_gfeat_dir.Rd man/refresh_feat_status.Rd man/reset_tracking_sqlite_db.Rd man/respecify_l2_models_by_subject.Rd man/rle_dt.Rd man/run_afni_command.Rd man/run_decon_alignment.Rd man/run_feat_sepjobs.Rd man/run_fsl_command.Rd man/run_glm_pipeline.Rd man/runmean.Rd man/sched_args_to_header.Rd man/setdiff_list_combn.Rd man/setup_compute_environment.Rd man/setup_glm_pipeline.Rd man/setup_l1_models.Rd man/setup_l2_models.Rd man/setup_l3_models.Rd man/sigmoid.Rd man/simulate_null_3dttest.Rd man/specify_contrasts.Rd man/submit_sqlite_query.Rd man/submit_tracking_query.Rd man/summarize_contrasts.Rd man/summary.bg_block_data.Rd man/summary.bg_subject_data.Rd man/summary.glm_pipeline_arguments.Rd man/summary.l1_model_set.Rd man/summary.l1_model_set_events.Rd man/summary.l1_model_set_models.Rd man/summary.l1_model_set_signals.Rd man/truncate_runs.Rd man/update_df.Rd man/update_tracked_job_status.Rd man/validate_block_data.Rd man/validate_dhms.Rd man/validate_input_data.Rd man/visualize_design_matrix.Rd man/voxelwise_deconvolution.Rd man/wait_for_job.Rd tests/testthat.R tests/testthat/setup.R tests/testthat/test-gpa.R tests/testthat/test-l3_covariate_order.R tests/testthat/test-r_batch_job.R vignettes/design.Rmd vignettes/fwe.Rmd vignettes/quickstart.Rmd