| add_baseline_regressors | Helper function to append baseline regressors to the... |
| add_custom_feat_syntax | Helper function to find/replace or insert additional... |
| add_tracked_job_parent | Add parent/child id relationship to tracking database |
| afni_3dclusterize | wrapper class for 3dClusterize |
| afni_3dclustsim | R6 class for 3dClustSim automation |
| afni_3dclustsim_list | R6 class for a list of 3dClustSim runs |
| afni_3dfwhmx | R6 class for running 3dFWHMx on a single input file based on... |
| afni_3dfwhmx_list | R6 class for running 3dFWHMx on a group of input files using... |
| afni_whereami | wrapper class for AFNI whereami |
| as.character.formula | S3 method to convert formula to character |
| as_dhms | helper function to convert a period object back into a... |
| bl1_build_events | helper function to build events consisting of onsets and... |
| bl1_build_models | helper function to create a set of level 1 models |
| bl1_build_signals | helper function to build level 1 signals |
| bl1_get_cols | Onset, duration, value column selection helper function |
| build_3dclustsim_permutation | helper function for setting up 3dClustSim objects for... |
| build_beta_extraction | helper function to prompt user to choose combinations of l1,... |
| build_design_matrix | Creates an fmri design matrix, including timing files for for... |
| build_fwe_correction | Function to walk user through setting up FWE corrections for... |
| build_l1_models | Interactive function to build an l1 model specification for... |
| build_l2_models | Interactive function to build an l2 model specification for... |
| build_l3_models | Interactive function to build an l3 model specification for... |
| calculate_subject_exclusions | small helper function to populate subject exclusions in... |
| check_nums | helper function to validate numbers in an input string or... |
| choose_glm_models | helper function to ask user to choose models at a given level... |
| choose_glm_set | helper function to guide user through process of choosing... |
| cleanup_glm_pipeline | helper function to refresh l3 model status and save gpa... |
| cleanup_regressor | Small utility function to handle any NAs in the regressor... |
| cluster_job_submit | This function submits a single script to a high-performance... |
| cluster_submit_shell_jobs | helper function to submit a set of shell jobs that are... |
| combine_feat_l3_to_afni | Function to combine Feat L3 analyses into AFNI BRIK+HEAD... |
| compress_mts_pca | Core function for computing multivariate time series... |
| compute_spike_regressors | compute spike regressors from a data.frame or matrix of... |
| concat_design_runs | Concatenate design matrices for each run to form a single... |
| convolve_cpp | Internal function to convolve two vectors using nested for... |
| convolve_dcv_hrf | This function takes in a matrix of generated neural events... |
| convolve_double_gamma | This function convolves a stimulus vector with the... |
| convolve_regressor | This function convolves a regressor with a normalized HRF... |
| create_fwe_spec | helper function to create an FWE object that specifies the... |
| create_new_hi_model | Internal function to walk through l2/l3 model setup,... |
| create_tracking_db | Internal helper function to create the tracking SQLite... |
| deconvolve_nlreg | C++ port of Bush and Cisler 2013, Magnetic Resonance Imaging... |
| deconvolve_nlreg_resample | This function deconvolves the BOLD signal using Bush 2011... |
| detrendts | Detrend a time series up to quadratic trend. Used by... |
| dhms | small helper function to parse duration syntax of... |
| do_convolve | Internal port of fsl do_convolve |
| dsigmoid | Dsigmoid transform |
| enforce_glms_complete | Helper function to create named data.frame from a set of... |
| event_lock_ts | function to get interpolated event locked data |
| evt_align_decon_files | Align a set of deconvolved time series files to an event of... |
| export_glm_config | Output GLM configuration to a '.yaml' or 'json' file |
| extract_bids_info | Function for extracting fields from BIDS filenames (mostly... |
| extract_fsl_betas | function to extract voxelwise betas from a given level of FSL... |
| extract_glm_betas_in_mask | Function to extract subject-level coefficients from an FSL... |
| feat_stats_to_brik | internal function to convert a feat level 1 directory to an... |
| fields_from_spec | internal function to populate l1_model_set onsets from spec... |
| file_ext | internal function for getting a file extension that may... |
| file_sans_ext | internal function for returning a file (and path) without its... |
| fill_atlas_with_stats | Populates parcel-wise statistics from an atlas or set of... |
| finalize_confound_settings | Helper function to populate confound information for pipeline... |
| finalize_pipeline_configuration | This is a small helper function to validate the... |
| fir1Bandpass | Apply a FIR-1 bandpass filter a signal. Can low- or high-pass... |
| fmri.design | fmri.design function from 'fmri' R package. Brought into this... |
| fmri.pipeline-package | fmri.pipeline: Analysis of fMRI Data on HPC clusters |
| fmri.stimulus | Convolve a regressor with a hemodynamic response function for... |
| fmri_ts | R6 class representing a multivariate time series object for... |
| fsl_generate_fsf_contrast_syntax | This function generates syntax for FSL Feat .fsf files for... |
| fsl_generate_fsf_ev_syntax | This function generates syntax for FSL Feat .fsf files for... |
| fsl_generate_fsf_lvl1_ev_syntax | This function generates syntax for FSL Feat .fsf files for... |
| fsl_l1_model | This function specifies a first-level GLM model in FSL based... |
| fsl_l2_model | Estimate a level 2 (subject) model using FSL FEAT with fixed... |
| fsl_l3_model | Estimate a level 2 (subject) model using FSL FEAT with fixed... |
| fwe_spec | R6 class for an FWE correction method that can apply to one... |
| generate_feature | This function creates K shifts of a neural events vector... |
| generate_feature_armadillo | This function creates K shifts of a neural events vector... |
| generate_mask_diagnostics | Generate a set of diagnostic images and plots for brain masks... |
| generate_motion_regressors | helper function for generating motion regressors from raw... |
| generate_run_data_from_bids | Function to generate a run_data object from a BIDS-compliant... |
| generate_subject_data_from_bids | Function to generate a subject_data object from a... |
| generate_trial_data_from_bids | Function to generate a trial_data object from a... |
| get_collin_events | Small helper function to calculate collinearity diagnostics... |
| get_contrasts_from_spec | helper function to generate a contrast matrix from an lm()... |
| get_feat_status | helper function to look at whether feat ingredients exist for... |
| get_l1_config | Function to output l1_models into '.yaml' object |
| get_l1_confounds | helper function to generate confounds txt file for inclusion... |
| get_l2_config | Helper function to output l2_models into '.yaml' object |
| get_l3_config | Get a list containing configuration settings for l3 models |
| get_medusa_compression_score | front-end function for taking a list of windowed time series... |
| get_medusa_interpolated_ts | front-end function for taking a list of windowed time series... |
| get_mr_abspath | small helper function to pull absolute paths to a given... |
| get_output_directory | small helper function to return the location of an l1... |
| get_tracked_job_status | Query job status in tracking SQLite database |
| hours_to_dhms | convert a number of hours to a days, hours, minutes, seconds... |
| insert_df_sqlite | helper function to insert a keyed data.frame into the sqlite... |
| insert_tracked_job | Internal helper funciton to insert a job into the tracking... |
| interpolate_fmri_epochs | Interpolate an aligned fmri_ts object onto a consistent time... |
| lookup_dim | Helper function to obtain the dimensions of a 4D file |
| lookup_nifti_inputs | helper function to locate nifti inputs for each run of data |
| lookup_nvoxels | Helper function to obtain the number of voxels in a 4D file... |
| lookup_run_volumes | Helper function to obtain the number of volumes in a 4D nifti... |
| meta_mixed_by | Function to run Bayesian random-effects meta-regression on... |
| mixed_by | Mixed by runs a set of mixed-effects models for each... |
| mobj_fit_lm | internal helper function to setup a linear model for a given... |
| mobj_refit_lm | Helper function to re-calculate the l3 design matrix for a... |
| names_to_internal | helper function to rename columns of input data.frame to... |
| ol_mean_min_max | Round and format the mean, min, and max as a single character... |
| ol_unique | Print the top n unique values and frequencies of an atomic... |
| path_sanitize | Sanitize a filename by removing directory paths and invalid... |
| pca_motion | small helper function for compressing motion parameters using... |
| place_dmat_on_time_grid | Function to convert dmat (runs x regressor list) to a... |
| populate_defaults | helper function to copy any missing fields in target |
| populate_last_events | Internal function to add last_onset and last_offset columns... |
| ptfce_spec | R6 class for pTFCE specification for one or more z-statistic... |
| R_batch_job | Description of R_batch_job R6 class |
| R_batch_sequence | Description of R_batch_sequence R6 class |
| read_df_sqlite | helper function to lookup a keyed data.frame from the sqlite... |
| read_feat_dir | helper function to look up core stats outputs from a .feat... |
| read_feat_inputs | This is a small helper function that returns the inputs... |
| read_gfeat_dir | helper function to look up core stats outputs from a .gfeat... |
| refresh_feat_status | small helper function to look at feat outputs and files to... |
| reset_tracking_sqlite_db | Internal helper function to reset tracking SQLite database |
| respecify_l2_models_by_subject | Helper function to run the requested GLM model for each... |
| rle_dt | R6 class for a keyed data.table object that uses run-length... |
| run_afni_command | Wrapper for running an AFNI command safely within R |
| run_decon_alignment | Align a set of deconvolved time series files from... |
| run_feat_sepjobs | function to submit a set of jobs on a cluster to estimate... |
| run_fsl_command | Wrapper for running an FSL command safely within R |
| run_glm_pipeline | primary function for running a GLM analysis pipeline |
| runmean | compute a moving average smooth over a time series (here, a... |
| sched_args_to_header | helper function to convert the $sched_args field to a vector... |
| setdiff_list_combn | internal function to print bidirectional set differences in a... |
| setup_compute_environment | Helper function for setting up and modifying the compute... |
| setup_glm_pipeline | Main worker function for setting up an analysis pipeline |
| setup_l1_models | Function for setting up level 1 model specifications and... |
| setup_l2_models | This function generates the inputs for an FSL level 2... |
| setup_l3_models | This function generates the inputs for level 3 analyses,... |
| sigmoid | Sigmoid transform |
| simulate_null_3dttest | helper class to generate 3dttest++ null datasets using... |
| specify_contrasts | Internal function to add, edit, rename, delete contrasts |
| submit_sqlite_query | helper function to establish sqlite connection and submit... |
| submit_tracking_query | Internal helper function to submit a query to the tracking... |
| summarize_contrasts | Internal helper function for printing a summary of a contrast... |
| summary.bg_block_data | Summarize the contents of the subject data |
| summary.bg_subject_data | Summarize the contents of the subject data |
| summary.glm_pipeline_arguments | Helper function to better summarize GPA object |
| summary.l1_model_set | Helper function to better summarize GPA object's L1 models |
| summary.l1_model_set_events | Helper function to better summarize GPA object's l1_models'... |
| summary.l1_model_set_models | Helper function to better summarize GPA object's l1_models'... |
| summary.l1_model_set_signals | Helper function to better summarize GPA object's l1_models'... |
| truncate_runs | Identify the last valid volume acquired in a given run.... |
| update_df | this helper function replaces matching rows of a current... |
| update_tracked_job_status | Update job status in tracking SQLite database |
| validate_block_data | internal function to validate the contents of a block... |
| validate_dhms | helper function to validate format of walltime inputs for HPC... |
| validate_input_data | helper function to verify contents of subject, run, block,... |
| visualize_design_matrix | Visualize design matrix, including event onset times and run... |
| voxelwise_deconvolution | Function to perform voxelwise deconvolution on an fMRI... |
| wait_for_job | This function pauses execution of an R script while a... |
