Man pages for fMRItools
Routines for Common fMRI Processing Tasks
| all_binary | All binary? |
| all_integers | All integers? |
| as.matrix_ifti | Convert CIFTI, NIFTI, or GIFTI input to T \times V matrix |
| bandstop_filter | Bandstop filter |
| carpetplot | Carpetplot |
| carpetplot_stack | Stacked carpetplot |
| check_req_ifti_pkg | Check required packages for the data format |
| colCenter | Center matrix columns |
| color_palette | Color palette |
| CompCor | Anatomical CompCor |
| CompCor_HCP | Anatomical CompCor for HCP NIFTI and CIFTI data |
| CompCor.noise_comps | CompCor: get noise components |
| coordlist_to_vol | Convert coordinate list to 3D array |
| cor_mat | Un-vectorize correlation matrix |
| crop_vol | Crop a 3D array |
| data_CompCor_Params | fMRI data for 'scrub' and 'CompCor' |
| dct_bases | Generate cosine bases for the DCT |
| dct_convert | DCT and frequency conversion |
| despike_3D | 3dDespike from AFNI |
| despike_3D.interpolate | 3dDespike from AFNI, step 2 |
| despike_3D.qreg | 3dDespike from AFNI, step 1 |
| dilate_mask_vol | Dilate 3D mask |
| dim_reduce | PCA-based Dimension Reduction and Prewhitening |
| dual_reg | Dual Regression |
| dual_reg_parc | Multiple regression for parcel data |
| erode_mask_vol | Erode 3D mask |
| expand_RPs | Expand realignment parameters (RPs) |
| fft_detrend | FFT detrending |
| fMRItools | fMRItools: Routines for Common fMRI Processing Tasks |
| format_data | Format data for pscrub and CompCor |
| format_path | Format a path |
| fsl_bptf | 'bptf' function from FSL |
| get_FORMAT | Get FORMAT from format |
| get_kwargs | Get kwargs |
| get_NIFTI_ROI_masks | Get NIFTI ROI masks |
| hat_matrix | Hat matrix |
| image_scale | image_scale |
| infer_format_ifti | Infer fMRI data format |
| infer_format_ifti_vec | Infer fMRI data format for several inputs |
| is_1 | Is this object the expected data type, and length one? |
| is_constant | Is this numeric vector constant? |
| is.fname | Is this an existing file path? |
| is_integer | Is this an integer? |
| is_posNum | Is this object a positive number? (Or non-negative) |
| make_mask | Create a mask based on vertices that are invalid |
| mat2UT | Matrix to Upper Triangular Vector |
| match_exactly | Do these character vectors match exactly? |
| match_input | Match user inputs to expected values |
| mean_squares | Compute mean squares from variance decomposition |
| merge_kwargs | Merges two kwargs |
| Mode | Mode of data vector |
| noise_Params | noise parameters for CompCor |
| norm_BOLD | Normalize BOLD data |
| nuisance_regression | Nuisance regression |
| pad_vol | Pad 3D Array |
| PCA | PCA for tall matrix |
| pct_sig | Convert data values to percent signal. |
| plot_FC | Plot FC |
| plot_FC_gg | Plot FC with ggplot2 |
| read_nifti | Wrapper to functions for reading NIFTIs |
| rowMedians2 | Row medians |
| scale_design_mat | Scale a design matrix |
| scale_med | Robust scaling |
| scale_timeseries | Scale the BOLD timeseries |
| sign_flip | Sign match ICA results |
| skew_pos | Positive skew? |
| sum_neighbors_vol | Sum of each voxel's neighbors |
| sys_path | Format a path for 'system' |
| temporal_filter | Temporal filtering (bandpass, highpass, lowpass) with DCT or... |
| unmask_mat | Unmask matrix data |
| unvec_mat | Transform vector data to image |
| unvec_vol | Convert vectorized data back to volume |
| UT2mat | Upper Triangular Vector to Matrix |
| validate_design_mat | Validate design matrix |
| var_decomp | Compute variance decomposition |
| vox_locations | Get coordinates of each voxel in a mask |
