R: Routines for Common fMRI Processing Tasks

# Routines for Common fMRI Processing Tasks

## Documentation for package ‘fMRItools’ version 0.7.2

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

fMRItools-package | 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
colCenter | Center matrix columns
color_palette | Color palette
CompCor | Anatomical CompCor
CompCor_HCP | Anatomical CompCor for HCP NIFTI and CIFTI data
coordlist_to_vol | Convert coordinate list to 3D array
crop_vol | Crop a 3D array
dct2Hz | DCT and frequency conversion
dct_bases | Generate cosine bases for the DCT
dct_convert | DCT and frequency conversion
despike_3D | 3dDespike from AFNI
detrend | Temporal filtering (bandpass, highpass, lowpass) with DCT or FFT
dice_overlap | Dice overlap
dilate_mask_vol | Dilate 3D mask
dual_reg | Dual Regression
dual_reg_parc | Multiple regression for parcel data
erode_mask_vol | Erode 3D mask
expand_RPs | Expand realignment parameters (RPs)
fMRItools | fMRItools: Routines for Common fMRI Processing Tasks
fsl_bptf | 'bptf' function from FSL
hat_matrix | Hat matrix
Hz2dct | DCT and frequency conversion
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_integer | Is this an integer?
is_posNum | Is this object a positive number? (Or non-negative)
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
Mode | Mode of data vector
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
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
temporal_filter | Temporal filtering (bandpass, highpass, lowpass) with DCT or FFT
uncrop_vol | Pad 3D Array
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