Routines for Common fMRI Processing Tasks

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Documentation for package ‘fMRItools’ version 0.6.0

• DESCRIPTION file.
• Package NEWS.

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
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)
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