Routines for Common fMRI Processing Tasks

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Documentation for package ‘fMRItools’ version 0.4.2

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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
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 Detrending with DCT or FFT
dim_reduce PCA-based Dimension Reduction and Prewhitening
dual_reg Dual Regression
erode_mask_vol Erode 3D mask
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)
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.
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
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
validate_design_mat Validate design matrix
var_decomp Compute variance decomposition
vox_locations Get coordinates of each voxel in a mask