Package: fMRItools 0.5.3

fMRItools: Routines for Common fMRI Processing Tasks

Supports fMRI (functional magnetic resonance imaging) analysis tasks including reading in 'CIFTI', 'GIFTI' and 'NIFTI' data, temporal filtering, nuisance regression, and aCompCor (anatomical Components Correction) (Muschelli et al. (2014) <doi:10.1016/j.neuroimage.2014.03.028>).

Authors:Amanda Mejia [aut, cre], Damon Pham [aut], Mark Fiecas [ctb]

fMRItools_0.5.3.tar.gz
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fMRItools.pdf |fMRItools.html✨
fMRItools/json (API)
NEWS

# Install 'fMRItools' in R:
install.packages('fMRItools', repos = c('https://mandymejia.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mandymejia/fmritools/issues

On CRAN:

Conda:

5.10 score 2 stars 4 packages 35 scripts 781 downloads 56 exports 1 dependencies

Last updated 23 days agofrom:58a3ed2f15. Checks:9 OK. Indexed: yes.

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Exports:all_binaryall_integersas.matrix_iftibandstop_filtercarpetplotcarpetplot_stackcolCentercolor_paletteCompCorCompCor_HCPcoordlist_to_volcrop_voldct_basesdct_convertdespike_3Ddetrenddilate_mask_voldim_reducedual_regdual_reg_parcerode_mask_volexpand_RPsfsl_bptfhat_matrixinfer_format_iftiinfer_format_ifti_vecis_1is_constantis_integeris_posNummat2UTmatch_exactlymatch_inputmean_squaresModenorm_BOLDnuisance_regressionpad_volPCApct_sigplot_FCread_niftiscale_design_matscale_medscale_timeseriessign_flipskew_possum_neighbors_voltemporal_filterunmask_matunvec_matunvec_volUT2matvalidate_design_matvar_decompvox_locations

Dependencies:matrixStats

Readme and manuals

Help Manual

Help pageTopics
All binary?all_binary
All integers?all_integers
Convert CIFTI, NIFTI, or GIFTI input to T \times V matrixas.matrix_ifti
Bandstop filterbandstop_filter
Carpetplotcarpetplot
Stacked carpetplotcarpetplot_stack
Center matrix columnscolCenter
Color palettecolor_palette
Anatomical CompCorCompCor
Anatomical CompCor for HCP NIFTI and CIFTI dataCompCor_HCP
Convert coordinate list to 3D arraycoordlist_to_vol
Crop a 3D arraycrop_vol
Generate cosine bases for the DCTdct_bases
DCT and frequency conversiondct2Hz dct_convert Hz2dct
3dDespike from AFNIdespike_3D
Dilate 3D maskdilate_mask_vol
PCA-based Dimension Reduction and Prewhiteningdim_reduce
Dual Regressiondual_reg
Multiple regression for parcel datadual_reg_parc
Erode 3D maskerode_mask_vol
Expand realignment parameters (RPs)expand_RPs
fMRItools: Routines for Common fMRI Processing TasksfMRItools-package fMRItools
'bptf' function from FSLfsl_bptf
Hat matrixhat_matrix
Infer fMRI data formatinfer_format_ifti
Infer fMRI data format for several inputsinfer_format_ifti_vec
Is this object the expected data type, and length one?is_1
Is this numeric vector constant?is_constant
Is this an integer?is_integer
Is this object a positive number? (Or non-negative)is_posNum
Matrix to Upper Triangular Vectormat2UT
Do these character vectors match exactly?match_exactly
Match user inputs to expected valuesmatch_input
Compute mean squares from variance decompositionmean_squares
Mode of data vectorMode
Normalize BOLD datanorm_BOLD
Nuisance regressionnuisance_regression
Pad 3D Arraypad_vol uncrop_vol
PCA for tall matrixPCA
Convert data values to percent signal.pct_sig
Plot FCplot_FC
Wrapper to functions for reading NIFTIsread_nifti
Scale a design matrixscale_design_mat
Robust scalingscale_med
Scale the BOLD timeseriesscale_timeseries
Sign match ICA resultssign_flip
Positive skew?skew_pos
Sum of each voxel's neighborssum_neighbors_vol
Temporal filtering (bandpass, highpass, lowpass) with DCT or FFTdetrend temporal_filter
Unmask matrix dataunmask_mat
Transform vector data to imageunvec_mat
Convert vectorized data back to volumeunvec_vol
Upper Triangular Vector to MatrixUT2mat
Validate design matrixvalidate_design_mat
Compute variance decompositionvar_decomp
Get coordinates of each voxel in a maskvox_locations