fMRI and behavioral analysis scripts for Ritz & Shenhav (in press) 'Orthogonal neural encoding of targets and distractors supports multivariate cognitive control'.

Includes code for Ecoding Geometry Analysis (EGA) and related multivariate functional connectivity.

Unprocessed fMRI data available at: https://doi.org/10.18112/openneuro.ds004909.v1.1.0

0_behavior

behavior & data files

• data files have all event information
• analyze_scanner_behav.m: analyze behavior

1_xnat2bids

Brown-specific files for getting data on sever + BIDS formatting

2_fmriprep

fmriprep preprocessing

3_preproc

moving files around & smoothing

4_wholeBrain

GLM analysis

batch scripts

• sh_wholeBrain_1_level1.sh: run first-level GLM
• sh_wholeBrain_2_level2.sh: run second-level GLM
• sh_wholeBrain_3_TFCE.sh: TFCE correction
• sh_wholeBrain_4_RSA.sh: just run first-level models for EGA

functions

• RDM_wholeBrain_1_1_estimateCat.m: core function for first-level analyses

5_ROI

Rostral-caudal analysis within dACC ROI

6_EGA

EGA analysis. First level models need to be fit block-wise for CV similarity. draws heavily from pcm_toolbox & especially rsatoolbox (see utils)

batch scripts

• sh_parcel_1_fit.sh: run EGA

functions

• RDM_parcel_1_1_fit.m: calculate similarity metrics for different models
• RDM_parcel_2_1_analyze.m: analyze similarity metrics
• RDM_parcel_2_3_mediation: run FC analyses

7_FC

• extract eigenvariate for FC analyses (drawing heavily from SPM's PPI)

simulations

EGA simulations

utils

lots of helpful packages.

• \pcm_toolbox\:

  • pcm_estGCrossval.m: core similarity metric function, adapted with more metrics

• \rsatoolbox\

  • basis of parcel-wise searchlight function
  • noise normalization

• bayesFactor: https://github.com/klabhub/bayesFactor

• palm: https://github.com/andersonwinkler/PALM

• pcm_toolbox: https://github.com/jdiedrichsen/pcm_toolbox

• rsatoolbox: https://github.com/rsagroup/rsatoolbox_matlab/tree/develop

• ScientificColourMaps7: https://www.fabiocrameri.ch/colourmaps/

• NIfTI_Toolbox: https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image

• rwls: https://github.com/jdiedrichsen/rwls

• surfing: https://github.com/nno/surfing

NOTE: requires an installation of SPM that you point to in batch scripts. https://www.fil.ion.ucl.ac.uk/spm/software/download/