A Computational Mechanism of Cue-Stimulus Integration for Pain in the Brain

https://doi.org/10.5061/dryad.41ns1rnpj

The codes and data for the manuscipt,

"A Computational Mechanism of Cue-Stimulus Integration for Pain in the Brain"

PEPSI stands for Pain Expectation and Pain Stimulus Integration.

Description of the data and file structure

codes

step1_CalcSubspacesEncodingperf.m

• Implements the processes and visualizations depicted in Figs. 2A-B (Calculation of subspaces and encoding performances).

step2_VisTraj.m

• Implements the visualization of the trajectories in subspaces.

step3_Traj2Behv.m

• Implements the processes and visualizations depicted in Fig. 5 (Reconstructing behavioral patterns from the neural trajectories).

data

data_for_replication.mat

• Contains all data necessary for implementing the steps in the codes folder.
  • neurAvg.FIR : subject averaged FIR response. comprising whole voxel.
  • neurAvg.CuetBeta, neurAvg.StimtBeta : temporal encoding weights using neurAvg.FIR as Y, and CueStimX as X
  • CueStimX : [Intercept, CueInfo, StimInfo]. Normalized. Condition ordered as in variable "condName"
  • parcelIndx: spatial index of each network
  • behvout: mat size of #cond X #sub. pain reports. condition is ordered as in variable "condName"
  • cmaps: color maps for "condName"
  • cmaps7: color maps for 7 large-scale functional networks. 

template.nii

• Provides the brain template for variable "neurAvg" in the data_for_replication.mat.
  • Example usage
    • obj = fmri_data(fullfile(basedir, 'data', 'template.nii')). This will results in same voxel size in data of the neurAvg.

Sharing/Access information

Links to other publicly accessible locations of the data:

• https://github.com/cocoanlab/PEPSI

Code/Software

Codes tested on Ubuntu 20.04, matlab R2021b.

Dependencies are...

• SPM12
• https://github.com/cocoanlab/cocoanCORE.git
• https://github.com/canlab/CanlabCore.git
• https://github.com/didch1789/yanchogosu_toolbox.git