Analysis Scripts for " A thalamic circuit represents dose-like responses induced by nicotine-related beliefs in human smokers"
I. SYSTEM REQUIREMENTS AND INSTALLATION GUIDE
Scripts were run on version 9.5 (R2018b) of the MATLAB Runtime is installed and are compatible with more recent versions as well.
Download and install SPM12 at https://www.fil.ion.ucl.ac.uk/spm/software/download/
Add the ‘helpers’ custom MATLAB function folder to MATLAB’s path.
Multiple regression was carried out in R (RStudio 1.1.463, 2018) using the ‘lmer’ function
General notes:
For simplicity we coded instructed belief levels with a single letter denoting each condition.
Whenever you come across folders names or code variables listed this way, they are referring to the following experimental conditions:
A – low belief
B – medium belief
C – high belief.
Moreover, the term ‘absr’ refers to the absolute value of market return (r) in the models employed throughout this study.
In this repository you may find:
Code:
• Reading participants’ behavioral data from scanning sessions
• R script for behavioral modelling
• SPM12 scripts:
o Preprocessing
o Generation of parametrical modulators by behavioral model for fMRI GLM.
o First- and second-level analysis for both GLM and PPI pipelines.
o Misc. helper functions
o
• Standalone scripts to generate all non-volumetric figures from spreadsheet data
Data:
Behavioral:
• Behavioral data from the stock market decision making task as a single CSV file.
• Control measurements (CO, Cotinine, cartridge weight)
• Self-report subjective belief rating
Functional:
GLM
• 1-st level maps (‘input’) and 2-nd level maps (‘output’):
o absr modeling
o button press modeling
o market reveal (visual stimulation)
• group-level maps:
o absr modeling
o button press modeling
o market reveal (visual stimulation)
o absr – belief conditions contrasted (A vs B vs C)
o absr – belief conditions combined (A+B+C)
PPI
• 1-st level maps (‘input’) and 2-nd level maps (‘output’):
o absr modeling
o absr – belief conditions contrasted (A vs B vs C)
ROI masks for thalamic nuclei
The THOMAS atlas nuclei, normalized to the study’s functional space.
GLM – no spatial smoothing
• 1-st level maps (‘input’) and 2-nd level maps (‘output’):
o absr modeling
o button press modeling
o market reveal (visual stimulation)
• group-level maps:
o absr modeling
o absr – belief conditions contrasted (A vs B vs C)
