# Trait disinhibition and NoGo event-related potentials in violent mentally disordered offenders and healthy controls --- ## Overview This repository contains all analysis code used for the manuscript **Trait disinhibition and NoGo event-related potentials in violent mentally disordered offenders and healthy controls**. Feel free to use and/or modify any code in this repository for your own research. --- ## Software used ### Bash [Bash](https://en.wikipedia.org/wiki/Bash_(Unix_shell)) is a Unix shell language used to interact with the computer. A Bash script (`preprocess.sh`) was used to run the EEG preprocessing scripts (themselves written in Python). ### Presentation [Presentation](https://www.neurobs.com) (Neurobehavioral Systems Inc.) is a stimulus delivery and experiment control program. Presentation was used to create and run the Go/NoGo task, and to send triggers to the EEG acquisition hardware. The code for the Go/NoGo task is available in the `paradigm` folder. ### Python [Python](https://www.python.org/) is a free, open source, general-purpose, high-level programming language. There are several so-called modules written for Python, which, for instance, contain various functions. Python and the [MNE-Python](https://mne.tools/stable/index.html) module was used for EEG data preprocessing. ### R [R](https://www.r-project.org/) is a free, open source, programming language primarily used for statistical modeling and analysis. R was used for data preparation and statistical analysis. ### Stan and brms [Stan](https://mc-stan.org/) is a free, open source, probabilistic programming language used for statistical inference and high-performance statistical computation. Stan was interfaced with R via the [brms](https://paul-buerkner.github.io/brms/) package, together used for Bayesian statistical analysis. --- ## Data availability Due to lack of explicit consent on behalf of the participants, we are unfortunately not able to share the data publicly. Requests for data may be sent to *carl.delfin [at] gu.se*. --- ## EEG data preprocessing All Python code used is found in the `preprocessing` folder. Preprocessing was carried out running 12 cores in parallel on a 12 core/24 thread AMD Ryzen 3900X workstation with 64 GB of 3600 MHz RAM. Most of the preprocessing time is dedicated to running [Autoreject](https://autoreject.github.io/). The final run was carried out on 2020-05-13 using the following environment and system specifications: ```bash ----- autoreject 0.2.1 matplotlib 3.2.1 mne 0.20.4 numpy 1.18.4 pandas 1.0.3 sinfo 0.3.1 ----- Python 3.8.2 (default, Apr 27 2020, 15:53:34) [GCC 9.3.0] Linux-5.4.0-7625-generic-x86_64-with-glibc2.29 24 logical CPU cores, x86_64 ----- Session information updated at 2020-05-13 09:16 ``` ```bash Linux kernel: Linux version 5.4.0-7625-generic (buildd@lcy01-amd64-015) (gcc version 9.3.0 (Ubuntu 9.3.0-10ubuntu2)) #29~1587437458~20.04~2960161-Ubuntu SMP Tue Apr 21 05:16:44 UTC CPU: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 43 bits physical, 48 bits virtual CPU(s): 24 On-line CPU(s) list: 0-23 Thread(s) per core: 2 Core(s) per socket: 12 Socket(s): 1 NUMA node(s): 1 Vendor ID: AuthenticAMD CPU family: 23 Model: 113 Model name: AMD Ryzen 9 3900X 12-Core Processor Stepping: 0 Frequency boost: enabled CPU MHz: 2116.134 CPU max MHz: 3800.0000 CPU min MHz: 2200.0000 BogoMIPS: 7586.39 Virtualization: AMD-V L1d cache: 384 KiB L1i cache: 384 KiB L2 cache: 6 MiB L3 cache: 64 MiB NUMA node0 CPU(s): 0-23 Vulnerability Itlb multihit: Not affected Vulnerability L1tf: Not affected Vulnerability Mds: Not affected Vulnerability Meltdown: Not affected Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp Vulnerability Spectre v1: Mitigation; usercopy/swapgs barriers and __user pointer sanitization Vulnerability Spectre v2: Mitigation; Full AMD retpoline, IBPB conditional, STIBP conditional, RSB filling Vulnerability Tsx async abort: Not affected Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate sme ssbd mba sev ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr wbnoinvd arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif umip rdpid overflow_recov succor smca ``` ### Statistical analysis --- The analysis is detailed in `analysis/analysis.Rmd`, which is knitted to a Word document containing all results. Quite a few helper functions and scripts are sourced in `analysis.Rmd`, please see `analysis/scripts`. The final run was carried out on 2020-05-13 using the following R environment: ```bash ─ Session info ─────────────────────────────────────────────────────────────── setting value version R version 4.0.0 (2020-04-24) os Pop!_OS 20.04 LTS system x86_64, linux-gnu ui X11 language en_US:en collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Stockholm date 2020-05-13 ─ Packages ─────────────────────────────────────────────────────────────────── package * version date lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.0.0) arrayhelpers 1.1-0 2020-02-04 [1] CRAN (R 4.0.0) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0) base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0) bayesplot 1.7.1 2019-12-01 [1] CRAN (R 4.0.0) bridgesampling 1.0-0 2020-02-26 [1] CRAN (R 4.0.0) brms * 2.12.0 2020-02-23 [1] CRAN (R 4.0.0) Brobdingnag 1.2-6 2018-08-13 [1] CRAN (R 4.0.0) broom * 0.5.6 2020-04-20 [1] CRAN (R 4.0.0) callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0) cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0) coda 0.19-3 2019-07-05 [1] CRAN (R 4.0.0) codetools 0.2-16 2018-12-24 [4] CRAN (R 4.0.0) colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0) colourpicker 1.0 2017-09-27 [1] CRAN (R 4.0.0) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) crosstalk 1.1.0.1 2020-03-13 [1] CRAN (R 4.0.0) data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0) DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0) dbplyr 1.4.3 2020-04-19 [1] CRAN (R 4.0.0) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0) devtools * 2.3.0 2020-04-10 [1] CRAN (R 4.0.0) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0) dplyr * 0.8.5 2020-03-07 [1] CRAN (R 4.0.0) DT 0.13 2020-03-23 [1] CRAN (R 4.0.0) dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.0) ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0) farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0) fastmap 1.0.1 2019-10-08 [1] CRAN (R 4.0.0) flextable * 0.5.9 2020-03-06 [1] CRAN (R 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2020-02-06 [1] CRAN (R 4.0.0) labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0) later 1.0.0 2019-10-04 [1] CRAN (R 4.0.0) lattice 0.20-41 2020-04-02 [4] CRAN (R 4.0.0) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0) loo 2.2.0 2019-12-19 [1] CRAN (R 4.0.0) lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0) markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0) Matrix 1.2-18 2019-11-27 [4] CRAN (R 4.0.0) matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0) mime 0.9 2020-02-04 [1] CRAN (R 4.0.0) miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.0) mnormt 1.5-7 2020-04-30 [1] CRAN (R 4.0.0) modelr 0.1.7 2020-04-30 [1] CRAN (R 4.0.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0) mvtnorm 1.1-0 2020-02-24 [1] CRAN (R 4.0.0) nlme 3.1-147 2020-04-13 [4] CRAN (R 4.0.0) officer * 0.3.9 2020-05-04 [1] CRAN (R 4.0.0) pander * 0.6.3 2018-11-06 [1] CRAN (R 4.0.0) patchwork * 1.0.0 2019-12-01 [1] CRAN (R 4.0.0) pillar 1.4.4 2020-05-05 [1] CRAN (R 4.0.0) 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2019-09-15 [1] CRAN (R 4.0.0) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0) rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0) scales * 1.1.1 2020-05-11 [1] CRAN (R 4.0.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) shiny 1.4.0.2 2020-03-13 [1] CRAN (R 4.0.0) shinyjs 1.1 2020-01-13 [1] CRAN (R 4.0.0) shinystan 2.5.0 2018-05-01 [1] CRAN (R 4.0.0) shinythemes 1.1.2 2018-11-06 [1] CRAN (R 4.0.0) StanHeaders * 2.19.2 2020-02-11 [1] CRAN (R 4.0.0) stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) svglite 1.2.3 2020-02-07 [1] CRAN (R 4.0.0) svUnit 1.0.3 2020-04-20 [1] CRAN (R 4.0.0) systemfonts 0.2.1 2020-04-29 [1] CRAN (R 4.0.0) testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0) threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.0) tibble * 3.0.1 2020-04-20 [1] CRAN (R 4.0.0) tidybayes * 2.0.3 2020-04-04 [1] CRAN (R 4.0.0) tidyr * 1.0.3 2020-05-07 [1] CRAN (R 4.0.0) tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0) tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0) usethis * 1.6.1 2020-04-29 [1] CRAN (R 4.0.0) uuid 0.1-4 2020-02-26 [1] CRAN (R 4.0.0) vctrs 0.3.0 2020-05-11 [1] CRAN (R 4.0.0) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.0) xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0) xts 0.12-0 2020-01-19 [1] CRAN (R 4.0.0) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0) zip 2.0.4 2019-09-01 [1] CRAN (R 4.0.0) zoo 1.8-8 2020-05-02 [1] CRAN (R 4.0.0) [1] /home/cmd/R/x86_64-pc-linux-gnu-library/4.0 [2] /usr/local/lib/R/site-library [3] /usr/lib/R/site-library [4] /usr/lib/R/library ```