Don’t deal with eccenctric software like AFNI and FSL. Try our all-in-one painless software for skull-stripping, atlas registration and warping. Supports humans and macaques (marmosets is in the works)
Reference: Nadian, Mohammad Hossein, Sepideh Farmani, and Ali Ghazizadeh. “A novel methodology for exact targeting of human and non-human primate brain structures and skull implants using atlas-based 3D reconstruction.” Journal of Neuroscience Methods 391 (2023): 109851.
Code:https://github.com/fmnh/MATres (courtesy of Mohammad Nadian)
Spiking Variability Decomposition
The code for parsing spiking variability: within trial variability nψ (aka φ) and between trial variability (nRV) using a pricinpled approach for a doubly stochastic process.
Reference: Fayyaz, S., Fakharian, M., & Ghazizadeh, A. (2021). Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions. bioRxiv
Code: var_decom (courtesy of Saleh Fayyaz & MohammadAmin Fakharian)
The code for constructing graph between nodes based on partial correlations and using PC-stable algorithm
1) Ghazizadeh, A., Fakharian, M. A., Amini, A., Griggs, W., Leopold, D. A., & Hikosaka, O. (2020). Brain networks sensitive to object novelty, value, and their combination. Cerebral cortex communications, 1(1), tgaa034
2) Attary T, Ghazizadeh A, (2021) Localizing sensory processing sensitivity and its subdomains within its relevant trait space: a data driven approach, Scientific Report
Neural Spiking Deconvolution
Code: Full and Partial deconvolution functions (courtesy of Setayesh Radkani)
First and Second-Order Multivariate Effects
The procedure for computing MVE and sMVE in fMRI data (we could not find sMVE in our fMRI datasets but you are welcome to prove us wrong)
Reference: Mansooreh Pakravan, Mojtaba Abbaszadeh, and Ali Ghazizadeh. “Coordinated multivoxel coding beyond univariate effects is not likely to be observable in fMRI data.” NeuroImage (2021): 118825.
Code: Crossnobis (MVE) and Geodesic (sMVE) Distances (courtesy of Mansooreh Pakravan)
Fractal Generation Code
The code for generating random fractal objects
Reference: Ghazizadeh, A, et al “Ecological origins of object salience: Reward, uncertainty, aversiveness, and novelty.” Frontiers in neuroscience 10 (2016): 378
Code: fractalmaker (courtesy of Shinya Yamamoto)