code/
├── data/         % all .mat files, usually results of cross validation and preprocessed data
│   ├── misc/     % .mat from non-VLR experiments
│   ├── train/    % .mat with preprocessed data to save recompute for during train-test runs
│   └── tmp/      % for temporary .mat files during performance analysis using performancebat
├── exp/          % (no files)
│   ├── hyp/      % hyperparameter definitions and variants for exploration
│   ├── toy/      % framework for single-voxel toy model exploration
│   └── ystd/     % framework for toy exploration of graylevel standardization 
├── fig/          % specific figures used in the thesis, do not use VLR results
│   └── utils/    % utilities for streamlining figure generation for this project
├── paper/        % compute stats for paper, copy necessary figures, ROI stuff that went unused
├── spm/          % genbatch.m: create SPM batch files using templates
│   ├── deform/   % files to warp images to/from MNI using SPM pre-computed transforms (2 ways)
│   ├── ran/      % batch files which were already run with SPM
│   └── templates/% template batch files for a single job. Replace wildcards using genbatch.m
├── utils/        % various utilities used by other functions throughout
│   ├── fig/      % utilities for figure generation (can be used for any project)
│   ├── mri/      % utilities for MRI info: scan parameters and image name lookup tables (lut)
│   └── nii/      % utilities for loading .nii files into matlab (+ the filexchange toolbox)
└── vlr/          % the VLR model: functions for training and testing it
    └── ops/      % functions used by the VLR model, but not specific to it.