These directories contain some MATLAB code I wrote for preprocessing and quality assessment of fMRI data. Here's a brief overview of how the code is organized and what it does:
├── fmri_multiecho_preprocessing <- Dir with code for fMRI preprocessing
│ ├── coreg_normalize_smooth.m <- SPM12 job for coregistration, normalization, and smoothing
│ ├── dicom_import.m <- SPM12 job for DICOM to NIfTI conversion
│ ├── preproc_mri_stpy.m <- Preprocesses functional and anatomical MRI data
│ ├── realign_estimate.m <- SPM12 job for realignment (estimation only)
│ ├── realign_reslice.m <- SPM12 job for realignment (estimation & reslicing)
│ └── run_preproc_mri_stpy.m <- Main script, calling preproc_mri_stpy.m
├── quality_check <- Dir with code for fMRI quality analysis
│ ├── bztbx_automask.m <- Creates a rough mask of the brain (based on code from ArtRepair toolbox)
│ ├── bztbx_bpfilt.m <- Bandpass filters fMRI time series
│ ├── bztbx_createmask.m <- Creates binary images (masks) of ROIs
│ ├── bztbx_extractts.m <- Extracts fMRI time series data
│ ├── bztbx_fmrifig.m <- Makes a figure with quality check results
│ ├── bztbx_multireg.m <- Makes a text file with multiple regressors (e.g. realigment parameters)
│ ├── bztbx_qa.m <- Main quality check function
│ ├── bztbx_truncrp.m <- Truncates realignment parameters
│ └── bztbx_tsnr.m <- Computes temporal signal to noise ratio of fMRI time series
├── README.md <- The file you're reading now