Denoiser: A nuisance regression tool for fMRI BOLD data

Denoiser is a tool for removing sources of noise from and performing temporal filtering of functional MRI data. It also provides visualization of the content of nuisance signals (including motion information, if provided), allowing the user to get a quick sense of data quality before and after noise removal.

Denoiser acts on 4D fMRI data (takes either a nifti file path or an already loaded nibabel object as input). Nuisance signal removal and temporal filtering are performed on a voxel-wise level, and a 'cleaned' 4D Nifti file (_NR file)/ nibabel object are created as outputs.

The specific noise signals to be removed are specified by the user (contained in a tsv file). This tool should be used only after BOLD data are minimally preprocessed (for example, after preprocessing the data using fmriprep, which creates a .tsv file containing nuisance signals).

For instructions on how to run, type: python run_denoise.py -h:

usage: run_denoise.py [-h] [--col_names COL_NAMES [COL_NAMES ...]] [--hp_filter HP_FILTER] [--lp_filter LP_FILTER] [--out_figure_path OUT_FIGURE_PATH] img_file tsv_file out_path

Function for performing nuisance regression. Saves resulting output nifti file, information about nuisance
regressors and motion (html report), and outputs nibabel object containing clean data

positional arguments:
  img_file              4d nifti img: file path or nibabel object loaded into memory
  tsv_file              tsv file containing nuisance regressors to be removed
  out_path              output directory for saving new data file

optional arguments:
  -h, --help            show this help message and exit
  --col_names COL_NAMES [COL_NAMES ...]
                        which columns of TSV file to include as nuisance regressors. defaults to ALL columns.
  --hp_filter HP_FILTER
                        frequency cut-off for high pass filter (removing low frequencies). Recommend .009 Hz
  --lp_filter LP_FILTER
                        frequency cut-off for low pass filter (removing high frequencies). Recommend .1 Hz for non-task data
  --out_figure_path OUT_FIGURE_PATH
                        output directory for saving figures. Defaults to location of out_path + _figures

If you run into troubles using the tool or have any questions please post them here.