density3d's Introduction

Density3D

Density Volumes for concatenated statistical maps of multi-subject, multi-run or surrogate fMRI datasets.

How to install

First, clone the repository:

git clone https://github.com/eurunuela/Density3D.git

Then, move into the cloned repository:

cd Density3D

Once inside the directory, install the package:

pip install .

Finally, make sure the installation was successful by checking the version.

❯ Density3D -v
Density3D v0.0.2-beta

To learn how to use it, make use of the help option:

❯ Density3D -h
usage: Density3D [-h] -i INPUT_FILE [-m INPUT_MASK] [-n N_BINS] [-r HIST_RANGE] [-o OUT_NAME] [-outdir OUT_DIR] [-indir IN_DIR] [-history] [-debug] [-quiet] [-v]

Required Argument::
  -i INPUT_FILE, --input INPUT_FILE
                        The name of the file to calculate densities on.

optional arguments:
  -h, --help            show this help message and exit
  -m INPUT_MASK, --mask INPUT_MASK
                        The filename of the mask to apply on <input>. Default is None (nilearn automatically creates the mask).
  -n N_BINS, --nbins N_BINS
                        Only output info about the file, don't process. Default is to process.
  -r HIST_RANGE, --range HIST_RANGE
                        Range to limit the densities. Default is "-0.01 0.01".
  -o OUT_NAME, --outname OUT_NAME
                        Name for the output file.Default is current density_volume.nii
  -outdir OUT_DIR, --outdir OUT_DIR
                        Output directory containing density volumes. Default is current directory.
  -indir IN_DIR, --indir IN_DIR
                        Input directory containing <input>. Default is current directory.
  -history, --history   Update the file history to contain the Density3D command.
  -debug, --debug       Only print debugging info to log file. Default is False.
  -quiet, --quiet       Only print warnings to log file. Default is False.
  -v, --version         show program's version number and exit