Command Line Interface usage¶

You can invoke the primary workflow of nigsp from the command line.

The `nigsp` command¶

NiGSP, a tool to apply Graph Signal Processing to MRI (functional and structural), and compute derivative metrics such as the Structural Decoupling Index and the coupled/decoupled FC. Version 0.19.0+5.gcfc1b19

usage: nigsp -f FNAME -s SCNAME [-sdi] [-dfc] [-a ATLASNAME] [-idx INDEX]
             [-odir OUTDIR] [-ofile OUTNAME] [-sci | -scu] [-n N_SURR]
             [-seed SEED] [-method METHOD] [-debug | -quiet] [-h] [-v]

Required Arguments¶

-f, --input-func: Complete path (absolute or relative) and name of the file containing fMRI signal. This file can be a nifti, 1D, txt, csv, or mat file. If a nifti file is selected, an atlas has to be specified.
-s, --input-structural: Complete path (absolute or relative) and name of the file containing the structural connectivity matrix. This file can be a 1D, txt, csv, or mat file.

Optional Arguments for metrics computation¶

Use these flag to select which metric should be computed. Note that the default behaviour is to compute all metrics.

-sdi, --structural-decoupling-index: Compute the structural decoupling index (see Preti et al, 2019, Nat. Commun.)
-dfc, --decoupled-functional-connectivity: Compute the decoupledd functional connectivity (see Griffa et al, 2022, NeuroImage)

Optional Arguments for data processing¶

-a, --input-atlas

Complete path (absolute or relative) and name of the file containing the desired atlas. This file MUST be a nifti file, and it is required if the functional input is a nifti file. It is also required if the desired output is nifti. Default is None.

-idx, --split-index

The index of the harmonic that should split the harmonics in two, or the method to estimate such index. Default is “median”, that invokes the estimation of the split index based on the energy of the graph.

Default: “median”

Optional Arguments for output¶

-odir, --output-directory: Complete path (absolute or relative) and name of the desired output directory. If it does not exist, it will be created. If it is not specified, a folder named “nigsp” will be created in the folder containing the functional file.
-ofile, --output-file: Name of, and if desired path to, the output files.Use this option to specify the file format of nigsp, and

Optional Arguments for statistical test¶

-sci, --informed-surrogates

Create surrogates informed of the structural connectivity matrix. Unless this option or the next one is selected, statistical test will be skipped

-scu, --uninformed-surrogates

Create surrogates ignoring the structural connectivity matrix. Unless this option or the previous one is selected, statistical test will be skipped

-n, --surrogates-number

Number of surrogates to create. Default is 1000.

Default: 1000

-seed, --random-seed

The seed to initialise. If None, internal seeds will be used depending on workflow, granting replicability. Default is None.

-method, --statistical-method

Type of statistical test to adopt. Possible options are “Bernoulli” (for a Bernoulli process test, group level only) or “frequentist” (for a frequentist approach, both group and subject level). Default is Bernoulli.

Default: “Bernoulli”

Other Optional Arguments¶

-debug, --debug

Only print debugging info to log file.

Default: “info”

-quiet, --quiet

Only print warnings to log file.