Overview

This module creates either component loadings or statsmaps of merged components. Most of the output is needed after doing dual regression, however it can created statsmaps of group level components.

Component loadings

This calculates loadings between individual subjects dual regression output and the group level components. Each loading is a pearson R of how similar an individual component is to the group level component.

Output

Output is a csv file or a npy file of subject by component.

Usage

nfact_stats loadings [-h] [-O] [-l LIST_OF_SUBJECTS]
[-o OUTDIR] [-d DIM] [-n NFACT_FOLDER] [-a ALGO] [-C]

General options:

-h, --help

Shows help message

-O, --overwrite

Overwrites previous file structure

Set Up Arguments:

-l, --list_of_subjects

Filepath to a list of subjects

-o, --outdir

Path to output directory

Decomp args:

-d, --dim

Number of dimensions/components that was used to generate nfact_decomp image

-n, --nfact_folder

Absolute path to nfact_decomp output folder.

-a, --algo

Which decomposition algorithm. Options are: NMF (default), or ICA. This is case insensitive

Stats args:

-t, --threshold

Threshold components so that component loadings reflect connectivity patterns not noise.

-C, --no_csv

Save Component Loadings as a npy file rather than as a csv file

Statsmap

This creates statistical maps to be used in PALM or Randomise. The statistical maps are 3D niftis (white matter) and ciftis (grey matter) of combined combined components. This can be done on a group level or on a subject level. If it is done on a group level then images are 3D of just combined components. If it is done on a subject level then output is a 4D image with subject as the 4th dim (ready for palm/randomise)

please note statsmap can currently only accept ciftis for the grey matter.

Usage

nfact_stats statsmap [-h] [-l LIST_OF_SUBJECTS] [-o OUTDIR] [-O] [-d DIM]
[-n NFACT_FOLDER] [-a ALGO] [-c COMPONENTS [COMPONENTS ...]] [-m MAP_NAME] [-G]

General options:

-h, --help

Shows help message and exit

-O, --overwrite

Overwrites previous file structure

Set Up options:

-l, --list_of_subjects

Filepath to a list of subjects

-o, --outdir

Path to output directory

Decomp options:

-d, --dim

Number of dimensions/components that was used to generate nfact_decomp image

-n, --nfact_folder

Absolute path to nfact_decomp output folder.

-a, --algo

Which decomposition algorithm. Options are: NMF (default), or ICA. This is case insensitive

Statsmap options:

-c, --components

Components to merge, Can accept any number

-m, --map_name

Name to call the maps (i.e if merging components asscoiated with a network call it networkx)

-G, --group-only

Only do group level stats map. Doesn’t need a subject list