CPACqc 0.2.2

A package to view Nifti files in a BIDS dataset and generate QC plots.

CPAC-QC Plotting App

Overview

The CPAC-qc Plotting App is a tool designed to generate quality control plots for the CPAC (Configurable Pipeline for the Analysis of Connectomes) outputs. This app helps in visualizing and assessing the quality of neuroimaging data processed through CPAC.

Features

• Generate bulk or subject specific plots

Requirements

• A html viewing tool or extension
• BIDS dir with .nii.gz images in it.

Installation

pip install CPACqc

Usage

1. Running Single Subject

cpacqc -d path/to/bids_dir -o path/to/output-qc-dir -s subject-id -n number-of-procs

2. Running all Subjects in the dir

cpacqc -d path/to/bids_dir -o path/to/output-qc-dir -n number-of-procs

or simply

cpacqc -d path/to/bids_dir -o path/to/output-qc-dir

3. Plotting Overlays

cpacqc -d path/to/bids_dir -o qc_dir -c ./overlay.csv

where overlay.csv can be in format

image_1,image_2
desc-preproc_bold, desc-preproc_T1w

and so on.