CPACqc 0.2.4

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 with defined number of procs

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

Note: if -n is not provided default is 8

2. Running multiple Subjects

cpacqc -d path/to/bids_dir -o path/to/output-qc-dir -s subject-id_1 subject-id_2

3. Running all Subjects in the dir

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

or simply

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

4. 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.

5. Generating PDF

You can generate pdf by loading the HTML report and then clicking Generate PDF button. or, you can generate pdf report directly by providing -pdf or --pdf flag

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

This will create pdf file named cpac_report.pdf in the output qc dir

Viewing

Use any .html viewer extension to view index.html