CPACqc 0.2.5

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
• Outputs PDF (default) and HTML report (with -html flag)

Requirements

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

Installation

pip install CPACqc

Usage

1. Minimal code

cpacqc -d bids_dir

This will output a pdf report report.pdf in your current directory.

2. HTML report

cpacqc -d bids_dir -html

This will create a pdf report.pdf along with a results dir with HTML report index.html and related files.

3. Running single/multiple Subjects

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

You can hand pick a singl or a few subjects with -s flag

4. 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

5. 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

6. 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.

Viewing

Use any .html viewer extension to view index.html