CPACqc 0.2.11

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

CPAC-QC Plotting App

PDF Report

example PDF report here: PDF REPORT

HTML Report

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.

Updates

• Outputs PDF (default) and HTML report (with -html flag) now.
• Default config has overlays.
• Images on PDF report will follow the order mentioned in overlay.csv provided or default.
• Added Bookmarks on PDF report for easy navigation.

Features

• Generate bulk or subject specific plots and reports.

Requirements

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

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 bids_dir -s subject-id_1 subject-id_2

You can hand pick a single or a multiple subjects with -s flag

4. Running with defined number of procs

cpacqc -d path/to/bids_dir  -n number-of-procs

Note: if -n is not provided default is 8

5. Running all Subjects in the dir

cpacqc -d /bids_dir 

6. Providing Overlays config

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

where overlay.csv can be in format

output,underlay,datatype
desc-preproc_bold,desc-preproc_T1w,func

and so on. If not provided a default config will be used.

Viewing

Use any PDF viewer to view *report.pdf file.

If -html enabled, Use any .html viewer extension to view index.html in the results dir.