Metadata-Version: 2.2
Name: CPACqc
Version: 0.2.2
Summary: A package to view Nifti files in a BIDS dataset and generate QC plots.
Home-page: https://github.com/birajstha/bids_qc
Author: Biraj Shrestha
Author-email: birajstha@gmail.com
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: backports.tarfile==1.2.0
Requires-Dist: certifi==2025.1.31
Requires-Dist: cffi==1.17.1
Requires-Dist: charset-normalizer==3.4.1
Requires-Dist: colorama==0.4.6
Requires-Dist: contourpy==1.3.1
Requires-Dist: cryptography==44.0.1
Requires-Dist: cycler==0.12.1
Requires-Dist: docutils==0.21.2
Requires-Dist: elbow==0.1.1
Requires-Dist: fonttools==4.56.0
Requires-Dist: id==1.5.0
Requires-Dist: idna==3.10
Requires-Dist: importlib_metadata==8.6.1
Requires-Dist: importlib_resources==6.5.2
Requires-Dist: jaraco.classes==3.4.0
Requires-Dist: jaraco.context==6.0.1
Requires-Dist: jaraco.functools==4.1.0
Requires-Dist: jeepney==0.9.0
Requires-Dist: joblib==1.4.2
Requires-Dist: keyring==25.6.0
Requires-Dist: kiwisolver==1.4.8
Requires-Dist: lxml==5.3.1
Requires-Dist: markdown-it-py==3.0.0
Requires-Dist: matplotlib==3.10.0
Requires-Dist: mdurl==0.1.2
Requires-Dist: more-itertools==10.6.0
Requires-Dist: nh3==0.2.21
Requires-Dist: nibabel==5.3.2
Requires-Dist: nilearn==0.11.1
Requires-Dist: numpy==2.2.3
Requires-Dist: packaging==24.2
Requires-Dist: pandas==2.2.3
Requires-Dist: pillow==11.1.0
Requires-Dist: pyarrow==19.0.0
Requires-Dist: pycparser==2.22
Requires-Dist: Pygments==2.19.1
Requires-Dist: pyparsing==3.2.1
Requires-Dist: python-dateutil==2.9.0.post0
Requires-Dist: pytz==2025.1
Requires-Dist: readme_renderer==44.0
Requires-Dist: requests==2.32.3
Requires-Dist: requests-toolbelt==1.0.0
Requires-Dist: rfc3986==2.0.0
Requires-Dist: rich==13.9.4
Requires-Dist: scikit-learn==1.6.1
Requires-Dist: scipy==1.15.2
Requires-Dist: SecretStorage==3.3.3
Requires-Dist: six==1.17.0
Requires-Dist: threadpoolctl==3.5.0
Requires-Dist: tqdm==4.67.1
Requires-Dist: twine==6.1.0
Requires-Dist: typing_extensions==4.12.2
Requires-Dist: tzdata==2025.1
Requires-Dist: urllib3==2.3.0
Requires-Dist: zipp==3.21.0
Requires-Dist: setuptools==75.8.2
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

# CPAC-QC Plotting App

![CPAC-QC](https://raw.githubusercontent.com/birajstha/bids_qc/main/static/cpac-qc.png)

## 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

```bash
pip install CPACqc
```

## Usage

1. **Running Single Subject**

```bash
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**

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

or simply

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

3. **Plotting Overlays**

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

where overlay.csv can be in format

```csv
image_1,image_2
desc-preproc_bold, desc-preproc_T1w
```

and so on.
