Metadata-Version: 2.1
Name: Ingress2QSIRecon
Version: 0.2.1
Summary: Tool to ingress data from other pipelines for use in QSIRecon
Author: Steven Meisler
Author-email: smeisler13@gmail.com
Requires-Python: >=3.10,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: SimpleITK (>=2.4.0,<3.0.0)
Requires-Dist: acres (>=0.1.0,<0.2.0)
Requires-Dist: beartype (>=0.18.5,<0.19.0)
Requires-Dist: icontract (>=2.6.6,<3.0.0)
Requires-Dist: loguru (>=0.7.2,<0.8.0)
Requires-Dist: nibabel (>=5.2.0,<6.0.0)
Requires-Dist: nilearn (>=0.10.1,<0.11.0)
Requires-Dist: nipype (>=1.8.6,<2.0.0)
Requires-Dist: niworkflows (>=1.9.0,<2.0.0)
Requires-Dist: pydantic (>=2.8,<3.0)
Requires-Dist: templateflow (>=24.2.0,<25.0.0)
Project-URL: homepage, https://github.com/PennLINC/ingress2qsirecon
Project-URL: repository, https://github.com/PennLINC/ingress2qsirecon
Description-Content-Type: text/markdown

# Ingress2QSIRecon
A tool for ingressing outputs from other processing pipelines (e.g., HCP, UKB) for use in QSIRecon.

## Overview
This tool can be used to import data from bespoke and widely-used DWI preprocessing pipelines (e.g., Human Connectome Project and UK Biobank) into QSIRecon for post-processing.

## Installation
This project can be installed via PyPi. In your virtual environment run
```
pip install Ingress2QSIRecon
```
For the master/development branch, you can clone the github repo, and run from within it:
```
pip install -e .
```

## Usage
Assuming you have the data to ingress locally availble, you can run the following:
```
ingress2qsirecon \
    /PATH/TO/INPUT/DATA \ # E.g., path to HCP1200 directory
    /PATH/TO/OUTPUT \ # BIDS directory with ingressed data will be made here
    PIPELINE_NAME \ # Currently support "hcpya" and "ukb" \
    -w /PATH/TO/WORKING/DIR \ # Where intermediate files and workflow information will be stored
    --participant-label 100307 # Name(s) of folder within /PATH/TO/INPUT/DATA. If not specified, will process everyone
```
