Tutorial

In this tutorial, you will download sample data, install pyalfe, configure it, and run it on this data. This tutorial requires git and python>=3.9.

Data download and directory setup

1. Download the tutorial data

git clone https://github.com/reghbali/pyalfe-test-data.git

This will create a directory named pyalfe-test-data and downloads the tutorial data inside it. The data is the MRI scan of a glioblastoma patient and is taken from the UPenn-GBM dataset.

2. Create the output directory

mkdir pyalfe-output

Installation

Create a python virtual environment and activate it

python3 -m venv venv
source venv/bin/activate

Install pyalfe

pip install pyalfe

Download models

pyalfe download models

Configure pyalfe by running

pyalfe configure

and simply pressing enter for all the prompts for default values.

Run

pyalfe run UPENNGBM0000511 --input-dir pyalfe-test-data  --output-dir pyalfe-output

Pipeline output

You can now inspect the pipeline output by changing directory to

cd pyalfe-output/UPENNGBM0000511

and exploring the FLAIR, T1, T1Post, T2, ADC subdirectories.

For instance, the individual FLAIR lesion measures can be found at:

FLAIR/quantification/UPENNGBM0000511_SummaryLesionMeasures.csv

FLAIR lesion segmentation can be found at:

FLAIR/abnormalmap/UPENNGBM0000511_FLAIR_abnormal_seg.nii.gz

Summary T1Post (enhancing) lesion measures can be found at:

T1Post/quantification/UPENNGBM0000511_IndividualLesionMeasures.csv

Brain volumetric measures can be found at:

T1/quantification/UPENNGBM0000511_volumeMeasures.csv

The tissue segmentation can be found at:

T1/UPENNGBM0000511_T1_tissue_seg.nii.gz