PABLO

PABLO (Publicly Available Brain image anaLysis tOolkit) is a general toolkit for brain MRI analysis.

PABLO is a versatile platform for analyzing combinations of methods consisting of three steps widely usde in MRI analysis; 1) spatial standardization, 2) dimension reduction and 3) classification. Because of the complex input and output, the pipeline is not fully automated. This repository contains the scripts for all steps used in our study. In mini PABLO, which can be downloaded through pip, only the scripts to compute image features are available.

Dependency (not fully)

FSL
NiBabel
ANTs
SPM12
pyradiomics

Install

Pip install is coming soon to compute image features from Nifti image.

pip install PABLO-MRI

Contents of PABLO

The full repository, which can be obtained via a command below, contains the scripts used in our study.

git clone https://github.com/carushi/PABLO

Scripts for DICOM conversion into Nifti (SPM)
Scripts for normalization of image data using SPM and ANTs
Scripts for skull stripping in each image
Computation of basic image features
Computation of image features using pyradiomics
Construction of classifiers for the data of multiple cohorts

Image Features available in mini PABLO

Basic features:
- Source: feature_calc.py
- Option: basic
Pyradiomic features
- Source: feature_calc.py
- Option: py
- Pyradiomics manual
Deep learning-based features: Inception-Resnet v2
- Source: process_nii.py
- Additional requirement: keras model
- Option: deep
Anatomical features
- feature_calc.py
- Option: ann

Input

3D Nifti file
DICOM file

Reference

Kawaguchi RK, Takahashi M, Miyake M, Kinoshita M, Takahashi S, Ichimura K, Hamamoto R, Narita Y, Sese J. Assessing Versatile Machine Learning Models for Glioma Radiogenomic Studies across Hospitals. Cancers (Basel). 2021 Jul 19;13(14):3611. doi: 10.3390/cancers13143611. PMID: 34298824; PMCID: PMC8306149.

zhangpeihao / PABLO