NeuroMorph-Assessment README

The project's README from github.com/ruoyuw22-byte/NeuroMorph-Assessment. As one markdown file: README.md.

NeuroMorph Assessment (NMA)

Screenshot

NeuroMorph Assessment Overview

Overview

NeuroMorph Assessment (NMA) is an automated structural MRI morphometry and CAT12-based brain volume analysis system.

The software integrates MRI data organization, CAT12 processing, quantitative brain tissue measurement, visualization, and automated report generation into a unified workflow.

Key Features

Automated MRI Workflow

Quantitative Morphometry

NMA extracts structural measurements including:

The system includes quantitative consistency validation during result extraction.

Visualization and Reporting

Features include:

Workflow

MRI Data
   |
   v
Data Import
   |
   v
T1 Image Detection
   |
   v
CAT12 Processing
   |
   v
Tissue Segmentation
   |
   v
Volume Quantification
   |
   v
Visualization and Report

Project Structure

NeuroMorph-Assessment/

├── src/
│   ├── app.py
│   ├── ui.html
│   ├── NMAWebView.m
│   ├── launcher.sh
│   └── Info.plist
│
├── resources/
├── scripts/
├── examples/
├── docs/
├── requirements.txt
└── README.md

Software Requirements

NeuroMorph Assessment requires MATLAB together with SPM12 and CAT12 for structural MRI processing.

The software was developed and tested under the following environment:

Software Version

MATLAB R2022b SPM12 SPM12 CAT12 CAT12.8

MATLAB

MATLAB is required for running SPM12 and CAT12 neuroimaging pipelines.

Recommended version:

MATLAB R2022b

Official website:

https://www.mathworks.com/products/matlab.html

SPM12

SPM12 (Statistical Parametric Mapping) is a MATLAB-based neuroimaging analysis toolbox required by NeuroMorph Assessment.

SPM12 is used for:

Official download:

https://www.fil.ion.ucl.ac.uk/spm/software/spm12/

After installation, add the SPM12 directory to MATLAB:

addpath('/path/to/spm12')

spm('Defaults','fMRI')
spm_jobman('initcfg')

CAT12

CAT12 (Computational Anatomy Toolbox 12) is an extension toolbox for SPM12.

NeuroMorph Assessment uses CAT12 for:

Official website:

https://neuro-jena.github.io/cat/

Recommended installation structure:

spm12/
│
└── toolbox/
    │
    └── cat12/

Add CAT12 path in MATLAB:

addpath('/path/to/spm12')
addpath('/path/to/spm12/toolbox/cat12')

Configuration

Before running NeuroMorph Assessment, please ensure:

  1. MATLAB is correctly installed.
  2. SPM12 is available in MATLAB path.
  3. CAT12 is installed under the SPM12 toolbox directory.
  4. Required paths are correctly configured in the application.

Installation

Requirements:

Python dependencies are provided in:

requirements.txt

Usage

  1. Import MRI data.
  2. Configure analysis environment.
  3. Run the processing workflow.
  4. Review quantitative results.
  5. Generate reports.

Documentation

Additional documentation is available in:

docs/

Version

Current version:

v0.11.1

Citation

Citation information will be updated with the final publication or software registration information.

License

License information will be added after dependency review.

Acknowledgements

This project uses open-source neuroimaging tools including SPM12 and CAT12.

NeuroMorph-Assessment (ruoyuw22-byte/NeuroMorph-Assessment)

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251 ·GitHub
NeuroMorph-Assessment
What is this?NeuroMorph Assessment (NMA) is an automated structural MRI morphometry system that integrates CAT12 processing, brain tissue quantification, visualization, and automated report generation into one workflow.
Is this a standalone app or does it depend on other software to actually work?It is a Python desktop application that acts as a wrapper and orchestrator around MATLAB, SPM12, and CAT12 — it does not do the MRI processing itself, it drives those external tools and then handles visualization and reporting.
How do I get it running?Install Python 3.x plus MATLAB with SPM12 and CAT12 and dcm2niix, then import your MRI data, configure the analysis environment, run the processing workflow, review the quantitative results, and generate reports.
What exactly do I need installed before this will work?You need macOS, Python 3.x, MATLAB with SPM12 on the MATLAB path, the CAT12 toolbox installed under SPM12, and dcm2niix for DICOM-to-NIfTI conversion.
Is this a lightweight, no-fuss install?No — it requires a paid MATLAB license plus manually installing and path-configuring two separate neuroimaging toolboxes (SPM12 and CAT12) before the app will even run, so setup is heavy and technical.
Who is this built for?Researchers and clinicians doing structural brain MRI morphometry who already work with SPM12/CAT12 pipelines and want the workflow automated end-to-end.
Does it only run on macOS?Yes, the listed requirements specify macOS as the platform.
Is the license finalized?Not yet — the repo currently lists MIT in GitHub metadata, but the README itself says license terms are still pending a dependency review.
What measurements does it actually extract from an MRI?It extracts total intracranial volume (TIV), gray matter volume, white matter volume, and cerebrospinal fluid volume, with built-in consistency validation during extraction.
Does it produce a shareable report?Yes, it includes three-plane MRI visualization, a quantitative result preview, processing progress monitoring, and generates an automated PDF report at the end.
Can I cite this in a paper right now?Not yet — the README states citation information will be added once the final publication or software registration is ready.
What are similar projects?fuck-cancer, damo-radar, Few-step-probabilistic-glucose-forecasting-from-continuous-glucose-monitoring-and-meal-images, Real-Time-Person-Elderly-Fall-Detection-System, presidio, langextract, matplotlib, HowToLiveBetter
Which topics is it in?medical-imaging, healthcare, desktop-application, health, visualization, desktop, research, gui, python, macos
Creator
ruoyuw22-byte
Size
1.5 MB
Stars
251
Updated
CommitAug 25Releasev0.11.1Aug 23
Age
1mo
Commits · 90 Days