Masks2Metrics (M2M)
Masks2Metrics (M2M): A Matlab Toolbox for Gold Standard Morphometrics - Published in JOSS (2018)
Science Score: 95.0%
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Published in Journal of Open Source Software
Repository
M2M is a matlab code to compute volume, surface, thickness from 2 manually traced masks (binary data)
Basic Info
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- Stars: 6
- Watchers: 4
- Forks: 2
- Open Issues: 0
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Metadata Files
README.md
Masks2Metrics (M2M)
Copyright (C) 2017 S. Mikhael and C. Gray.
Table of Contents
- What is M2M for
- License
- Installation Instructions
- Getting Started
- Authors
- Contributors
- Contributing
- Code of Conduct
- Road Map
What is M2M for?
Masks2Metrics (M2M) is a Matlab based tool that is used to calculate 3 metrics for a given region-of-interest (ROI) in a 3D image: thickness, volume and surface area. While many software packages that automatically compute such metrics exist, it is also necessary to compare the results from automated software with manually-traced ROIs. The current software takes such manually-traced ROIs and computes the metrics automatically.
We (the authors and contributors) use M2M to compute those metrics on images acquired by a Magnetic Resonance Imaging (MRI) machine. The ROI is defined by pairs of 3-dimensional (3D) binary masks (in NIfTI format) that represent the inner and outer borders of the ROI, and are drawn continuously along one direction (x-, y- or z-axis). For the special case of brain images, if the ROI describes a gyrus, the paired masks would be the corresponding grey matter (GM) and white matter curves (WM). Paired ROI NIfTI (.nii) masks are expected to be of the form subjroihemgm/wmsegments.nii. An example of a pair corresponding to subject 1 right superior frontal gyrus (SFG) would be 1sfgrgm1.nii and 1sfgr_wm1.nii. A special feature of M2M is that multiple segments can be used rather than a single continuous ROI (see Wiki help). The ROI metrics calculated are grey matter thickness (GMth), grey matter volume (GMvol),and white matter surface area (WMsa).
License
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License, the license.txt file, and http://www.gnu.org/licenses for more details.
Installation Instructions
Download M2M into a folder called Masks2Metrics. In addition to the Masks2Metrics code, the folder includes external code that is called by the tool, including a NIfTI Matlab tools and pre-existing distance code (Euclidean, Fréchet and the Modified Hausdorff Distance).
Getting Started
- Add the Masks2Metrics folder and subfolders to your list of Matlab paths.
- To calculate your ROI's metrics call the function
'masks2metrics'with the appropriate parameters.
For more details, please refer to our Wiki. It includes a short tutorial demonstrating how the tool can be used as well as a workflow highlighting communication between all functions.
Authors
Shadia Mikhael, Edinburgh Imaging, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
Calum Gray, Edinburgh Imaging and Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK.
Contributors
Maria del C. Valdés Hernández, Edinburgh Imaging, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
Corne, Hoogendoorn, Toshiba Medical Visualization Systems Edinburgh, Edinburgh, UK.
Cyril R. Pernet, Edinburgh Imaging, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
Contributing
See CONTRIBUTING
Code of Conduct
See CODEOFCONDUCT
Roadmap
Owner
- Name: Edinburgh Imaging
- Login: Edinburgh-Imaging
- Kind: user
- Location: Edinburgh
- Company: Edinburgh Imaging
- Website: www.ed.ac.uk/edinburgh-imaging
- Repositories: 4
- Profile: https://github.com/Edinburgh-Imaging
JOSS Publication
Masks2Metrics (M2M): A Matlab Toolbox for Gold Standard Morphometrics
Authors
Edinburgh Imaging, The Chancellor’s Building, 1st floor, FU303e, 49 Little France Crescent, Edinburgh, Scotland, UK, EH16 4SB.
Edinburgh Imaging, The Chancellor’s Building, 1st floor, FU303e, 49 Little France Crescent, Edinburgh, Scotland, UK, EH16 4SB., Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK.
Editor
Christopher R. Madan
Tags
metrics gyrus masks thickness volume surface areaGitHub Events
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